P. Pradeepkumar

发表

Qualitative SERS analysis of G-quadruplex DNAs using selective stabilising ligands.

K. Faulds, D. Graham, K. Gracie, 2014, The Analyst.

Site‐Specific N 2 ‐dG DNA Adducts: Formation, Synthesis, and TLS Polymerase‐Mediated Bypass

P. Pradeepkumar, P. Ghodke, 2020 .

Mechanism of Error-Free DNA Replication Past Lucidin-Derived DNA Damage by Human DNA Polymerase κ.

V. Jha, H. Ling, Linlin Zhao, 2017, Chemical research in toxicology.

The 3′-modified antisense oligos promote faster hydrolysis of the target RNA by RNase H than the natural counterpart

J. Chattopadhyaya, N. Amirkhanov, E. Zamaratski, 2001 .

G-quadruplex forming structural motifs in the genome of Deinococcus radiodurans and their regulatory roles in promoter functions

V. Dhamodharan, H. Misra, Swathi Kota, 2015, Applied Microbiology and Biotechnology.

Oligonucleotides: Synthesis, Physicochemical and Biochemical Properties of their Duplexes with DNA and RNA

P. Pradeepkumar, 2004 .

Oxetane modified, conformationally constrained, antisense oligodeoxyribonucleotides function efficiently as gene silencing molecules.

Lida K. Gifford, P. Lu, K. Jen, 2004, Nucleic acids research.

Targeting Parallel Topology of G-Quadruplex Structures by Indole- Fused Quindoline Scaffolds.

Satendra Kumar, Sruthi Sudhakar, Sushma B Singh, 2022, Biochemistry.

Bisindolylmaleimide Ligands Stabilize c-MYC G-Quadruplex DNA Structure and Downregulate Gene Expression.

Satendra Kumar, Bharathwaj Sathyamoorthy, R. Ramanathan, 2022, Biochemistry.

A critical survey of the structure-function of the antisense oligo/RNA heteroduplex as substrate for RNase H.

J. Chattopadhyaya, E. Zamaratski, P. Pradeepkumar, 2001, Journal of biochemical and biophysical methods.

Antisense oligonuclotides with oxetane-constrained cytidine enhance heteroduplex stability, and elicit satisfactory RNase H response as well as showing improved resistance to both exo and endonucleases.

J. Chattopadhyaya, N. Amirkhanov, P. Pradeepkumar, 2003, Organic & biomolecular chemistry.

Kinetic analysis of the RNA cleavage of the conformationally-constrained oxetane-modified antisense-RNA hybrid duplex by RNase HElectronic supplementary information (ESI) available: autoradiograms of denaturing PAGE gels. See http://www.rsc.org/suppdata/p2/b1/b111438g/

J. Chattopadhyaya, N. Amirkhanov, P. Pradeepkumar, 2002 .

Oxetane modified antisense oligonucleotides promote RNase H cleavage of the complementary RNA strand in the hybrid duplex as efficiently as the native, and offer improved endonuclease resistance

J. Chattopadhyaya, P. Pradeepkumar, 2001 .

Unique structural features in DNA polymerase IV enable efficient bypass of the N2 adduct induced by the nitrofurazone antibiotic.

D. Nair, Kiran R. Gore, J. Kottur, 2015, Structure.

Specific Stabilization of c-MYC and c-KIT G-Quadruplex DNA Structures by Indolylmethyleneindanone Scaffolds.

F. Rosu, S. Harikrishna, Saaz Sakrikar, 2016, Biochemistry.

Synthesis of [Ru(phen)(2)dppz](2+)-tethered oligo-DNA and studies on the metallointercalation mode into the DNA duplex.

J. Chattopadhyaya, P. Pradeepkumar, D. Ossipov, 2001, Journal of the American Chemical Society.

Benzothiazole hydrazones of furylbenzamides preferentially stabilize c-MYC and c-KIT1 promoter G-quadruplex DNAs.

P. Pradeepkumar, S. P. Pany, K. V. Diveshkumar, 2016, Organic & biomolecular chemistry.

Selective G-quadruplex DNA stabilizing agents based on bisquinolinium and bispyridinium derivatives of 1,8-naphthyridine.

V. Dhamodharan, S. Harikrishna, K. Halder, 2012, The Journal of organic chemistry.

Thioflavin T as an efficient inducer and selective fluorescent sensor for the human telomeric G-quadruplex DNA.

P. I. Pradeepkumar, S Harikrishna, V. Dhamodharan, 2013, Journal of the American Chemical Society.

Oxetane Locked Thymidine in the Dickerson-Drew Dodecamer Causes Local Base Pairing Distortions—An NMR Structure and Hydration Study

S. Chatterjee, W. Pathmasiri, P. Shrivastava, 2005, Journal of biomolecular structure & dynamics.

3'-endo/4'-exo Locked Thymidine in the Dickerson-Drew Dodecamer Causes Local Base Pairing Distortions – An NMR Structure and Hydration Study

W. Pathmasiri, J. Isaksson, J. Chattopadhyaya, 2005 .

Topology specific stabilization of promoter over telomeric G-quadruplex DNAs by bisbenzimidazole carboxamide derivatives.

