@article { ISI:000263373600066, title = {Dendritic effect of ligand-coated nanoparticles: enhanced apoptotic activity of silica-berberine nanoconjugates}, journal = {Langmuir}, volume = {25}, number = {4}, year = {2009}, month = {FEB}, pages = {2339-2347}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

We describe the synthesis and biological characterization of a novel prototype, namely, silica nanoconjugates bearing a covalently linked berberine, a plant alkaloid known to have antiproliferative activity. The effect of synthesized nanoconjugates on cell proliferation, the cell cycle profile, and apoptosis in the human cervical carcinoma cell line (HeLa), human hepatocellular liver carcinoma cell line (HepG2), and human embryonic kidney (HEK) 293T cell line has been studied and compared with the results obtained for free berberine. Our results show that all the nanoconjugates display higher antiproliferative activity than free berberine. The ability of these nanoconjugates to inhibit cellular proliferation is mediated by the cell cycle arrest at the G1 phase. Moreover, silica nanoconugates caused selective apoptotic arrest with a higher efficiency than free berberine followed by apoptotic cell death as shown by quantitative fluorescence-activated cell sorting analyses. Efficiency of the nanoconjugates increases upon an increase in the linker chain length, demonstrating the distinct role of the spacer chain that conjugates nanoparticles and ligands. The actual reason to show enhanced efficiency by the nanoconjugates has not been elucidated in the present study; however, we hypothesize that an increase in local concentration due to the confinement of a ligand on the nanosurface ({\textquoteright}{\textquoteright}dendritic{\textquoteright}{\textquoteright} effect) might have led to the observed effect.

}, issn = {0743-7463}, doi = {10.1021/la802761b}, author = {Halimani, Mahantappa and Chandran, S. Prathap and Kashyap, Sudhir and Jadhav, V. M. and Bhagavatula L. V. Prasad and Hotha, Srinivas and Maiti, Souvik} } @article { ISI:000263732700047, title = {Effects for the incorporation of five-atom thioacetamido nucleic acid (TANA) backbone on hybridization thermodynamics and kinetics of DNA duplexes}, journal = {Journal of Physical Chemistry B}, volume = {113}, number = {9}, year = {2009}, month = {MAR}, pages = {2944-2951}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

Thermodynamic studies of nucleic acids serve not only to widen our understanding on the nature and strength of forces that stabilize nucleic acids in a myriad of structural states they assume but also to facilitate the development of databases that could be used to predict the stability and selectivity of probe/primer-sets required in a broad range of nucleic acid-based diagnostic and therapeutic protocols. In the current study, we investigated the effect of a novel, backbone-modified {\textquoteleft}{\textquoteleft}thioacetamido linkage{\textquoteright}{\textquoteright} (TANA) on thermodynamics of hybridization, binding kinetics, and conformation of a DNA duplex. The modification comprises of an extended five-atom amide (N3{\textquoteright}-CO-CH(2)-S-CH(2)) linker, as opposed to four-atom phosphodiester linker backbone present in DNA. One to three TANA-substitutions have been introduced in the linker backbone of two thymidine residues of one of the strand of the DNA duplex. Using spectroscopic and calorimetric techniques, we observed that TANA destabilizes the DNA helix by lowering the favorable enthalpy parameter of duplex formation. TANA center dot DNA duplexes were found to adopt a conformation toward an A-type duplex as shown by circular dichroism spectroscopy studies. Analysis of differential scanning calorimetry data indicated a nonzero heat capacity change, Delta C(p), accompanying the duplex formation. The average Delta C(p) change per duplex was found to be 832.5 cal mol(-1) K(-1), giving an average base-pair change of 59.5 cal (mol of base pairs)(-1) K(-1). Hybridization kinetic measurements using surface plasmon resonance indicated a decrease in binding affinity parameter (K(A)) that originates from higher dissociation rate constants (k(d)). Furthermore, optical melting studies showed that increasing the number of modifications results in a modest change in the number of counterions taken up during duplex formation.

}, issn = {1520-6106}, doi = {10.1021/jp808747g}, author = {Kaur, Harleen and Arora, Amit and Gogoi, K. and Solanke, P. and Gunjal, Anita D. and Kumar, Vaijayanti A. and Maiti, Souvik} } @article { ISI:000287627200012, title = {Single nucleotide polymorphism in transcobalamin II (15V) induces structural changes in the protein as revealed by molecular modeling studies}, journal = {Biochemistry}, volume = {50}, number = {8}, year = {2011}, month = {MAR}, pages = {1396-1402}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

Cobalamin is an essential micronutrient in mammals. Deficiencies of this micronutrient have been implicated as risk factors for various complex diseases. Cobalamin is transported to the cells by the transport protein transcobalamin II (TCII), and hence genetic variations (like single nucleotide polymorphisms) in TCII could be perceived to affect the binding of cobalamin to TCII, thereby modulating the intracellular concentrations of cobalamin. To understand whether three nonsynonymous mutations in TCII (I5V, P241R, and R381Q) alter the structure of the protein which could potentially affect cobalamin binding, we performed molecular dynamics simulation in silico. Superimposition of active sites of the four simulated models (wild type and three variants) with the human TCII crystal structure revealed that the distance between the N epsilon nitrogen atom of His-173 and the cobalt ion of cobalamin deviated considerably in the I5V model as compared to wild type and other variants. His-173 directly coordinates with the cobalt ion of cobalamin. Further, from our dynamic cross-correlation and principal component analysis it appears that in the I5V model the beta-domain moves apart from the alpha-domain creating a wide gap between the two domains. This might facilitate the initial binding of cobalamin in the I5V model as cobalamin enters the binding site through the gap between the two domains. These observations were not found in the other variants. We thus speculate that binding of cobalamin will be more facile in the I5V variant.

}, issn = {0006-2960}, doi = {10.1021/bi101095g}, author = {Silla, Yumnam and Chandamouli, Balasubramanian and Maiti, Souvik and Sengupta, Shantanu} } @article { ISI:000300871600018, title = {Antagonism of microRNA function in zebrafish embryos by using locked nucleic acid enzymes (LNAzymes)}, journal = {Chembiochem}, volume = {13}, number = {4}, year = {2012}, month = {MAR}, pages = {584-589}, publisher = {WILEY-V C H VERLAG GMBH}, address = {PO BOX 10 11 61, D-69451 WEINHEIM, GERMANY}, abstract = {

MicroRNAs (miRNAs) have crucial functions in many cellular processes, such as differentiation, proliferation and apoptosis; aberrant expression of miRNAs has been linked to human diseases, including cancer. Tools that allow specific and efficient knockdown of miRNAs would be of immense importance for exploring miRNA function. Zebrafish serves as an excellent vertebrate model system to understand the functions of miRNAs involved in a variety of biological processes. We designed and employed a strategy based on locked nucleic acid enzymes (LNAzymes) for in vivo knockdown of miRNA in zebrafish embryos. We demonstrate that LNAzyme can efficiently knockdown miRNAs with minimal toxicity to the zebrafish embryos.

}, keywords = {enzymes, locked nucleic acids, microRNA, morpholino, zebrafish}, issn = {1439-4227}, doi = {10.1002/cbic.201100789}, author = {Suryawanshi, Hemant and Lalwani, Mukesh Kumar and Ramasamy, Soundhar and Rana, Rajiv and Scaria, Vinod and Sivasubbu, Sridhar and Maiti, Souvik} } @article { ISI:000311832900049, title = {Improved inhibition of telomerase by short twisted intercalating nucleic acids under molecular crowding conditions}, journal = {Nucleic Acid Therapeutics}, volume = {22}, number = {6}, year = {2012}, month = {DEC}, pages = {399-404}, publisher = {MARY ANN LIEBERT INC}, address = {140 HUGUENOT STREET, 3RD FL, NEW ROCHELLE, NY 10801 USA}, abstract = {

Human telomeric DNA has the ability to fold into a 4-stranded G-quadruplex structure. Several G-quadruplex ligands are known to stabilize the structure and thereby inhibit telomerase activity. Such ligands have demonstrated efficient telomerase inhibition in dilute conditions, but under molecular crowding conditions mimicking physiological milieu, stabilization of the telomeric G-quadruplex is often lost. We attempted to demonstrate the enhanced G-quadruplex stabilizing ability under molecular conditions by using twisted intercalating nucleic acids (TINA)-modified oligonucleotides. We have shown using circular dichroism and ultraviolet spectroscopic methods that these TINA-modified short oligonucleotides function as G-quadruplex, inducing agents and participate in the formation of stabilized 3:1 G-quadruplex with the human telomeric oligonucleotide. Using enzyme-linked immunosorbent assay-based telomerase repeat amplification assay (TRAP) assay as well as nondenaturing polyacrylamide gel electrophoresis-based TRAP, we demonstrate remarkable enhancement in their anti-telomerase activity even under molecular crowding conditions. This is the first time in which a G-quadruplex stabilizing agent has demonstrated enhanced activity even under molecular crowding conditions.

