Publications

66.Bagale, S. S.; Deshmukh, P. U.; Mandal, S.; Malvi, H.; Kondabagil, K.; Pradeepkumar, P.I."Synthesis of N6-dA damaged DNAs to probe the replication ability of human translesion polymerases" J. Org. Chem. 2024 (Under revision)

65.Kumari, M.; Jaiswal, S.; Shankar, U.; Gupta, S.; Pradeepkumar, P.I.; Kumar, A.; Nayak, D.; Yadav, V.; Yadav, P."Characterization of G‐quadruplexes in the Helicobacter pylori genome and assessment of therapeutic potential of G4 ligands " Biotechnol Appl Biochem. 2024, e2644.

64.Bagale, S.S.; Deshmukh, P.U.; Lad, S.B.; Sudarsan, A.; Sudhakar, S. Kondabagil, K.; Pradeepkumar, P.I. "Synthesis of N2-trans-isosafrole-dG-adduct Bearing DNAs and the Bypass Studies with Human TLS Polymerases κ and η" J. Org. Chem. 2024, 89, 11, 7680-7691.

63.Roy, S.; Majee, P. Sudhakar, S.; Mishra, S.; Kalia, J.; Pradeepkumar, P.I.; Srivatsan, S.G. "Structural elucidation of HIV-1 G-quadruplexes in a cellular environment and their ligand binding using responsive 19F-labeled nucleoside probes" Chem. Sci. 2024, 15, 7982–7991.

62.Kumar, S.; Biswas, A.; Sudhakar, S.; Kumari, D.; Pradeepkumar, P.I. "Estrone-Based Derivatives Stabilize the c-MYC and c-KIT G-Quadruplex DNA Structures" ACS Omega 2024, 9, 6616–6616.

61.Deshmukh, P. U.; Lad, S. B.; Sudarsan, A.; Sudhakar, S.; Aggarwal, T.; Mandal, S.; Bagale, S.S.; Kondabagil, K.; Pradeepkumar, P.I. "Human TLS polymerases polκ and polη perform error-free replication across N2-dG methyleugenol and estragole DNA adducts" Biochemistry 2023, 62(16), 2391–2406.

60. Lad, S. B.; Upadhyay, M.; Thorat, P.; Nair, D.; Moseley, G. W.; Srivastava, S.; Pradeepkumar, P. I.; Kondabagil, K. "Biochemical Reconstitution of the Mimiviral Base Excision Repair Pathway." J. Mol. Biol. 2023, 435 (17), 168188.

59. Sudhakar, S.; Barkau, C. L.; Chilamkurthy, R.; Barber, H. M.; Pater, A. A.; Moran, S. D.; Damha, M. J.; Pradeepkumar, P. I.; Gagnon, K. T. "Binding to the Conserved and Stably Folded Guide RNA Pseudoknot Induces Cas12a Conformational Changes During Ribonucleoprotein Assembly."J. Biol. Chem. 2023, 104700.

58. Khatik, S.Y., Sudhakar,S.; Mishra, S.; Kalia, J.; Pradeepkumar, P.I.; Srivatsan, S.G. "Probing juxtaposed G-quadruplex and hairpin motifs using a responsive nucleoside probe: a unique scaffold for chemotherapy." Chem. Sci. 2023

57. Boldinova, E. O.; Ghodke, P. P.; Sudhakar, S.; Mishra, V. K.; Manukyan, A. A.; Miropolskaya, N.; Pradeepkumar, P. I.; Makarova, A. V. "Translesion Synthesis across the N2-Ethyl-Deoxyguanosine Adduct by Human PrimPol."ACS Chem. Biol. 2022, 17, 11, 3238–3250.

56. Kumar, S.; Pany, S.P.; Todankar, C. S.; Sudhakar, S.; Singh,S. B.; Todankar, C. S.; Pradeepkumar, P.I. "Targeting Parallel Topology of G-Quadruplex Structures by Indole- Fused Quindoline Scaffolds." Biochemistry 2022, 61, 22, 2546-2549.

