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Publications 2016

  1. Nagaraja, V., Godbole, A.A., Henderson, S.R., Maxwell, A.(2016) DNA topoisomerase I and DNA gyrase as targets for TB therapy. Drug Discov Today.    [Epub ahead of print] Review]  PubMed

  2. Dey, D., Nagaraja, V., Ramakumar, S.(2016) Structural and evolutionary analyses reveal determinants of DNA binding specificities of nucleoid-associated proteins HU and IHF. Mol Phylogenet Evol.  [Epub ahead of print] PubMed

  3. Kakade, P., Sadhale, P., Sanyal, K., Nagaraja, V. (2016) ZCF32, a fungus specific Zn(II)2 Cys6 transcription factor, is a repressor of the biofilm development in the human pathogen Candida albicans. Sci Rep. 6, 31124 PubMed

  4. Ghosh S, Padmanabhan B, Godbole AA, Tare P, Ahmed W, Vasu K, China A, Kumar R, Mitra A, Nagaraja V. (2016) Transcriptional regulation of topology modulators and transcription regulators of Mycobacterium tuberculosis.  Biochem Biophys Res Commun. 475,257-263 PubMed

  5. Ghosh S, Padmanabhan B, Anand C, Nagaraja V. (2016) Lysine acetylation of the Mycobacterium tuberculosis HU protein modulates its DNA binding and genome organization. Mol Microbiol. 100, 577-588. PubMed

  6. Trivedi, U., Kaushik, S., Kunjadia, P., Saravanan, M., Nagaraja, V., Archana, G., Nareshkumar, G. (2016) Functional expression and purification of Anabaena PCC 7120 XisA protein. Protein Expr Purif., 118, 64-69.  PubMed

  7. Ahmed, W., Menon, S., D. N. B. Karthik, P.V., Nagaraja, V. (2016)  Autoregulation of topoisomerase expression by supercoiling sensitive transcription. .Nucleic Acids Res. 44, 1541-1552 PubMed

  8. Jepsen, M.L., Harmsen, C., Godbole, A.A., Nagaraja, V., Knudsen, B.R., Ho, Y.P. (2016) Specific detection of the cleavage activity of mycobacterial enzymes using a quantum dot based DNA nanosensor. Nanoscale. 8, 358-364  PubMed

Publications 2015

  1. Kurthkoti, K., Tare, P., Paitchowdhury, R., Gowthami, V.N., Garcia, M.J., Colangeli, R., Chatterji, D., Nagaraja, V., Rodriguez, G.M. (2015)  The mycobacterial iron-dependent regulator IdeR induces ferritin (bfrB) by alleviating Lsr2 repression. Mol Microbiol. 98, 864-877.  PubMed

  2. Swapna, G., Kumari, V. and  Nagaraja, V.(2015) Different Modes of Transactivation of Bacteriophage Mu Late Promoters by Transcription Factor C. PLoS One.  10, e0129504. PubMed

  3. Sipos, A., Pató, J., Székely, R., Hartkoorn, R.C., Kékesi, L., Orfi, L., Szántai-Kis, C., Mikušová, K., Svetlíková, Z., Korduláková, J., Nagaraja, V., Godbole, A.A., Bush, N., Collin, F., Maxwell. A,, Cole, S.T., Kéri, G. (2015)  Lead selection and characterization of antitubercular compounds using the Nested Chemical  Library.  Tuberculosis (Edinb). 95, S200-206. PubMed

  4. Godbole,  A.A., Ahmed, W., Bhat, R., Bradley, E., Ekins, S., and  Nagaraja, V.(2014)  Targeting Mycobacterium tuberculosis topoisomerase I by small molecule inhibitors   Antimicrob Agents Chemother 59, 1549-1557 PubMed

  5. Ahmed, W., Menon, S., Pullela, K .V.D.N.B. and Nagaraja, V.(2015)  Reduction in DNA topoisomerase I level affects growth, phenotype and nucleoid architecture of Mycobacterium smegmatis. Microbiology 151, 341-353  PubMed

Publications 2014

  1. Pradeep, B.E., Mahalingam, N., Manivannan, B., Padmanabhan, K., Nilawe, P., Gurung, G., Chhabra, A. and Nagaraja V. (2014) Draft Genome Sequence of Elizabethkingia meningoseptica, Isolated from a Postoperative Endophthalmitis Patient. Genome Announc. 2, e01335-013314. PubMed

  2. Mitra, A., Misquitta, R. and  Nagaraja, V. (2014). Mycobacterium tuberculosis Rho is an NTPase with   distinct kinetic properties and a novel RNA-binding subdomain. PLoS One. 9, e107474. PubMed

  3. Ghosh, S., Mallick, B. and  Nagaraja, V. (2014)  Direct regulation of topoisomerase activity by a nucleoid-associated protein. Nucl. Acids Res.. 42, 11156-11165. PubMed