}, issn = {2159-3337}, doi = {10.1089/nat.2012.0372}, author = {Agarwal, Tani and Pradhan, Devranjan and Geci, Imrich and El-Madani, Amro M. and Petersen, Michael and Pedersen, Erik B. and Maiti, Souvik} } @article { ISI:000304338300004, title = {Kinetic studies of amino acid-based surfactant binding to DNA}, journal = {Journal of Physical Chemistry B}, volume = {116}, number = {20}, year = {2012}, month = {MAY}, pages = {5831-5837}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

In this work, the binding kinetics of amino acid-based surfactants, presenting different linkers and head groups, with calf thymus (CT)-DNA was studied using stopped-flow fluorescence spectroscopy. The kinetic studies were carried out as a function of Na+ concentration and surfactant-to-DNA charge ratio. The surfactant binding on DNA took place in two consecutive steps, for which the corresponding first and second relative rate constants (k(1) and k(2)) were determined. The fast step was attributed to the surfactant binding to DNA and micelle formation in its vicinity, the slower step to DNA condensation and possible rearrangement of the surfactant aggregates. In general, both relative rate constants increase with surfactant concentration and decrease with the ionic strength of the medium. The architecture of the surfactant was found to have a significant impact on the kinetics of the DNA surfactant complexation. Surfactants with amide linkers showed larger relative rate constants than those with ester linkers. The variation of the relative rate constants with the head groups of the surfactants, alanine and proline, was found to be less obvious, being partially dependent on the surfactant concentration.

}, issn = {1520-6106}, doi = {10.1021/jp301069t}, author = {Santhiya, Deenan and Dias, Rita S. and Dutta, Sounak and Das, Prasanta Kumar and Miguel, Maria G. and Lindman, Bjorn and Maiti, Souvik} } @article { ISI:000299158700036, title = {Tuberculosis drug streptomycin as a potential cancer therapeutic: inhibition of miR-21 function by directly targeting its precursor}, journal = {Angewandte Chemie-International Edition}, volume = {51}, number = {4}, year = {2012}, month = {DEC}, pages = {1019-1023}, publisher = {WILEY-BLACKWELL}, type = {Article}, address = {COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA}, keywords = {Apoptosis, drug discovery, Gene expression, inhibitors, RNA}, issn = {1433-7851}, doi = {10.1002/anie.201106455}, author = {Bose, Debojit and Jayaraj, Gopal Gunanathan and Suryawanshi, Hemant and Agarwala, Prachi and Pore, Subrata Kumar and Banerjee, Rajkumar and Maiti, Souvik} } @article { ISI:000320836600009, title = {Effect of different arginine methylations on the thermodynamics of tat peptide binding to HIV-1 TAR RNA}, journal = {Biochimie}, volume = {95}, number = {7}, year = {2013}, month = {JUL}, pages = {1422-1431}, publisher = {ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER}, address = {23 RUE LINOIS, 75724 PARIS, FRANCE}, abstract = {

RNA-binding proteins are an important class of mediators that regulate cell function and differentiation. Methylation of arginine, a post-translational modification (PTM) found in these proteins, can modulate their function. Arginine can be monomethylated or dimethylated, depending on the type of methyl transferases involved. This paper describes a comparative study of the thermodynamics of unmodified and modified Tat peptide interaction with TAR RNA, where the peptide is methylated at epsilon (epsilon) and eta (eta) nitrogen atoms of guanidinium group of arginine side chain at position 52 or 53. The results indicate that monomethylation of arginine at epsilon (epsilon) nitrogen atom enhances binding affinity, owing to a more favourable enthalpy component which overrides the less favourable entropy change. In contrast, monomethylation of arginine residue at eta nitrogen results in reduced binding affinity originating exclusively from a less favourable enthalpy change leaving entropic component unaffected. However, in case of simultaneous methylation at epsilon and eta positions, the binding parameters remain almost unaffected, when compared to the unmodified peptide. In case of symmetric dimethylation at eta position the observed enthalpy change of the binding was found to be smaller than the values obtained for the unmodified peptide. Asymmetric dimethylation at eta position showed the most reduced binding affinities owing to less favourable enthalpy changes. These results provide insights that enable elucidation of the biological outcome of arginine methylation as PTMs that regulate protein function, and will contribute to our understanding of how these PTMs are established in vitro and in vivo. (C) 2013 Elsevier Masson SAS. All rights reserved.

}, keywords = {HIV-1, Post-translational modification, Protein methylation, RNA-protein interaction, Thermodynamics}, issn = {0300-9084}, doi = {10.1016/j.biochi.2013.03.008}, author = {Kumar, Santosh and Maiti, Souvik} } @article { ISI:000320640600005, title = {Effect of loops and G-quartets on the stability of RNA G-quadruplexes}, journal = {Journal of Physical Chemistry B}, volume = {117}, number = {23}, year = {2013}, month = {JUN}, pages = {6896-6905}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

The loop length, loop composition, salt concentration, and number of G-quartets are major determinants of G-quadruplex stability. We examined the effect of each of these factors on the thermal stability and folding topology of a library of RNA quadruplexes. The thermal stability of G2 and G3 RNA quadruplexes was investigated upon varying the loop length (from 1-1-1 to 15-15-15) and salt concentration (from sequence 1 to 100 mM KCl), while the effect of loop composition was explored using 18 naturally occurring potential RNA quadruplexes predicted in untranslated regions (UTRs). We found loop length and quadruplex stability to be inversely related for G2 RNA quadruplexes and G3 RNA quadruplexes with shorter loops. However, melting temperature saturates for G3 RNA quadruplexes with longer loops. RNA G-quadruplexes with longer loops (G3 15-15-15) displayed T-m values significantly higher than the physiological temperature. This study thus highlights the need to modify the consensus motif presently used by quadruplex prediction tools. An increase in the loop size from 7 bases to IS bases in the consensus motif will add to its predictive value for the discovery of potential RNA quadruplexes across transcriptomes.

}, issn = {1520-6106}, doi = {10.1021/jp401739m}, author = {Pandey, Satyaprakash and Agarwala, Prachi and Maiti, Souvik} } @article { ISI:000326022200050, title = {Effect of N-acetylation and N-methylation of lysine residue of tat peptide on its interaction with HIV-1 TAR RNA}, journal = {Plos One}, volume = {8}, number = {10}, year = {2013}, month = {OCT}, pages = {UNSP e77595}, publisher = {PUBLIC LIBRARY SCIENCE}, address = {1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA}, abstract = {

Post-translational modification (PTM) of RNA binding proteins (RBPs) play a very important role in determining their binding to cognate RNAs and therefore regulate the downstream effects. Lysine can undergo various PTMs and thereby contribute to the regulation of different cellular processes. It can be reversibly acetylated and methylated using a pool of respective enzymes, to act as a switch for controlling the binding efficiency of RBPs. Here we have delineated the thermodynamic and kinetic effects of N-acetylation and N-monomethylation of lysine on interaction between HIV-1 TAR RNA and its cognate binder Tat peptide (a model system). Our results indicate that acetylation of lysine 50 (K50), leads to eight-fold reduction in binding affinity, originating exclusively from entropy changes whereas, lysine 51 (K51) acetylation resulted only in three fold decrease with large enthalpy-entropy compensation. The measurement of kinetic parameters indicated major change (4.5 fold) in dissociation rate in case of K50 acetylation however, K51 acetylation showed similar effect on both association and dissociation rates. In contrast, lysine methylation did not affect the binding affinity of Tat peptide to TAR RNA at K50, nonetheless three fold enhancement in binding affinity was observed at K51 position. In spite of large enthalpy-entropy compensation, lysine methylation seems to have more pronounced position specific effect on the kinetic parameters. In case of K50 methylation, simultaneous increase was observed in the rate of association and dissociation leaving binding affinity unaffected. The increased binding affinity for methylated Tat at K51 stems from faster association rate with slightly slower dissociation rate.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0077595}, author = {Kumar, Santosh and Maiti, Souvik} } @article { ISI:000315844500003, title = {G-quadruplex augments translation in the 5 {\textquoteleft} untranslated region of transforming growth factor beta 2}, journal = {Biochemistry}, volume = {52}, number = {9}, year = {2013}, month = {MAR}, pages = {1528-1538}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

