Dr. Deepak T Nair - Publications
NCBS (2007-present)
- Surana, P., Vijaya, S. and Nair, D. T.§ RNA-dependent RNA polymerase of Japanese Encephalitis Virus binds the initiator nucleotide GTP to form a mechanistically important pre-initiation state. (2013) Nucleic Acids Research(http://nar.oxfordjournals.org/content/early/2013/11/28/nar.gkt1106.full)
- Sharma A., Kottur, J., Narayanan, N. and Nair, D. T.§ A strategically located serine residue is critical for the mutator activity of DNA Polymerase IV from Escherichia coli. Nucleic Acids Research (Featured article on the NAR website-http://www.oxfordjournals.org/our_journals/nar/2013_featured_articles.ht...)
- Jain, D. and Nair, D. T.§ (2013) Spacing between core recognition motifs determines relative orientation of AraR monomers on bipartite operators. Nucleic Acids Research 41:639 (http://nar.oxfordjournals.org/content/41/1/639.long)
- Sharma, A., Subramanian, V. and Nair, D. T.§ (2012) The PAD region in the mycobacterial dinB homolog MsPolIV exhibits positional heterogeneity. Acta Crystallogr D Biol Crystallogr. 68:960
- Sharma, A. and Nair, D. T.§ (2012) MsDpo4—a DinB Homolog from Mycobacterium smegmatis—is an Error-Prone DNA Polymerase that can Promote G:T and T:G Mismatches. Journal of Nucleic Acids, vol. 2012, Article ID 285481. (http://www.hindawi.com/journals/jna/2012/285481/)
- Sharma A. and Nair, D. T.§ (2011) Cloning, expression, purification, crystallization and preliminary crystallographic analysis of MsDpo4: a Y-family DNA polymerase from Mycobacterium smegmatis. Acta Crystallogr Sect F Struct Biol Cryst Commun. 67:812.
- Nair, D. T., Johnson, R. E., Prakash, L., Prakash, S. and Aggarwal, A. K. (2011) DNA Synthesis across an Abasic Lesion by Yeast Rev1 DNA Polymerase. J Mol Biol. 406:18.
- Namadurai, S.*, Jain, D.*, Kulkarni, D. S.*, Tabib, C. R., Friedhoff, P., Rao, D. N. and Nair, D. T.§ (2010) The C-terminal domain of the MutL homolog from Neisseria gonorrhoeae forms an inverted homodimer. PLoS One. 5:e13726. (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0013726)
- Jain, R., Nair, D.T., Johnson, R. E., Prakash, S., Prakash, L. and Aggarwal, A. K. (2009) Replication across template T/U by human DNA polymerase-iota. Structure. 17:974.
- Nair, D.T., Johnson, R. E., Prakash, S., Prakash, L. and Aggarwal, A. K. (2009) DNA synthesis across an abasic lesion by human DNA polymerase iota. Structure. 17:530.
- Gupta, Y.K., Nair, D.T., Wharton, R. P., and Aggarwal, A. K. (2008). Structures of Human Pumilio with Noncognate RNAs Reveal Molecular Mechanisms for Binding Promiscuity. Structure. 16:549.
- Nair, D.T.*, Johnson, R. E.*, Prakash, S., Prakash, L. and Aggarwal, A. K. (2008) Protein-template directed synthesis across an acrolein-derived DNA adduct by yeast Rev1 DNA Polymerase. Structure. 16:239.
(§= corresponding author; *Equal contribution)
Structures Deposited in the PDB from NCBS: 3NCV, 4DEZ, 4EGY, 4EGZ, 4H0E, 4IRC, 4IR9, 4IR1, 4IRD and 4IRK.
Mount Sinai Medical Centre (2002-2007)
- Lone, S.*, Townson, S. A.*, Uljon, S. N.*, Johnson, R. E., Brahma, A., Nair, D.T., Prakash, S., Prakash, L. and Aggarwal, A. K. (2007) Human DNA Polymerase kappa encircles DNA: implications for mismatch extension and lesion bypass.Mol. Cell. 25:601
- Nair, D.T.*, Johnson, R. E.*, Prakash, S., Prakash, L. and Aggarwal, A. K. (2006) Hoogsteen base pair formation promotes synthesis opposite the 1,N6-ethenodeoxyadenosine lesion by human DNA Polymerase iota. Nat. Struct. Mol. Biol. 13:619
- Nair, D.T., Johnson, R. E., Prakash, S., Prakash, L. and Aggarwal, A. K. (2006) Incoming nucleotide imposes a syn conformation on templating purine in the human DNA polymerase iota active site. Structure (Camb). 14:749
- Nair, D.T., Johnson, R. E., Prakash, S., Prakash, L. and Aggarwal, A. K. (2005) Human DNA Polymerase iota incorporates dCTP opposite template G via a G.C+ Hoogsteen base pair. Structure (Camb). 13:1569
- Nair, D.T., Johnson, R. E., Prakash, S., Prakash, L. and Aggarwal, A. K. (2005) Rev1 employs a novel mechanism of DNA synthesis using a protein template. Science. 309:2219
- Nair, D.T., Johnson, R. E., Prakash, S., Prakash, L. and Aggarwal, A. K. (2004) Replication by human DNA polymerase-iota occurs by Hoogsteen base- pairing. Nature. 430:377.
(*Equal contribution)
National Institute of Immunology (1996-2001)
- Nair, D.T., Kaur, K. J., Singh, K., Mukherjee, P., Rajagopal, D., George, A., Bal, V., Rath, S., Rao, K. V. and Salunke, D. M. (2003) Mimicry of native peptide antigens by the corresponding retro-inverso analogs is dependent on their intrinsic structure and interaction propensities. J. Immunol. 170:1362
- Nair, D.T., Singh, K., Siddiqui, Z., Nayak, B. P., Rao, K. V. S. and Salunke, D. M. (2002) Epitope recognition by diverse antibodies suggests conformational convergence in an antibody response. J. Immunol. 168:2371
- Nayak, S.K., Bagga, S., Gaur, D., Nair, D.T., Salunke, D.M. and Batra, J.K. Mechanism of specific target recognition and RNA hydrolysis by ribonucleolytictoxin restrictocin. (2001) Biochemistry. 40:9115
- *Jain, D., *Nair, D.T., Swaminathan, G. J., Abraham, E.G., Nagaraju, J. and Salunke, D.M. (2001) Structure of the Induced Antibacterial Protein from Tasar Silkworm, Antherea mylitta: Implications to molecular evolution. (2001) J. Biol. Chem. 276:41377
- Nair, D.T., Singh, K., Shahu, N., Rao, K. V. S. and Salunke, D. M. (2000). Crystal structure of an antibody bound to an immunodominant peptide epitope: novel features in peptide-antibody recognition. J. Immunol. 165:6949
(*Equal contribution)
Fellowships, Awards and Honors
1. Ramanujan Fellowship (2008-2013): Deepak T. Nair
2. Innovative Young Biotechnology Award (2012-2015): Deepti Jain
3. CSIR Student Fellowship: Amit Sharma, Shivlee Nirwal, Jithesh Kottur, Manhar Singh Rawat
4. UGC Student Fellowship: Rahul Sharma
5. ICMR Student Fellowship: Naveen Narayanan
6. Best Poster Award at the NCBS Annual Talks (2012): Dr. Deepti Jain
7. Prof. K. Venkatesan Award at the 42nd National Seminar on Crystallography (2013): Shivlee Nirwal
8. Award for Best Oral Presentation at the 42nd National Seminar on Crystallography(2013): Parag Surana