Dr. P.I. Pradeepkumar’s Researcher ID link

Year

Authors/Title/Journal

Pdf

2015 Kottur, J.; Sharma, A.; Gore, K.R.; Narayanan, N.; Samanta, S.; 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, (in press)
publi
2014 Diveshkumar, K.V.; Sakrikar, S.; Harikrisna, S.; Dhamodharan, V.; Pradeepkumar, P. I.Targeting Promoter Quadruplex DNAs by Indenopyramidine Based Ligands. ChemMedChem, (in press: DOI: 10.1002/cmdc.201402394)
publi
2014 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, 118, 10035-10044..
publi
2014 Gracie, K.; Dhamodharan, V.; Pradeepkumar, P.I.; Faulds, K.; Graham, D. Qualitative SERS Analysis of G-quadruplex DNAs Using Selective Stabilising Ligands. Analyst, 139, 4458-4465.
publi
2013
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., 78, 9956-9962.
publi
2013
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, 11, 5853-5865
publi
2013
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., 135, 367-376
publi
2012

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

publi

2012

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, 77, 3233-3245

publi

2012

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., 77, 229-242

publi

2012

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 Weblink: http://as.wiley.com/WileyCDA/WileyTitle/productCd-3527330909,descCd-tableOfContents.html

publi

2012

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 Weblink: http://www.springer.com/biomed/molecular/book/978-3-642-27425-1

publi

2011

Wong, O. Y.; Pradeepkumar. P. I.; Silverman. S. K. DNA-Catalyzed Covalent Modification of Amino Acid Side Chains in Tethered and Free Peptide Substrates. Biochemistry, 50, 4741-4749

publi

2010

Shukla, S.; Sumaria, C.; Pradeepkumar, P.I. Exploring Chemical Modifications for siRNA Therapeutics: A Structural and Functional Outlook, Chem Med Chem,  3, 328-349.

publi

2008

Kost, D. M.; Gerdt, J. P.; Pradeepkumar, P. I.; Silverman, S. K. Controlling the direction of site-selectivity and regioselectivity in RNA ligation by Zn2+-dependent deoxyribozymes that use 2',3'-cyclic phosphate RNA substrates, Org. Biomol. Chem., 6,4391-4398

publi

2008

Pradeepkumar, P. I.; Hobartner, C.; Baum, A.; Silverman, S. K. DNA-catalyzed formation of nucleopeptide linkages, Angew. Chem. Int. Ed., 47, 1753-1757

publi

2007

 Hobartner, C.; Pradeepkumar, P. I.; Silverman, S. K. Site-selective depurination by a periodate-dependent deoxyribozyme, Chem. Commun., 14, 2255-2257

publi

2005

Isaksson, J.; Plashkevych, O.; Pradeepkumar, P. I.; Chatterjee, S.; Barman, J.; Pathmasri, W.; Shrivastava, P.; Petit, C.; Chattopadhyaya, J. Oxetane locked thymidine in the Dickerson-Drew dodecamer causes local base pairing distortions - an NMR structure and hydration study, J. Biomol. Struct. Dyn., 23, 299-330

publi

2004

Pradeepkumar, P. I.; Cheruku, P.; Plashkevych, O.; Acharya, P.; Gohil, S.; Chattopadhyaya, J. 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 analogs, J. Am. Chem. Soc, 126, 11484-11499

publi

2004

Opalinska, J. B.; Kalota, A.; Rodriquez, L.; Henningson, C.; Gifford, L. K.; Lu,P.; Jen, K-Y.; Paradeepkumar, P. I.; Barman, J.; Kim, T. K.; Swider, C.;Chattopadhyaya, J.; Gewirtz, A.M. Rationally targeted, conformationally constrained, oxetane modified oligonucleotides are highly efficient gene silencing molecules, Nucleic Acids Res., 32, 5791-5799

publi

2003

Pradeepkumar, P. I.; Amirkhanov, N. V.; Chattopadhyaya, J. Antisense oligonucleotides with oxetane-constrained cytidine enhance heteroduplex stability, elicit satisfactory RNase H response as well as show improved resistance to both exo and endonucleases, Org. Biomol. Chem., 1, 81-92

publi

2003

Acharya, P.: Isaksson, J.; Pradeepkumar, P. I.; Chattopadhyaya, J. Three distinct sets of evidences show the importance of stereoelectronics as one of the major forces responsible for the self-assembly of DNA and RNA, Collect. Czech. Chem. Commun., 5, 99-120. (review)

publi

2003

Amirkhanov, N.V.; Pradeepkumar, P. I.; Chattopadhyaya, J. Kinetic analysis of the RNA cleavage of the conformationally-constrained oxetane-modified antisense-RNA hybrid duplex by  RNase H , J. Chem. Soc., Perkin Trans. 2, 976-984

publi

2003

Boon, E.M.; Barton, J.K.; Pradeepkumar, P. I.; Isaksson, J.; Petit, C.; Chattopadhyaya, J. An electrochemical probe of DNA stacking in an antisense oligonucleotide containing C3'-endo locked sugar, Angew. Chem. Int. Ed, 41, 3402-3405

publi

2001

Ossipov, D.; Pradeepkumar, P. I.; Holmer, M.; Chattopadhyaya, J. Synthesis of [Ru(phen)2DPPZ]2+-tethered oligo-DNA and studies on the metallointercalation mode into the DNA duplex, J. Am. Chem. Soc., 123, 3551-3562

publi

2001

Zamaratski, E.; Ossipov, D.; Pradeepkumar, P. I.; Amirkhanov, N. V.;Chattopadhyaya, J. The 3'-modified antisense oligos promote faster hydrolysis of the target RNA by RNase H than the natural counterpart, Tetrahedron, 57, 593-606

publi

2001

Pradeepkumar, P. I.; Zamaratski, E.; Foldesi, A.; Chattopadhyaya, J. Conformation-specific cleavage of antisense oligonucleotide-RNA duplexes by RNase H, J. Chem. Soc., Perkin Trans. 2, 402-408

publi

2001

Pradeepkumar, P. I.; Chattopadhyaya J. 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. Chem. Soc., Perkin Trans. 2, 2074-2083

publi

2001

Zamaratski, E.; Pradeepkumar, P. I.; Chattopadhyaya, J. A critical survey of the structure-function of the antisense oligo/RNA heteroduplex as substrate for RNase H, J. Biochem. Biophys. Methods, 48, 189-208. (review)

publi

2000

Pradeepkumar, P. I.; Zamaratski, E.; Foldesi, A.; Chattopadhyaya, J. Transmission of the conformational information in the antisense/RNA hybrid duplex influences the pattern of the RNase H cleavage reaction, Tetrahedon Lett.,41, 8601-8607

publi

 

 

Research Group Teaching

Go home