Transforming growth factor beta 2 (TGF beta 2) is a versatile cytokine with a prominent role in cell migration, invasion, cellular development, and immunomodulation. TGF beta 2 promotes the malignancy of tumors by inducing epithelial-mesenchymal transition, angiogenesis, and immunosuppression. As it is well-documented that nucleic acid secondary structure can regulate gene expression, we assessed whether any secondary motif regulates its expression at the post-transcriptional level. Bioinformatics analysis predicts an existence of a 23-nucleotide putative G-quadruplex sequence (PG4) in the 5{\textquoteright} untranslated region (UTR) of TGF beta 2 mRNA. The ability of this stretch of sequence to form a highly stable, intramolecular parallel quadruplex was demonstrated using ultraviolet and circular dichroism spectroscopy. Footprinting studies further validated its existence in the presence of a neighboring nucleotide sequence. Following structural characterization, we evaluated the biological relevance of this secondary motif using a dual luciferase assay. Although PG4 inhibits the expression of the reporter gene, its presence in the context of the entire 5{\textquoteright} UTR sequence interestingly enhances gene expression. Mutation or removal of the G-quadruplex sequence from the 5{\textquoteright} UTR of the gene diminished the level of expression of this gene at the translational level. Thus, here we highlight an activating role of the G-quadruplex in modulating gene expression of TGF beta 2 at the translational level and its potential to be used as a target for the development of therapeutics against cancer.

}, issn = {0006-2960}, doi = {10.1021/bi301365g}, author = {Agarwala, Prachi and Pandey, Satyaprakash and Mapa, Koyeli and Maiti, Souvik} } @article { ISI:000326292100005, title = {G-Quadruplexes as tools for synthetic biology}, journal = {Chembiochem}, volume = {14}, number = {16}, year = {2013}, month = {NOV}, pages = {2077-2081}, publisher = {WILEY-V C H VERLAG GMBH}, address = {BOSCHSTRASSE 12, D-69469 WEINHEIM, GERMANY}, abstract = {

With the potential to engineer biological systems, synthetic biology is an emerging field that combines various disciplines of sciences. It encompasses combinations of DNA, RNA and protein modules for constructing desired systems and the rewiring of existing signalling networks. Despite recent advances, this field still lags behind in the artificial reconstruction of cellular processes, and thus demands new modules and switches to create genetic circuits. The widely characterised noncanonical nucleic acid secondary structures, G-quadruplexes are promising candidates to be used as biological modules in synthetic biology. Structural plasticity and functional versatility are significant G-quadruplex traits for its integration into a biological system and for diverse applications in synthetic circuits.

}, keywords = {G-quadruplexes, ribozymes, synthetic biology, topology, zipcodes}, issn = {1439-4227}, doi = {10.1002/cbic.201300456}, author = {Agarwala, Prachi and Pandey, Satyaprakash and Maiti, Souvik} } @article { ISI:000319720700012, title = {Molecular-beacon-based screen for small molecule inhibitors of miRNA maturation}, journal = {ACS Chemical Biology}, volume = {8}, number = {5}, year = {2013}, month = {MAY}, pages = {930-938}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

miRNAs are small non-coding RNAs that regulate about 60\% of mammalian genes by modulating their transcript levels. Network scale studies of miRNA-mediated regulatory circuits demonstrate the central importance of this class of small RNA in the maintenance of biological robustness. More recently, several reports have described the deregulation of numerous miRNA to be causally associated with many diseases, including cancer. These studies have highlighted the potential for development of therapeutic modalities against miRNA. Previous screening protocols, for small molecules targeting miRNA function, are either costly or technically too complex to be applied in a high-throughput manner in standard chemical laboratories. We describe a simple in vitro screening method using a DNA-based molecular beacon that overcomes the limitations associated with earlier screens. We used this method to identify inhibitors of miR-27a function from a library of 14 aminoglycosides as a pilot study. Inhibitory molecules identified were further scrutinized to identify the validity of screen. With this proof of concept we illustrate the utility of a scalable molecular-beacon-based screening strategy for miRNA inhibitors.

}, issn = {1554-8929}, doi = {10.1021/cb300650y}, author = {Bose, Debojit and Jayaraj, Gopal Gunanathan and Kumar, Santosh and Maiti, Souvik} } @article { ISI:000311822100011, title = {Thermodynamics and solvation dynamics of BIV TAR RNA-Tat peptide interaction}, journal = {Molecular Biosystems}, volume = {9}, number = {1}, year = {2013}, month = {OCT}, pages = {88-98}, publisher = {ROYAL SOC CHEMISTRY}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

The interaction of the trans-activation responsive (TAR) region of bovine immunodeficiency virus (BIV) RNA with the Tat peptide is known to play important role in viral replication. Despite being thoroughly studied through a structural point of view, the nature of binding between BIV TAR RNA and the BIV Tat peptide requires information related to its thermodynamics and the nature of hydration around the TAR-Tat complex. In this context, we carried out the thermodynamic study of binding of the Tat peptide to the BIV TAR RNA hairpin through different calorimetric and spectroscopic measurements. Fluorescence titration of 2-aminopurine tagged BIV TAR RNA with the Tat peptide gives their binding affinity. The isothermal titration calorimetric experiment reveals the enthalpy of binding between BIV TAR RNA and the Tat peptide to be largely exothermic with the value of -11.7 (SEM 0.2) kcal mol(-1). Solvation dynamics measurements of BIV TAR RNA having 2-AP located at the bulge region have been carried out in the absence and presence of the BIV Tat peptide using the time correlated single photon counting technique. The solvent cage around the Tat binding site of RNA appears to be more rigid in the presence of the Tat peptide as compared to the free RNA. The displacement of solvent and ions on RNA due to peptide binding influences the entropic contributions to the total binding energy.

}, issn = {1742-206X}, doi = {10.1039/c2mb25357g}, author = {Goel, Teena and Kumar, Santosh and Maiti, Souvik} } @article { ISI:000334599800029, title = {Anti-cancer therapeutic potential of quinazoline based small molecules via global upregulation of miRNAs}, journal = {Chemical Communications}, volume = {50}, number = {35}, year = {2014}, month = {MAR}, pages = {4639-4642}, publisher = {ROYAL SOC CHEMISTRY}, type = {Article}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

Three quinazoline based small molecules showed global upregulation of miRNA expression with a selective enrichment of tumor suppressor miRNAs. The target genes of the upregulated miRNAs were predicted to be enriched for apoptotic pathways. Apoptotic induction following treatment with quinazoline compounds was confirmed by in cellulo studies. Thus, these small molecules having the core structural moiety (2,4-diphenyl-quinazoline) can be used as scaffolds to design activators of miRNA expression paving the way for novel anti-cancer drugs.

}, issn = {1359-7345}, doi = {10.1039/c3cc49337g}, author = {Nahar, Smita and Bose, Debojit and Panja, Sumit Kumar and Saha, Satyen and Maiti, Souvik} } @article { ISI:000337645600001, title = {In the sense of transcription regulation by G-quadruplexes: asymmetric effects in sense and antisense strands}, journal = {Biochemistry}, volume = {53}, number = {23}, year = {2014}, month = {JUN}, pages = {3711-3718}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

G-Quadruplexes occupy important regulatory regions in the genome. DNA G-quadruplexes in the promoter regions and RNA quadruplexes in the UTRs (untranslated regions) have been individually studied and variously implicated at different regulatory levels of gene expression. However, the formation of G-quadruplexes in the sense and antisense strands and their corresponding roles in gene regulation have not been studied in much detail. In the present study, we have elucidated the effect of strand asymmetry in this context. Using biophysical methods, we have demonstrated the formation of stable G-quadruplex structure in vitro using CD and UV melting. Additionally, ITC was employed to demonstrate that a previously reported selective G-quadruplex ligand was able to bind and stabilize the G-quadruplex in the present sequence. Further, we have shown using reporter constructs that although the DNA G-quadruplex in either strand can reduce translation efficiency, transcriptional regulation differs when G-quadruplex is present in the sense or antisense strand. We demonstrate that the G-quadruplex motif in the antisense strand substantially inhibits transcription, while when in the sense strand, it does not affect transcription, although it does ultimately reduce translation. Further, it is also shown that the G-quadruplex stabilizing ligand can enhance this asymmetric transcription regulation as a result of the increased stabilization of the G-quadruplex.