55. Kumar, S.; Reddy Sannapureddi, R. K.; Todankar, C. S.; Ramanathan, R.; Biswas, A.; Sathyamoorthy, B.; Pradeepkumar, P.I. "Bisindolylmaleimide ligands stabilize c-MYC DNA G-quadruplex DNA structures and downregulate gene expression." Biochemistry 2022, 61, 11, 1064-1076.

54. Jana, S.K.; Harikrishna, S.; Sudhakar, S. El-Khoury, R.; Pradeepkumar, P.I.; Damha, M. J. "Nucleoside Analogues with a Seven-Membered Sugar Ring: Synthesis and Structural Compatibility in DNA–RNA Hybrids"J. Org. Chem. 2022, 87, 5, 2367–2379.

53. Biswas, A.; Singh,S. B.; Todankar, C. S.; Sudhakar, S.; Pany, S.P.P.; Pradeepkumar, P.I. "Stabilization and fluorescence light-up of G-quadruplex nucleic acids using indolyl-quinolinium based probes" Phys. Chem. Chem. Phys., 2022, 24, 6238-6255.

52.Pratibha P. Ghodke; Pradeepkumar, P. I."Site-Specific N2-dG DNA Adducts: Formation, Synthesis, and TLS Polymerase-Mediated Bypass"Eur. J. Org. Chem. 2020, 6831–6844.

51. Habibian,M.; Harikrishna, S.; Fakhoury, J.; Barton, M.; Ageely, E. A.; Cencic, R.; Fakih, H. H.; Katolik, A.; Takahashi, M.; Rossi, J.; Pelletier, J.; Gagnon, K.T. Pradeepkumar, P.I.; Damha, M. J."Effect of 2′-5′/3′-5′ phosphodiester linkage heterogeneity on RNA interference"Nucleic Acids Res. 2020, 48, 4643–4657.

50.Pratibha P. Ghodke; Pradeepkumar, P. I."N2-Aryl-Deoxyguanosine modified phosphoramidites and oligonucleotides."Curr. Proto. Nucleic Acids Chem. 2019, 78.

49. Pany, S. P. P.; Sapra, M.; Sharma, J. Dhamodharan, V.; Patankar, S.; Pradeepkumar, P.I."Presence of Potential G-Quadruplex RNA-Forming Motifs at the 5’-UTR of PP2Aca mRNA Repress Translation"ChemBioChem 2019, 20, 2955 –2960.

48. Gupta, A.; Lad, S. B.; Ghodke, P. P.; Pradeepkumar, P.I.; Kondabagil K. "Mimivirus encodes a multifunctional primase with DNA/RNA polymerase,terminal transferase and translesion synthesis activities."Nucleic Acids Res. 2019, 47, 6932-6945.

47. Dhamodharan, V. ; Pradeepkumar, P. I. "Specific Recognition of Promoter G-Quadruplex DNAs by Small Molecule Ligands and Light-up Probes"ACS Chem. Biol. 2019, 14, 2102–2114.

46. Pratibha P. Ghodke; Bommisetti,P.; Nair, D.T.; Pradeepkumar, P. I."Synthesis of N2-Deoxyguanosine Modified DNAs and the Studies on Their Translesion Synthesis by the E. coli DNA Polymerase IV"J. Org. Chem. 2019, 84,1734–1747.

45. B Kumari, A Yadav, SP Pany, Pradeepkumar, P.I.; S Kanvah"Cationic red emitting fluorophore: A light up NIR fluorescent probe for G4-DNA"J. Photochem. Photobiol B , 2019, 190, 128-136.