V. Dhamodharan, A. C. Bhasikuttan, S. Harikrishna, 2015, ACS chemical biology.

Targeting Promoter G‐Quadruplex DNAs by Indenopyrimidine‐Based Ligands

V. Dhamodharan, S. Harikrishna, Saaz Sakrikar, 2014, ChemMedChem.

Ligand-induced conformational preorganization of loops of c-MYC G-quadruplex DNA and its implications in structure-specific drug design.

S. Harikrishna, P. Pradeepkumar, Saikiran Kotaru, 2017, Molecular bioSystems.

Effect of 2′-5′/3′-5′ phosphodiester linkage heterogeneity on RNA interference

R. Cencic, J. Pelletier, J. Rossi, 2020, Nucleic acids research.

Cationic red emitting fluorophore: A light up NIR fluorescent probe for G4-DNA.

B. Kumari, Sriram Kanvah, Akanksha Yadav, 2019, Journal of photochemistry and photobiology. B, Biology.

Probing the Binding Interactions between Chemically Modified siRNAs and Human Argonaute 2 Using Microsecond Molecular Dynamics Simulations

S. Harikrishna, P. I. Pradeepkumar, S. Harikrishna, 2017, J. Chem. Inf. Model..

Nucleoside Analogues with a Seven-Membered Sugar Ring: Synthesis and Structural Compatibility in DNA-RNA Hybrids.

M. Damha, Sruthi Sudhakar, S. Harikrishna, 2022, Journal of Organic Chemistry.

Synthesis, physicochemical and biochemical studies of 1',2'-oxetane constrained adenosine and guanosine modified oligonucleotides, and their comparison with those of the corresponding cytidine and thymidine analogues.

J. Chattopadhyaya, P. Acharya, O. Plashkevych, 2004, Journal of the American Chemical Society.

An electrochemical probe of DNA stacking in an antisense oligonucleotide containing a C3'-endo-locked sugar.

J. Barton, E. Boon, J. Isaksson, 2002, Angewandte Chemie.

Conformation-specific cleavage of antisense oligonucleotide-RNA duplexes by RNase H

P. I. Pradeepkumar, J. Chattopadhyaya, A. Földesi, 2001 .

The N(2)-Furfuryl-deoxyguanosine Adduct Does Not Alter the Structure of B-DNA.

D. Nair, S. Harikrishna, Kiran R. Gore, 2016, The Journal of organic chemistry.

Influence of 2'-fluoro versus 2'-O-methyl substituent on the sugar puckering of 4'-C-aminomethyluridine.

S. Harikrishna, Kiran R. Gore, P. Pradeepkumar, 2013, The Journal of organic chemistry.

Synthesis, gene silencing, and molecular modeling studies of 4'-C-aminomethyl-2'-O-methyl modified small interfering RNAs.

V. G. Chittoor, S. Patankar, C. Höbartner, 2012, The Journal of organic chemistry.

DNA Catalysts for Synthetic Applications in Biomolecular Chemistry

C. Höbartner, P. Pradeepkumar, 2012 .

Design, synthesis, biophysical and primer extension studies of novel acyclic butyl nucleic acid (BuNA).

P. I. Pradeepkumar, V. Kesavan, Vipin Kumar, 2013, Organic & biomolecular chemistry.

Incorporation of 4'-C-aminomethyl-2'-O-methylthymidine into DNA by thermophilic DNA polymerases.

C. Höbartner, Kiran R. Gore, P. Pradeepkumar, 2012, Chemical communications.

Synthesis and polymerase-mediated bypass studies of the N2-deoxyguanosine DNA damage caused by a lucidin analogue.

S. Harikrishna, P. Pradeepkumar, P. Ghodke, 2015, The Journal of organic chemistry.

Mimivirus encodes a multifunctional primase with DNA/RNA polymerase, terminal transferase and translesion synthesis activities

Ankita Gupta, Kiran Kondabagil, P. Pradeepkumar, 2019, Nucleic acids research.

RNA-Cleaving DNA Enzymes and Their Potential Therapeutic Applications as Antibacterial and Antiviral Agents

P. I. Pradeepkumar, C. Höbartner, P. Pradeepkumar, 2012, From Nucleic Acids Sequences to Molecular Medicine.

Exploring Chemical Modifications for siRNA Therapeutics: A Structural and Functional Outlook

S. Shukla, P. Pradeepkumar, Chintan S. Sumaria, 2010, ChemMedChem.

Specific Recognition of Promoter G-quadruplex DNAs by Small Molecule Ligands and Light-up Probes.

P. I. Pradeepkumar, V. Dhamodharan, P. Pradeepkumar, 2019, ACS chemical biology.

Stabilization and fluorescence light-up of G-quadruplex nucleic acids using indolyl-quinolinium based probes.

Sruthi Sudhakar, Sushma B Singh, P. Pradeepkumar, 2022, Physical chemistry chemical physics : PCCP.