}, issn = {0006-2960}, doi = {10.1021/bi401451q}, author = {Agarwal, Tani and Roy, Saumya and Kumar, Santosh and Chakraborty, Tushar Kanti and Maiti, Souvik} } @article { ISI:000332059600003, title = {Morphological effects of G-quadruplex stabilization using a small molecule in zebrafish}, journal = {Biochemistry}, volume = {53}, number = {7}, year = {2014}, month = {FEB}, pages = {1117-1124}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

Zebrafish (Danio rerio) embryos are transparent and advantageous for studying early developmental changes due to ex utero development, making them an appropriate model for studying gene expression changes as a result of molecular targeting. Zebrafish embryos were injected with a previously reported G-quadruplex selective ligand, and the phenotypic changes were recorded. We report marked discrepancies in the development of intersegmental vessels. In silico analysis determined that the putative G-quadruplex motif occur in the upstream promoter region of the Cdh5 (N-cadherin) gene. A real-time polymerase chain reaction-based investigation indicated that in zebrafish, CDH-2 (ZN-cad) was significantly downregulated in the ligand-treated embryos. Biophysical characterization of the interaction of the ligand with the G-quadruplex motif found in this promoter yielded strong binding and stabilization of the G-quadruplex with this ligand. Hence, we report for the first time the phenotypic impact of G-quadruplex targeting with a ligand in a vertebrate organism. This study has unveiled not only G-quadruplex targeting in non-human animal species but also the potential that G-quadruplexes can provide a ready tool for understanding the phenotypic effects of targeting certain important genes involved in differentiation and developmental processes in a living eukaryotic organism.

}, issn = {0006-2960}, doi = {10.1021/bi4009352}, author = {Agarwal, Tani and Lalwani, Mukesh Kumar and Kumar, Santosh and Roy, Saumya and Chakraborty, Tushar Kanti and Sivasubbu, Sridhar and Maiti, Souvik} } @article { ISI:000343847000023, title = {Role of G-quadruplex located at 5 end of mRNAs}, journal = {Biochimica Et Biophysica Acta-General Subjects}, volume = {1840}, number = {12}, year = {2014}, month = {DEC}, pages = {3503-3510}, publisher = {ELSEVIER SCIENCE BV}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {

Background: Secondary structures in 5{\textquoteright} UTR of mRNAs play a critical role in regulating protein synthesis. Though studies have indicated the role of secondary structure G-quadruplex in translational regulation, position-specific effect of G-quadruplex in naturally occurring mRNAs is still not understood. As a pre-initiation complex recognises 5{\textquoteright} cap of the mRNA and scans along the untranslated region (UTR) before initiating translation, the presence of G-quadruplex in 5{\textquoteright} region may have a significant contribution in regulating translation. Here, we investigate the role of G-quadruplex located at the 5{\textquoteright} end of an mRNA. Methods: Biophysical characterisation of putative G-quadruplexes was performed using UV and CD spectroscopy. Functional implication of G-quadruplex in the context of their location was assessed in cellulo using gRT-PCR and dual luciferase assay system. Results: PG4 sequences in 5{\textquoteright} UTR of AICT interacting protein (AKTIP), cathepsin B (CTSB) and forkhead box E3 (FOXE3) mRNAs form G-quadruplex whereas it is unable to form G-quadruplex in apolipoprotein A-I binding protein (APOA1BP). Our results demonstrated diverse roles of G-quadruplex located at 5{\textquoteright} end of mRNAs. Though G-quadruplex in AKTIP and CTSB mRNA act as inhibitory modules, it activates translation in FOXE3 mRNA. Conclusions: Our works suggests that G-quadruplex present at the 5{\textquoteright} terminal of an mRNA behaves differently in a different gene context. It can activate or inhibit gene expression. General significance: This study demonstrated that it is difficult to predict the role of G-quadruplex on the basis of its position in 5{\textquoteright} UTR. The neighbouring nucleotide sequence, the intracellular milieu and the interacting partners might render diverse functions to this secondary structure. (C) 2014 Elsevier B.V. All rights reserved.

}, keywords = {AKTIP, APOA1BP, CTSB, FOXE3, G-quadruplex, UTR}, issn = {0304-4165}, doi = {10.1016/j.bbagen.2014.08.017}, author = {Agarwala, Prachi and Pandey, Satyaprakash and Maiti, Souvik} } @article { ISI:000333235600009, title = {Understanding the effect of locked nucleic acid and 2 {\textquoteleft}-O-methyl modification on the hybridization thermodynamics of a miRNA-mRNA pair in the presence and absence of AfPiwi protein}, journal = {Biochemistry}, volume = {53}, number = {10}, year = {2014}, month = {MAR}, pages = {1607-1615}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

miRNAs are some of the key epigenetic regulators of gene expression. They act through hybridization with their target mRNA and modulate the level of respective proteins via different mechanisms. Various cancer conditions are known to be associated with up- and downregulation of the oncogenic and tumor suppressor miRNAs, respectively. The levels of aberrantly expressed oncogenic miRNAs can be downregulated in different ways. Similarly, restoration of tumor suppressor miRNAs to their normal levels can be achieved using miRNA mimics. However, the use of miRNA mimics is limited by their reduced biostability and function. We have studied the hybridization thermodynamics of the miRNA 26a (11-mer, including the seed sequence) guide strand with the mRNA (11-mer) target strand in the absence and presence of AfPiwi protein. We have also inserted locked nucleic acids (LNAs) and 2{\textquoteright}-O-methyl-modified nucleotides into the guide strand, in a walk-through manner, to assess their effect on the binding efficiency between guide and target RNA. Insertion of LNA and 2{\textquoteright}-O-methyl-modified nucleotides into the guide strand helped to strengthen the binding affinity irrespective of the position of insertion. However, in the presence of AfPiwi protein, these modifications reduced the binding affinity to different extents depending on the position of insertion. Insertion of a modification leads to an increase in the enthalpic contribution with an increased unfavorable entropic contribution, which negatively compensates for the higher favorable enthalpy.

}, issn = {0006-2960}, doi = {10.1021/bi401677d}, author = {Kumar, Santosh and Mapa, Koyeli and Maiti, Souvik} } @article { ISI:000353218700026, title = {Beta, gamma-Bis-substituted PNA with configurational and conformational switch: preferred binding to cDNA/RNA and cell-uptake studies}, journal = {Chemical Communications}, volume = {51}, number = {36}, year = {2015}, month = {MAR}, pages = {7693-7696}, publisher = {ROYAL SOC CHEMISTRY}, type = {Article}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

(S,S)- and (R,R)-beta,gamma-Bis-substituted PNAs were synthesized from the C-2 symmetric vicinal diamine system embedded in 1,4 dihydroxybutane and 1,4-dimethoxybutane scaffolds. (R,R)-beta,gamma-Bis-methoxymethyl-PNA derived from D-tartaric acid was found to be in the right configuration and conformation to be an excellent mimic of PNA, endowed with superior ability to enter into cells.

}, issn = {1359-7345}, doi = {10.1039/c5cc00891c}, author = {Bose, Tanaya and Banerjee, Anjan and Nahar, Smita and Maiti, Souvik and Kumar, Vaijayanti A.} } @article { ISI:000365529900006, title = {Cyclic cationic peptides containing sugar amino acids selectively distinguishes and inhibits maturation of pre-mirnas of the same family}, journal = {Nucleic Acid Therapeutics}, volume = {25}, number = {6}, year = {2015}, month = {DEC}, pages = {323-329}, publisher = {MARY ANN LIEBERT, INC}, address = {140 HUGUENOT STREET, 3RD FL, NEW ROCHELLE, NY 10801 USA}, abstract = {

The discovery of microRNAs (miRNAs) has added a new dimension to the gene regulatory networks, making aberrantly expressed miRNAs as therapeutically important targets. Small molecules that can selectively target and modulate miRNA levels can thus serve as lead structures. Cationic cyclic peptides containing sugar amino acids represent a new class of small molecules that can target miRNA selectively. Upon treatment of these small molecules in breast cancer cell line, we profiled 96 therapeutically important miRNAs associated with cancer and observed that these peptides can selectively target paralogous miRNAs of the same seed family. This selective inhibition is of prime significance in cases when miRNAs of the same family have tissue-specific expression and perform different functions. During these conditions, targeting an entire miRNA family could lead to undesired adverse effects. The selective targeting is attributable to the difference in the three-dimensional structures of precursor miRNAs. Hence, the core structure of these peptides can be used as a scaffold for designing more potent inhibitors of miRNA maturation and hence function.