44. Pratibha P. Ghodke; Pradeepkumar, P. I."Nucleosides Modification Using Buchwald-Hartwig Amination Reactions""Palladium-Catalyzed Modification of Nucleosides, Nucleotides and Oligonucleotides", Elsevier, Chapter 10, pp 295-334 2018

43. Mohammad Anas, Sharma, R.; Dhamodaran, V.; Pradeepkumar, P.I.; Manhas, A.; Srivastava, K.; Ahmed, S.; Kumar, N."Investigating pharmacological targeting of G-quadruplexes in human malaria parasite"Biochemistry, 2017, 56 (51), pp 6691–6699

42. Yockey, O.; Jha, V.; Ghodke, P. P.; Xu, T.; Xu, W.; Ling, H.; Pradeepkumar, P.I.; Zhao, L."Mechanism of Error-Free DNA Replication Past Lucidin-Derived DNA Damage by Human DNA Polymerase κ"Chem. Res. Toxicol., 2017, 30 (11), pp 2023–2032.

41. Malhotra, R.; Rarhi, C.; Diveshkumar, K.V. ; Bommisetti P.; Pany, S.P.P.; Subho Roy, S.; Pradeepkumar, P.I.; Kundu, M."Pyridopyrimidinone Derivatives as G-Quadruplex DNA Stabilizing Agents: Design, Synthesis and Biophysical Studies"ChemistrySelect, 2017, 2, 5206 – 5213

40. Harikrishna, S.; Saikiran, K.; Pradeepkumar , P. I."Ligand Induced Conformational Preorganization of Loops of c-MYC G-Quadruplex DNA and its Implications in Structure Specific Drug Design "Mol. BioSyst., 2017, 13, 1458–1468

39. Harikrishna, S.; Pradeepkumar , P. I."Probing the Atomic Level Interactions between Chemically Modified siRNAs and Human Argonaute 2 Using Microsecond MD Simulations "J. Chem. Inf. Model., 2017, 57 (4), 883–896

38. Malhotra, R.; Rarhia, C.; Diveshkumar , K.V.; Barikb, R.; D’cunha, R.; Dharb, P.; Kundu, M.; Chattopadhyay, S.; Royb, S; Basub, S.; Pradeepkumar, P.I.,Hajrad, S."Dihydrochelerythrine and its Derivatives: Synthesis and Their Application as Potential G-quadruplex DNA Stabilizing agents"Bioorg. Med. Chem., 2016, 24, 2887–2896

37. Diveshkumar, K.V.; Sakrikar, S.; Rosu, F.; Gabelica, V.; Pradeepkumar P. I."Specific Stabilization of Parallel G-quadruplex DNA Structures by Indolylmethyleneindanone Scaffolds"Biochemistry 2016, 55, 3571-3585

36. Pany, S. P. P.; Bommisetti, P.; Diveshkumar, K. V. ; Pradeepkumar , P. I."Benzothiazole Hydrazone of Furylbenzamides Preferentially Stabilize c-MYC and c-KIT1 Promoter G-quadruplex DNAs"Org. Biomol. Chem., 2016, 14, 5779-5793

35. Ghodke, P.P.; Gore, K.R.; Harikrishna, S.; Samanta, B.; Kottur, J.; Nair, D.T.; Pradeepkumar P. I."The N2‑Furfuryl-deoxyguanosine Adduct Does Not Alter The Structure of B‑DNA"J. Org. Chem., 2016, 81, 502−511

34. Swathi, K.; Dhamodharan, V.; Pradeepkumar P. I.; Hari S. Misra"G-quadruplex Forming Structural Motifs in the Genome of Deinococcus radiodurans and their Regulatory Roles in Promoter functions"Appl. Microbiol. Biotechnol., 2015, 99, 9761–9769

33. Ghodke, P. P.; Harikrishna, S.; Pradeepkumar, P. I."Synthesis and Polymerase Mediated Bypass Studies of the N2-Deoxyguanosine DNA Damage Caused by a Lucidin Analogue"J. Org. Chem., 2015, 80, 2128–2138

32. Kottur, J.; Sharma, A.; Gore, K.R.; Narayanan, N.; Samanta, B.; Pradeepkumar, P. I.; Nair, D. T"Unique Structural Features in DNA Polymerase IV Enable Efficient Bypass of the N2-Adduct induced by the Nitrofurazone Antibiotic."Structure, 2015, 23, 56-67