Presence of Potential G‐Quadruplex RNA‐Forming Motifs at the 5′‐UTR of PP2Acα mRNA Repress Translation

S. Patankar, V. Dhamodharan, M. Sapra, 2019, Chembiochem : a European journal of chemical biology.

Investigating Pharmacological Targeting of G-Quadruplexes in the Human Malaria Parasite.

K. Srivastava, Richa Sharma, Shakil Ahmed, 2017, Biochemistry.

Synthesis of N2‐Aryl‐2′‐Deoxyguanosine Modified Phosphoramidites and Oligonucleotides

P. Pradeepkumar, P. Ghodke, 2019, Current protocols in nucleic acid chemistry.

Synthesis of N2-Deoxyguanosine Modified DNAs and the Studies on Their Translesion Synthesis by the E. coli DNA Polymerase IV.

D. Nair, P. Pradeepkumar, P. Ghodke, 2019, The Journal of organic chemistry.

Nucleoside Modification Using Buchwald-Hartwig Amination Reactions

P. Pradeepkumar, P. Ghodke, 2018 .

G-quadruplex forming structural motifs in the genome of Deinococcus radiodurans and their regulatory roles in promoter functions

V. Dhamodharan, H. Misra, Swathi Kota, 2015, Applied Microbiology and Biotechnology.

DNA-catalyzed covalent modification of amino acid side chains in tethered and free peptide substrates.

S. Silverman, On Yi Wong, P. Pradeepkumar, 2011, Biochemistry.

DNA-catalyzed formation of nucleopeptide linkages.

S. Silverman, C. Höbartner, D. A. Baum, 2008, Angewandte Chemie.

Translesion Synthesis across the N2-Ethyl-deoxyguanosine Adduct by Human PrimPol.

Sruthi Sudhakar, Vipin Mishra, P. Pradeepkumar, 2022, ACS chemical biology.

Biochemical reconstitution of the mimiviral base excision repair pathway.

G. Moseley, Sanjeeva Srivastava, Kiran Kondabagil, 2023, Journal of molecular biology.

Binding to the conserved and stably folded guide RNA pseudoknot induces Cas12a conformational changes during ribonucleoprotein assembly

M. Damha, Sruthi Sudhakar, Keith T. Gagnon, 2023, The Journal of biological chemistry.

Controlling the direction of site-selectivity and regioselectivity in RNA ligation by Zn2+-dependent deoxyribozymes that use 2',3'-cyclic phosphate RNA substrates.

S. Silverman, J. P. Gerdt, P. Pradeepkumar, 2008, Organic & biomolecular chemistry.

Site-selective depurination by a periodate-dependent deoxyribozyme.

S. Silverman, Scott K Silverman, C. Höbartner, 2007, Chemical communications.

Fluorescence quenching studies of γ-butyrolactone binding protein (CprB) from Streptomyces coelicolor A3(2).

P. I. Pradeepkumar, R. Anand, G. Patwari, 2014, The journal of physical chemistry. B.

Influence of 2'-fluoro versus 2'-O-methyl substituent on the sugar puckering of 4'-C-aminomethyluridine.

S. Harikrishna, Kiran R. Gore, P. Pradeepkumar, 2013, The Journal of organic chemistry.

Light induced damage and repair in nucleic acids and proteins: general discussion.

Tolga N. V. Karsili, R. Improta, I. Schlichting, 2018, Faraday discussions.

Estrone-Based Derivatives Stabilize the c-MYC and c-KIT G-Quadruplex DNA Structures

Sruthi Sudhakar, P. Pradeepkumar, Annyesha Biswas, 2024, ACS omega.

Pyridopyrimidinone Derivatives as DNAG‐Quadruplex‐Stabilizing Agents: Design, Synthesis and Biophysical Studies

R. Malhotra, Subho Roy, P. Pradeepkumar, 2017 .

Selective G-quadruplex DNA stabilizing agents based on bisquinolinium and bispyridinium derivatives of 1,8-naphthyridine.

V. Dhamodharan, S. Harikrishna, K. Halder, 2012, The Journal of organic chemistry.

Synthesis of N2-trans-isosafrole-dG-adduct Bearing DNAs and the Bypass Studies with Human TLS Polymerases κ and η.

Kiran Kondabagil, Sruthi Sudhakar, P. Pradeepkumar, 2024, The Journal of organic chemistry.

Characterization of G-quadruplexes in the Helicobacter pylori genome and assessment of therapeutic potential of G4 ligands.

P. Pradeepkumar, Puja Yadav, Amit Kumar, 2024, Biotechnology and applied biochemistry.

Controlling the direction of site-selectivity and regioselectivity in RNA ligation by Zn2+-dependent deoxyribozymes that use 2',3'-cyclic phosphate RNA substrates.

S. Silverman, J. P. Gerdt, P. Pradeepkumar, 2008, Organic and biomolecular chemistry.

Electronic Supplementary Information Site-selective Depurination by a Periodate-dependent Deoxyribozyme

S. Silverman, C. Höbartner, P. Pradeepkumar, 2022 .