}, issn = {2159-3337}, doi = {10.1089/nat.2015.0554}, author = {Nahar, Smita and Bose, Debojit and Pal, Sudip and Chakraborty, Tushar Kanti and Maiti, Souvik} } @article { ISI:000352329300007, title = {Human telomeric RNA G-quadruplex response to point mutation in the G-quartets}, journal = {Journal of Physical Chemistry B}, volume = {119}, number = {13}, year = {2015}, month = {APR}, pages = {4617-4627}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

Many putative G-quadruplex forming sequences have been predicted to exist in the human genome and transcriptome. As these sequences are subject to point mutations or SNPs (single nucleotide polymorphisms) during the course of evolution, we attempt to understand impact of these mutations in context of RNA G-quadruplex formation using human telomeric RNA (TERRA) as a model sequence. Our studies suggest that G-quadruplex stability is sensitive to substitution of the guanines comprising G-quartets. While central G-quartet plays a crucial role in maintaining the DNA G-quadruplex stability as evident in literature, there is equal importance of three G-quartets in the stability of RNA quadruplex structure. The work here highlights the alterations in the G-quartet are detrimental to the integrity of overall RNA G-quadruplex structure. Furthermore, TmPyP4 molecules are shown to exhibit similar binding behavior toward telomeric RNA G-quadruplex harboring base substitutions employing CD titrations and isothermal titration calorimetry; well indicating that mutation does not influence TmPyP4 recognition ability as it affects the stability of RNA G-quadruplex. Thus, our study implicates that mutation in G-quartets causes destabilization of RNA G-quadruplex without affecting its trans factor binding ability.

}, issn = {1520-6106}, doi = {10.1021/acs.jpcb.5b00619}, author = {Agarwala, Prachi and Kumar, Santosh and Pandey, Satyaprakash and Maiti, Souvik} } @article { ISI:000346408800001, title = {Nonconventional chemical inhibitors of microRNA: therapeutic scope}, journal = {Chemical Communications}, volume = {51}, number = {5}, year = {2015}, month = {OCT}, pages = {820-831}, publisher = {ROYAL SOC CHEMISTRY}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

MicroRNAs (miRNAs) are a class of genomically encoded small RNA molecules (similar to 22nts in length), which regulate gene expression post transcriptionally. The term microRNA or miRNA was coined in 2001, and research in the past decade has shed light on their widespread occurrence, evolutionary conservation and tissue specific functions. It is estimated that they modulate the gene expression of approximately 60\% of the mammalian genes by regulating the levels of target mRNAs to which they can bind on the basis of sequence complementarities. miRNAs are produced in a well coordinated series of steps from being transcribed in the nucleus to exerting their function in the cytoplasm. miRNAs are now implicated in diverse biological phenomena ranging from development to stress response which makes miRNAs one of the central regulatory molecules which modulate information flow along the central dogma of gene expression. More importantly, like any regulatory molecule, deregulation of miRNAs is causally associated with several diseases (mainly cancer) and is directly involved in a variety of pathophysiologies owing to their aberrant expression. Thus, modulation of miRNA levels is of prime therapeutic importance. Conventional methods of miRNA knockdown using chemically modified antisense-oligonucleotides have been explored extensively but face the challenges of modes of delivery, biostability and biodistribution. This calls for the development of more alternative and non-conventional methods to target miRNA. Small molecules targeting RNA chemical and structural space provide one such timely opportunity. In this article we first provide a brief overview of miRNA biogenesis and its disease associations. We then summarize the major developments in conventional oligonucleotide based approaches to miRNA knockdown and its status. We then focus on the more non-conventional methods like oligonucleotide enzymes and small molecules and provide an outlook on the future of such methods.

}, issn = {1359-7345}, doi = {10.1039/c4cc04514a}, author = {Jayaraj, Gopal Gunanathan and Nahar, Smita and Maiti, Souvik} } @article { ISI:000361212000060, title = {Potent inhibition of miR-27a by neomycin-bisbenzimidazole conjugates}, journal = {Chemical Science}, volume = {6}, number = {10}, year = {2015}, month = {JUL}, pages = {5837-5846}, publisher = {ROYAL SOC CHEMISTRY}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

miRNAs are important components of regulatory networks that control gene expression and have implications in various diseases including cancer. Targeting oncogenic miRNAs with small molecules is currently being explored to develop cancer therapeutics. Here, we report the development of dual binding neomycin-bisbenzimidazole conjugates that target oncogenic miR-27a with high affinity (K-a = 1.2 to 7.4 x 10(8) M-1). These conjugates bring significant reduction (similar to 65\% at 5 mu M) in mature miRNA levels and penetrate easily in the cells where they localise both in the cytoplasm and the nucleus. Cell cycle analysis showed significant increase in the G0/G1 phase (similar to 15\%) and decrease in the S phase (similar to 7\%) upon treatment with neomycin-bisbenzimidazole conjugates, suggesting inhibition of cell proliferation. Using the conjugation approach, we show that moderately binding ligands can be covalently combined into high affinity binders. This study also highlights the role of linker optimization in designing high affinity ligands for miR-27a targeting.

}, issn = {2041-6520}, doi = {10.1039/c5sc01969a}, author = {Nahar, Smita and Ranjan, Nihar and Ray, Arjun and Arya, Dev P. and Maiti, Souvik} } @article { ISI:000366339300003, title = {RNA stem-loop to G-quadruplex equilibrium controls mature MicroRNA production inside the cell}, journal = {Biochemistry}, volume = {54}, number = {48}, year = {2015}, month = {DEC}, pages = {7067-7078}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

The biological role of the existence of overlapping structures in RNA is possible yet remains very unexplored. G-Rich tracts of RNA form G-quadruplexes, while GC-rich sequences prefer stem-loop structures. The equilibrium between alternate structures within RNA may occur and influence its functionality. We tested the equilibrium between G-quadruplex and stem-loop structure in RNA and its effect on biological processes using pre-miRNA as a model system. Dicer enzyme recognizes canonical stem-loop structures in pre-miRNA to produce mature miRNAs. Deviation from stem-loop leads to deregulated mature miRNA levels, providing readout of the existence of an alternate structure per se G-quadruplex-mediated structural interference in miRNA maturation. In vitro analysis using beacon and Dicer cleavage assays indicated that mature miRNA levels depend on relative amounts of K+: and Mg2+ ions, suggesting an ion-dependent structural shift. Further in cellulo studies with and without TmPyP4 (RNA G-quadruplex destabilizer) demonstrated that miRNA biogenesis is modulated by G-quadruplex to stem-loop equilibrium in a subset of pre-miRNAs. Our combined analysis thus provides evidence of the formation of noncanonical G-quaciruplexes in competition with canonical stem-loop structure inside the cell and its effect on miRNA maturation in a comprehensive manner.

}, issn = {0006-2960}, doi = {10.1021/acs.biochem.5b00574}, author = {Pandey, Satyaprakash and Agarwala, Prachi and Jayaraj, Gopal Gunanathan and Gargallo, Raimundo and Maiti, Souvik} } @article { ISI:000355317200045, title = {Selective inhibition of miR-21 by phage display screened peptide}, journal = {Nucleic Acids Research}, volume = {43}, number = {8}, year = {2015}, month = {APR}, pages = {4342-4352}, publisher = {OXFORD UNIV PRESS}, address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND}, abstract = {

miRNAs are nodal regulators of gene expression and deregulation of miRNAs is causally associated with different diseases, including cancer. Modulation of miRNA expression is thus of therapeutic importance. Small molecules are currently being explored for their potential to downregulate miRNAs. Peptides have shown to have better potency and selectivity toward their targets but their potential in targeting and modulating miRNAs remain unexplored. Herein, using phage display we found a very selective peptide against pre-miR-21. Interestingly, the peptide has the potential to downregulate miR-21, by binding to pre-miR-21 and hindering Dicer processing. It is selective towards miR-21 inside the cell. By antagonising miR-21 function, the peptide is able to increase the expression of its target proteins and thereby increase apoptosis and suppress cell proliferation, invasion and migration. This peptide can further be explored for its anti-cancer activity in vivo and may be even extended to clinical studies.