31. Dhamodharan, V.; Harikrishna, S.; Bhasikuttan, A. C.; Pradeepkumar, P. I."Topology Specific Stabilization of Promoter Over Telomeric G-quadruplex DNAs by Bisbenzimidazole Carboxamide Derivatives"ACS Chem. Biol., 2015, 10 (3), 821–833

30.Diveshkumar, K.V.; Sakrikar, S.; Harikrisna, S.; Dhamodharan, V.; Pradeepkumar, P. I."Targeting Promoter Quadruplex DNAs by Indenopyramidine Based Ligands"Chem.Med.Chem 2014, 9, 2754–2765

29. Biswas, A.; Swarnkar, R.K.; Hussain, B.; Sahoo, S.K.; Pradeepkumar, P. I.; Patwari, G. N.; Anand R"Fluorescence Quenching Studies of γ-Butyrolactone Binding Protein (CprB) from Streptomyces Coelicolor A3(2). "J. Phys. Chem. B. 2014, 118, 10035-10044

28. Gracie, K.; Dhamodharan, V.; Pradeepkumar, P.I.; Faulds, K.; Graham, D."Qualitative SERS Analysis of G-quadruplex DNAs Using Selective Stabilising Ligands"Analyst, 2014 139, 4458-4465

27. Gore, K. R.; Harikrishna, S.; Pradeepkumar, P. I."Influence of 2′-Fluoro versus 2′ O-Methyl Substituent on the Sugar puckering of 4′ C-Aminomethyluridine"J. Org. Chem. 2013, 78, 9956-9962.

26. Kumar, V.;Gore, K. R.;Pradeepkumar, P. I.; Kesavan, V."Design, synthesis, biophysical and primer extension studies of novel acyclic butyl nucleic acid."Org. Biomol. Chem. 2013, 11, 5853-5865.

25. Mohanty, J; Barooh, N; Dhamodharan,V.; Harikrishna, S.;Pradeepkumar, P. I.; Bhasikuttan, A. C."Thioflavin T as an Efficient Inducer and Selective Sensor for the Human Telomeric G-Quadruplex DNA"J. Am. Chem. Soc. 2013, 135, 367-376

24. Gore K.R ; Nair D.T ; Pradeepkumar P.I.; "Synthesis of N2-furfuryl doxyguanosine phosphoramidite and modified oligonucleotides "Indian Patent Application No.: 0454/MUM/2013 dated February 18, 2013

23. Nawale, G.; Gore, K. R.; Hobartner, C.; Pradeepkumar, P.I."Incorporation of 4'-C-aminomethyl-2'-O-methylthymidine into DNA by thermophilic DNA polymerases."Chem. Commun. 2012, 48, 9619-9621

22. Gore, K. R.; Nawale, G.; Harikrishna, S.; Chittoor, V; Pandey, S.; Hobartner, C; Patankar, S; Pradeepkumar, P. I."Synthesis, Gene Silencing and Molecular Modeling Studies of 4’-C-Aminomethyl, 2’-O-Methyl Modified Small Interfering RNAs"J. Org. Chem. 2012, 77, 3233-3245

21. Dhamodharan,V.; Harikrishna, S.; Jagadeeswaran, C; Halder, K; Pradeepkumar, P. I."Selective G-quadruplex DNA Stabilizing Agents Based on Bisquinolinium and Bispyridinium Derivatives of 1, 8-Naphthyridine."J. Org. Chem. 2012, 77, 229-242

20. Hobartner, C; Pradeepkumar, P. I."DNA Catalysts for Practical Application in Bioorganic Chemistry in New Strategies in Chemical Synthesis and Catalysis (Pigantaro, B. Ed.)"Wiley-VCH. Chapter 6, pp 129-150 2012

19. Pradeepkumar, P. I.; Hobartner, C."RNA Cleaving DNA Enzymes and their Potential Therapeutic Applications as Antibacterial and Antiviral Agents in From Nucleic Acids Sequences to Molecular Medicine(Erdmann, V. A, Barciszewski, J. Eds.)"Springer Book Series in RNA Technologies, Springer DE. Chapter 15, pp 371-410 2012