}, issn = {0305-1048}, doi = {10.1093/nar/gkv185}, author = {Bose, Debojit and Nahar, Smita and Rai, Manish Kumar and Ray, Arjun and Chakraborty, Kausik and Maiti, Souvik} } @article { ISI:000354438400001, title = {Tale of RNA G-quadruplex}, journal = {Organic \& Biomolecular Chemistry}, volume = {13}, number = {20}, year = {2015}, month = {APR}, pages = {5570-5585}, publisher = {ROYAL SOC CHEMISTRY}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

G-quadruplexes are non-canonical secondary structures found in guanine rich regions of DNA and RNA. Reports have indicated the wide occurrence of RNA G-quadruplexes across the transcriptome in various regions of mRNAs and non-coding RNAs. RNA G-quadruplexes have been implicated in playing an important role in translational regulation, mRNA processing events and maintenance of chromosomal end integrity. In this review, we summarize the structural and functional aspects of RNA G-quadruplexes with emphasis on recent progress to understand the protein/trans factors binding these motifs. With the revelation of the importance of these secondary structures as regulatory modules in biology, we have also evaluated the various advancements towards targeting these structures and the challenges associated with them. Apart from this, numerous potential applications of this secondary motif have also been discussed.

}, issn = {1477-0520}, doi = {10.1039/c4ob02681k}, author = {Agarwala, Prachi and Pandey, Satyaprakash and Maiti, Souvik} } @article { ISI:000372562000005, title = {Influence of ionic liquids on thermodynamics of small molecule DNA interaction: the binding of ethidium bromide to calf thymus DNA}, journal = {Journal of Physical Chemistry B}, volume = {120}, number = {10}, year = {2016}, month = {MAR}, pages = {2691-2700}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

Ionic liquids (ILs) are salts with poor ionic coordination, resultantly remaining in liquid state below 100 degrees C and some may retain liquid state even at room temperature. ILs are known to provide a conducive environment for many biological enzymatic reactions, but their interaction with biomacromolecules are poorly understood. In the present study, we investigate the effect of various ionic liquids on DNA small molecule interaction using calf thymus DNA (ctDNA) ethidium bromide (EB) as a model system. The effect of various ionic liquids on these interactions is studied by an array of techniques such as circular dichroism (CD), UV melting, fluorescence exclusion and isothermal titration calorimetry. Interestingly, we observed that presence of IL increased the stability of ctDNA without altering its structure. The binding affinities Kbs for EB binding to ctDNA in the presence of 300 mM ILs are about half order of magnitude smaller than the Kbs in absence of ILs and correspond to a less favorable free energy. We noted that, when adjusted to corresponding buffer condition, the unfavorable shift in AG of ctDNA-EB interaction is attributed to decreased entropy in the case of ILs, whereas the same effect by NaCI was due to increased enthalpy.

}, issn = {1520-6106}, doi = {10.1021/acs.jpcb.5b11823}, author = {Mishra, Arpit and Ekka, Mary Krishna and Maiti, Souvik} } @article {45641, title = {Inhibition of miR-21 by 3 {\textquoteleft}/5 {\textquoteleft}-serinyl-capped 2 {\textquoteleft}-O-Methyl RNA Interspersed with 2 {\textquoteleft}-O-(2-Amino-3-Methoxypropyl) uridine units}, journal = {Nucleic Acid Therapeutics}, volume = {26}, year = {2016}, month = {OCT}, pages = {327-334}, type = {Article}, abstract = {

miRNAs are highly conserved class of small ncRNAs whose involvement in human pathophysiologies is extensively investigated. MiR-21 is a well established oncogenic miRNA whose deregulation plays a significant role in onset and progression of cancer. The need of novel approaches to downregulate miR-21 is rapidly expanding. Potent inhibition of miR-21 is achieved by chemically modified 2-O-methyl RNA oligonucleotide. The serinol capping at 3 and 5ends and the interspersed 2-O-(R-2-amino-3-methoxypropyl) uridine units enhance the nuclease resistance and efficacy of 2-O-methyl RNA for the inhibition of miR-21. This represents a simple and novel modification for developing oligonucleotide-based therapeutics.

}, keywords = {antagomirs, cancer, microRNA, noncoding RNA, oligonucleotides}, issn = {2159-3337}, doi = {10.1089/nat.2015.0591}, author = {Nahar, Smita and Kotikam, Venubabu and Kumar, Vaijayanti A. and Maiti, Souvik} } @article {43406, title = {Systematic evaluation of biophysical and functional characteristics of selenomethylene-locked nucleic acid-mediated inhibition of miR-21}, journal = {Biochemistry}, volume = {55}, year = {2016}, month = {DEC}, pages = {7023-7032}, abstract = {miRNAs constitute an important layer of gene regulation mediated by sequence-specific targeting of mRNAs. Aberrant expression of miRNAs contributes to a host of pathological states. Promoting cancer, miR-21 is upregulated in variety of cancers and promotes tumor progresion by suppressing a network of tumor suppressor genes. Here we describe a novel class of bicyclic RNA analogues, selenomethylene-locked nucleic acid (SeLNA), that display high affinity, improved metabolic stability, and increased potency for miR-21 inhibition. The thermal stability (T-m) for duplexes was increased significantly with incorporation of SeLNA monomers as compared to that of the unmodified DNA RNA hybrid. A comprehensive thermodynamic profile obtained by isothermal titration calorimetry revealed a favorable increase in the enthalpy of hybridization for SeLNA containing DNA and target RNA heteroduplexes. SeLNA modifications displayed remarkable binding affinity for miR-21 target RNA with a K-a of <= 1.05 x 10(8) M-1. We also observed enhanced serum stability for SeLNA RNA duplexes with a half-life of <= 36 h. These in vitro results were well correlated with the antisense activity in cancer cells imparting up to similar to 91\% inhibition of miR-21. The functional impact of SeLNA modifications on miR-21 inhibition was further gauged by investigating the migration and invasion characterisitics of cancer cells, which were drastically reduced to similar to 49 and similar to 55\%, respectively, with SeLNA having four such modifications. Our findings demonstrate SeLNA as a promising candidate for therapeutics for disease associated miRNAs.}, doi = {10.1021/acs.biochem.6b00895}, author = {Nahar, Smita and Singh, Amrita and Morihiro, Kunihiko and Moai, Yoshihiro and Kodama, Tetsuya and Obika, Satoshi and Maiti, Souvik} } @article {44489, title = {G-quadruplex motif at the 3{\textquoteright} end of sgRNAs improves CRISPR-Cas9 based genome editing efficiency}, journal = {Chemical Communications}, volume = {54}, year = {2018}, month = {MAR}, pages = {2377-2380}, abstract = {Originating as a component of prokaryotic adaptive immunity, the type II CRISPR/Cas9 system has been repurposed for targeted genome editing in various organisms. Although Cas9 can bind and cleave DNA efficiently under in vitro conditions, its activity inside a cell can vary dramatically between targets owing to differences between genomic loci and availability of enough Cas9/sgRNA (single guide RNA) complex molecules for cleavage. Most methods to improve CRISPR/Cas9 activity have so far relied on Cas9 protein engineering or base modifications in the sgRNA sequence. Here we demonstrate that a structure based rational design of sgRNAs can enhance the efficiency of Cas9 cleavage in vivo. By appending a naturally forming RNA G-quadruplex motif to the 3' end of sgRNAs we can improve its stability and target cleavage efficiency in zebrafish embryos without inducing off-target activity, thereby underscoring its value in the design of better and optimized genome editing triggers.}, issn = {1359-7345}, doi = {10.1039/C7CC08893K}, author = {Nahar, Smita and Sehgal, Paras and Azhar, Mohammad and Rai, Manish and Singh, Amrita and Sivasubbu, Sridhar and Chakraborty, Debojyoti and Maiti, Souvik} } @article {44188, title = {Superior HIV-1 TAR binders with conformationally constrained R52 arginine mimics in the Tat(48-57) peptide}, journal = {Chemmedchem}, volume = {13}, year = {2018}, month = {FEB }, pages = {220-226}, type = {Article}, abstract = {

We report a 100-fold increase in binding affinity of the Tat(48-57) peptide to HIV-1 transcriptional activator-responsive element (TAR) RNA by replacing Arg52, an essential and critical residue for Tat{\textquoteright}s specific binding, with (2S,4S)-4-guanidinoproline. The resulting Tat1M peptide is a far superior binder than Tat1M, a peptide containing another conformationally constrained arginine mimic, (2S,4S)-4-amino-N-(3-guanidinopropyl)proline, or even the control Tat peptide (CtrlTat) itself. Our observations are supported by circular dichroism (CD), isothermal titration calorimetry (ITC), gel electrophoresis and UV spectroscopy studies. Molecular dynamics simulations suggest increased interactions between the more compact Tat1M and TAR RNA, relative to CtrlTat. The CD signature of the RNA itself remains largely unchanged upon binding of the peptides. The Tat mimetics further have better cell uptake properties than the control Tat peptide, thus increasing their potential application as specific TAR-binding molecules.

}, keywords = {antiviral agents, arginine mimics, RNA, Tat peptide analogues, Tat-TAR binding}, issn = {1860-7179}, doi = {10.1002/cmdc.201700653}, author = {Bhosle, Govind S. and Kharche, Shalmali and Kumar, Santosh and Sengupta, Durba and Maiti, Souvik and Fernandes, Moneesha} } @article {46331, title = {Francisella novicida Cas9 interrogates genomic DNA with very high specificity and can be used for mammalian genome editing}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, year = {2019}, month = {OCT}, pages = {20959-20968}, type = {Article}, abstract = {

Genome editing using the CRISPR/Cas9 system has been used to make precise heritable changes in the DNA of organisms. Although the widely used Streptococcus pyogenes Cas9 (SpCas9) and its engineered variants have been efficiently harnessed for numerous gene-editing applications across different platforms, concerns remain regarding their putative off-targeting at multiple loci across the genome. Here we report that Francisella novicida Cas9 (FnCas9) shows a very high specificity of binding to its intended targets and negligible binding to off-target loci. The specificity is determined by its minimal binding affinity with DNA when mismatches to the target single-guide RNA (sgRNA) are present in the sgRNA:DNA heteroduplex. FnCas9 produces staggered cleavage, higher homology-directed repair rates, and very low nonspecific genome editing compared to SpCas9. We demonstrate FnCas9-mediated correction of the sickle cell mutation in patient-derived induced pluripotent stem cells and propose that it can be used for precise therapeutic genome editing for a wide variety of genetic disorders.

}, keywords = {CRISPR Cas9, gene therapy, Genome editing, iPSCs, sickle cell anemia}, issn = {0027-8424}, doi = {10.1073/pnas.1818461116}, author = {Acharya, Sundaram and Mishra, Arpit and Paul, Deepanjan and Ansari, Asgar Hussain and Azhar, Mohd and Kumar, Manoj and Rauthan, Riya and Sharma, Namrata and Aich, Meghali and Sinha, Dipanjali and Sharma, Saumya and Jain, Shivani and Ray, Arjun and Jain, Suman and Ramalingam, Sivaprakash and Maiti, Souvik and Chakraborty, Debojyoti} } @article {46741, title = {Terminal uridylyl transferase mediated site-directed access to clickable chromatin employing CRISPR-dCas9}, journal = {Journal of the American Chemical Society}, volume = {142}, year = {2020}, month = {AUG}, pages = {13954-13965}, type = {Article}, abstract = {

Locus-specific interrogation of target genes employing functional probes such as proteins and small molecules is paramount in decoding the molecular basis of gene function and designing tools to modulate its downstream effects. In this context, CRISPR-based gene editing and targeting technologies have proved tremendously useful, as they can be programmed to target any gene of interest by simply changing the sequence of the single guide RNA (sgRNA). Although these technologies are widely utilized in recruiting genetically encoded functional proteins, display of small molecules using CRISPR system is not well developed due to the lack of adequate techniques. Here, we have devised an innovative technology called sgRNA-Click (sgR-CLK) that harnesses the power of bioorthogonal click chemistry for remodeling guide RNA to display synthetic molecules on target genes. sgR-CLK employs a novel posttranscriptional chemoenzymatic labeling platform wherein a terminal uridylyl transferase (TUTase) was repurposed to generate clickable sgRNA of choice by site-specific tailoring of multiple azide-modified nucleotide analogues at the 3{\textquoteright} end. The presence of a minimally invasive azide handle assured that the sgRNAs are indeed functional. Notably, an azide-tailed sgRNA targeting the telomeric repeat served as a Trojan horse on the CRISPR-dCas9 system to guide synthetic tags (biotin) site-specifically on chromatin employing copper-catalyzed or strain-promoted click reactions. Taken together, sgR-CLK presents a significant advancement on the utility of bioorthogonal chemistry, TUTase, and the CRISPR toolbox, which could offer a simplified solution for site-directed display of small molecule probes and diagnostic tools on target genes.

}, issn = {0002-7863}, doi = {10.1021/jacs.0c06541}, author = {George, Jerrin Thomas and Azhar, Mohd and Aich, Meghali and Sinha, Dipanjali and Ambi, Uddhav B. and Maiti, Souvik and Chakraborty, Debojyoti and Srivatsan, Seergazhi G.} } @article {47694, title = {FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip}, journal = {eLife}, volume = {10}, year = {2021}, month = {JUN }, pages = {e67130}, type = {Article}, abstract = {The COVID-19 pandemic originating in the Wuhan province of China in late 2019 has impacted global health, causing increased mortality among elderly patients and individuals with comorbid conditions. During the passage of the virus through affected populations, it has undergone mutations, some of which have recently been linked with increased viral load and prognostic complexities. Several of these variants are point mutations that are difficult to diagnose using the gold standard quantitative real-time PCR (qRT-PCR) method and necessitates widespread sequencing which is expensive, has long turn-around times, and requires high viral load for calling mutations accurately. Here, we repurpose the high specificity of Francisella novicida Cas9 (FnCas9) to identify mismatches in the target for developing a lateral flow assay that can be successfully adapted for the simultaneous detection of SARS-CoV-2 infection as well as for detecting point mutations in the sequence of the virus obtained from patient samples. We report the detection of the S gene mutation N501Y (present across multiple variant lineages of SARS-CoV-2) within an hour using lateral flow paper strip chemistry. The results were corroborated using deep sequencing on multiple wild-type (n = 37) and mutant (n = 22) virus infected patient samples with a sensitivity of 87\% and specificity of 97\%. The design principle can be rapidly adapted for other mutations (as shown also for E484K and T716I) highlighting the advantages of quick optimization and roll-out of CRISPR diagnostics (CRISPRDx) for disease surveillance even beyond COVID-19. This study was funded by Council for Scientific and Industrial Research, India.}, issn = {2050-084X}, doi = {10.7554/eLife.67130}, author = {Kumar, Manoj and Gulati, Sneha and Ansari, Asgar H. and Phutela, Rhythm and Acharya, Sundaram and Azhar, Mohd and Murthy, Jayaram and Kathpalia, Poorti and Kanakan, Akshay and Maurya, Ranjeet and Vasudevan, Janani Srinivasa and Aparna, S. and Pandey, Rajesh and Maiti, Souvik and Chakraborty, Debojyoti} } @article {47346, title = {Rapid and accurate nucleobase detection using FnCas9 and its application in COVID-19 diagnosis}, journal = {Biosensors \& Bioelectronics}, volume = {183}, year = {2021}, month = {JUL }, pages = {113207}, type = {Article}, abstract = {

Rapid detection of DNA/RNA pathogenic sequences or variants through point-of-care diagnostics is valuable for accelerated clinical prognosis, as witnessed during the recent COVID-19 outbreak. Traditional methods relying on qPCR or sequencing are tough to implement with limited resources, necessitating the development of accurate and robust alternative strategies. Here, we report FnCas9 Editor Linked Uniform Detection Assay (FELUDA) that utilizes a direct Cas9 based enzymatic readout for detecting nucleobase and nucleotide sequences without transcleavage of reporter molecules. We also demonstrate that FELUDA is 100\% accurate in detecting single nucleotide variants (SNVs), including heterozygous carriers, and present a simple web-tool JATAYU to aid end-users. FELUDA is semi-quantitative, can adapt to multiple signal detection platforms, and deploy for versatile applications such as molecular diagnosis during infectious disease outbreaks like COVID-19. Employing a lateral flow readout, FELUDA shows 100\% sensitivity and 97\% specificity across all ranges of viral loads in clinical samples within 1hr. In combination with RT-RPA and a smartphone application True Outcome Predicted via Strip Evaluation (TOPSE), we present a prototype for FELUDA for CoV-2 detection closer to home.

}, keywords = {CRISPRDx, FELUDA, FnCas9, LFA, SARS-CoV2, SNV detection}, issn = {0956-5663}, doi = {10.1016/j.bios.2021.113207}, author = {Azhar, Mohd and Phutela, Rhythm and Kumar, Manoj and Ansari, Asgar Hussain and Rauthan, Riya and Gulati, Sneha and Sharma, Namrata and Sinha, Dipanjali and Sharma, Saumya and Singh, Sunaina and Acharya, Sundaram and Sarkar, Sajal and Paul, Deepanjan and Kathpalia, Poorti and Aich, Meghali and Sehgal, Paras and Ranjan, Gyan and Bhoyar, Rahul C. and Singhal, Khushboo and Lad, Harsha and Patra, Pradeep Kumar and Makharia, Govind and Chandak, Giriraj Ratan and Pesala, Bala and Chakraborty, Debojyoti and Maiti, Souvik and Indian CoV2 Genomics Genetic Epide} } @article {47401, title = {Rapid identification and tracking of SARS-CoV-2 variants of concern}, journal = {Lancet}, volume = {397}, year = {2021}, month = {APR}, pages = {1346-1347}, type = {Letter}, issn = {0140-6736}, doi = {10.1016/S0140-6736(21)00470-0}, author = {Chakraborty, Debojyoti and Agrawal, Anurag and Maiti, Souvik} } @article {47766, title = {Alternative splicing modulation mediated by G-quadruplex structures in MALAT1 lncRNA}, journal = {Nucleic Acids Research}, volume = {50}, year = {2022}, month = {JAN}, pages = {378-396}, type = {Article}, abstract = {MALAT1, an abundant lncRNA specifically localized to nuclear speckles, regulates alternative-splicing (AS). The molecular basis of its role in AS remains poorly understood. Here, we report three conserved, thermodynamically stable, parallel RNAG-quadruplexes (rG4s) present in the 3{\textquoteright} region of MALAT1 which regulates this function. Using rG4 domain-specific RNA-pull-down followed by mass-spectrometry, RNA-immuno-precipitation, and imaging, we demonstrate the rG4 dependent localization of Nucleolin (NCL) and Nucleophosmin (NPM) to nuclear speckles. Specific G-to-A mutations that abolish rG4 structures, result in the localization loss of both the proteins from speckles. Functionally, disruption of rG4 in MALAT1 phenocopies NCL knockdown resulting in altered pre-mRNA splicing of endogenous genes. These results reveal a central role of rG4s within the 3{\textquoteright} region of MALAT1 orchestrating AS.}, issn = {0305-1048}, doi = {10.1093/nar/gkab1066}, author = {Ghosh, Arpita and Pandey, Satya Prakash and Ansari, Asgar Hussain and Sundar, Jennifer Seematti and Singh, Praveen and Khan, Yasmeen and Ekka, Mary Krishna and Chakraborty, Debojyoti and Maiti, Souvik} } @article {48338, title = {G4-binding drugs, chlorpromazine and prochlorperazine, repurposed against COVID-19 infection in hamsters}, journal = {Frontiers in Molecular Biosciences}, volume = {10}, year = {2023}, month = {MAR }, pages = {1133123}, type = {Article}, abstract = {

The COVID-19 pandemic caused by SARS-CoV-2 has caused millions of infections and deaths worldwide. Limited treatment options and the threat from emerging variants underline the need for novel and widely accessible therapeutics. G-quadruplexes (G4s) are nucleic acid secondary structures known to affect many cellular processes including viral replication and transcription. We identified heretofore not reported G4s with remarkably low mutation frequency across \>5 million SARS-CoV-2 genomes. The G4 structure was targeted using FDA-approved drugs that can bind G4s - Chlorpromazine (CPZ) and Prochlorperazine (PCZ). We found significant inhibition in lung pathology and lung viral load of SARS-CoV-2 challenged hamsters when treated with CPZ or PCZ that was comparable to the widely used antiviral drug Remdesivir. In support, in vitro G4 binding, inhibition of reverse transcription from RNA isolated from COVID-infected humans, and attenuated viral replication and infectivity in Vero cell cultures were clear in case of both CPZ and PCZ. Apart from the wide accessibility of CPZ/PCZ, targeting relatively invariant nucleic acid structures poses an attractive strategy against viruses like SARS-CoV-2, which spread fast and accumulate mutations quickly.

}, keywords = {Conserved motif, FDA-approved drugs, G-quadruplex binding drugs, hamster model of COVID-19, RNA G-quadruplex}, doi = {10.3389/fmolb.2023.1133123}, author = {Roy, Shuvra Shekhar and Sharma, Shalu and Rizvi, Zaigham Abbas and Sinha, Dipanjali and Gupta, Divya and Rophina, Mercy and Sehgal, Paras and Sadhu, Srikanth and Tripathy, Manas Ranjan and Samal, Sweety and Maiti, Souvik and Scaria, Vinod and Sivasubbu, Sridhar and Awasthi, Amit and Harshan, Krishnan H. and Jain, Sanjeev and Chowdhury, Shantanu} } @article {48754, title = {Identification of G-quadruplex structures in MALAT1 lncRNA that interact with nucleolin and nucleophosmin}, journal = {Nucleic Acids Research}, volume = {51}, year = {2023}, month = {SEP}, pages = {9415-9431}, type = {Article}, abstract = {

Nuclear-retained long non-coding RNAs (lncRNAs) including MALAT1 have emerged as critical regulators of many molecular processes including transcription, alternative splicing and chromatin organization. Here, we report the presence of three conserved and thermodynamically stable RNA G-quadruplexes (rG4s) located in the 3 \& PRIME; region of MALAT1. Using rG4 domain-specific RNA pull-down followed by mass spectrometry and RNA immunoprecipitation, we demonstrated that the MALAT1 rG4 structures are specifically bound by two nucleolar proteins, Nucleolin (NCL) and Nucleophosmin (NPM). Using imaging, we found that the MALAT1 rG4s facilitate the localization of both NCL and NPM to nuclear speckles, and specific G-to-A mutations that disrupt the rG4 structures compromised the localization of both NCL and NPM in speckles. In vitro biophysical studies established that a truncated version of NCL (\& UDelta;NCL) binds tightly to all three rG4s. Overall, our study revealed new rG4s within MALAT1, established that they are specifically recognized by NCL and NPM, and showed that disrupting the rG4s abolished localization of these proteins to nuclear speckles

}, issn = {0305-1048}, doi = {10.1093/nar/gkad639}, author = {Ghosh, Arpita and Pandey, Satya Prakash and Joshi, Dheeraj Chandra and Rana, Priya and Ansari, Asgar Hussain and Sundar, Jennifer Seematti and Singh, Praveen and Khan, Yasmeen and Ekka, Mary Krishna and Chakraborty, Debojyoti and Maiti, Souvik} } @article {49559, title = {Molecular modeling of non-canonical intramolecular RNA triple helix structures predicted from TRIPinRNA and their in vitro biophysical structure validation}, journal = {Journal of Physical Chemistry B}, volume = {129}, year = {2025}, month = {APR}, pages = {4298-4308}, type = {Article}, abstract = {

RNA triple helices have traditionally been characterized by pyrimidine-type UA-U or CG-C triplets, with other base triplets considered to be destabilizing. However, the presence of non-canonical triplets in riboswitches and self-splicing introns suggests that triplexes containing longer stretches of such triplets may exist in the human genome too. Using molecular modeling, we investigated a chimeric triple helix derived from the FLRT2-AS1 lncRNA, confirming its stability over a 500 ns simulation. Biophysical analyses further support the formation of this triplex in vitro. Although these non-canonical structures exhibit less thermal stability compared to traditional UA-U triplets found in lncRNAs like metastasis associated lung adenocarcinoma transcript 1 and NEAT1, they may serve distinct biological functions, suggesting a dynamic and more temporal role in cellular processes. The triplex selected for this study is found in a human long non-coding RNA gene, paving the way for investigating the intriguing roles of these triple helices in cell biology.

}, issn = {1520-6106}, doi = {10.1021/acs.jpcb.5c00160}, author = {Rakheja, Isha and Panda, Gayatri and Maiti, Souvik and Ray, Arjun} }