  4. Bhowmick,T., Ghosh, S., Dixit, K., Ganesan, V., Ramagopal, U.A.,Dey, D. , Sarma S.P.,  Ramakumar, S. and Nagaraja, V. (2014) Targeting Mycobacterium tuberculosis nucleoid- associated protein HU with structure based inhibitors. Nat Commun. 5, 4124.(DOI: 10.1038/ncomms5124). PubMed

  5. Vos, S.M., Lyubimov, A.Y., Hershey, D.M., Schoeffler, A.J., Sengupta, S., Nagaraja, V. and Berger, J.M. (2014).  Direct control of type IIA topoisomerase activity by a chromosomally encoded regulatory protein. Genes Dev. 28, 1485-1497. PubMed

  6. Kundu, P.P., Bhowmick, T., Swapna, G., Pavan Kumar, G.V., Nagaraja, V. and  Narayana, C. (2014). Allosteric Transition Induced by Mg(2+) Ion in a Transactivator Monitored by SERS. J Phys Chem B. 118, 5322-5330. PubMed  

  7. Gupta, M., Sajid, A., Sharma, K., Ghosh, S., Arora, G., Singh, R, Nagaraja, V., Tandon, V. and  Singh Y.(2014). HupB, a nucleoid associated protein of Mycobacterium tuberculosis, is modified by Serine/Threonine Protein Kinases in vivo. J Bacteriol. [Epub ahead of print].    PubMed   

  8. Godbole, A.A., Ahmed, W., Bhat, R.S., Bradley, E.K., Ekins, S. and  Nagaraja, V. (2014) Inhibition of Mycobacterium tuberculosis topoisomerase I by m-AMSA, a eukaryotic type II topoisomerase poison. Biochem Biophys Res Commun.  446, 916-920. PubMed

  9. Ahmed, W., Menon, S., Godbole, A.A., Karthik, P.V. and  Nagaraja, V.(2014)  Conditional silencing of topoisomerase I gene of Mycobacterium tuberculosis validates its essentiality for cell survival. FEMS Microbiol Lett. 353, 116–123. PubMed

  10. Kumar, R., Madhumathi, B.S. and Nagaraja, V. (2014) Molecular basis for the differential quinolone susceptibility of Mycobacterium tuberculosis DNA gyrase. Antimicrob. Agents Chemother,  58, 2013-2020. PubMed

Publications 2013

  1. Ghosh, S., Indi, S.S. and Nagaraja, V. (2013)  Regulation of lipid biosynthesis, sliding motility, and biofilm formation by a membrane-anchored nucleoid-associated protein of Mycobacterium tuberculosis.  J Bacteriol. 195, 1769-1778. PubMed

  2. Vasu, K. and Nagaraja, V. (2013)  Diverse functions of restriction-modification systems in addition to cellular defense. Microbiol .Mol. Biol. Rev. 77, 53-72. PubMed

  3. Leelaram, M.N., Bhat, A.G., Godbole, A.A., Bhat, R.S., Manjunath, R. and  Nagaraja, V. (2013). Type IA topoisomerase inhibition by clamp closure. FASEB J. 27, 3030-3038. PubMed

  4. Ahmed, W.,  Bhat, AG, ,Leelaram, MN,  Menon, S.  and  Nagaraja, V. (2013) Carboxyl terminal domain basic amino acids of mycobacterial topoisomerase I bind DNA to promote strand passage. Nucl. Acids Research,  41, 7462-7471. PubMed

  5. Tare, P. and Nagaraja, V. (2013) Regulation of transcription initiation in mycobacteria. Curr. Sci. 105, 632-642.

  6. Vasu, K.,  Nagamalleswari, E., Zahran, Z,  Imhof, P, Xu, S.Y., Hong, S. and Nagaraja, V. (2013) Increasing cleavage specificity and activity of restriction endonuclease KpnI. Nucl. Acids Res. 41, 9812-9824. PubMed

  7. Tare, P., Mullick, B.  and Nagaraja, V. (2013)  Co - evolution of specific amino acids in sigma 1.2 region and nucleotide bases in the discriminator to act as sensors of small molecule effectors of transcription initiation. Mol. Microbiol., 90, 569-583. PubMed

Publications 2012

  1. Vasu, K., Nagamalleswari, E. and Nagaraja, V. (2012) Promiscuous restriction is a cellular defense strategy that confers fitness advantage to bacteria. Proc Natl Acad Sci USA. 109, E1287-1293. PubMed

  2. Karambelkar. S., Swapna, G. and  Nagaraja, V.(2012) Silencing of toxic gene expression by Fis. Nucl. Acids Res. 40, 4358-4367. PubMed

  3. Mitra, A. and Nagaraja, V. (2012). Under-representation of intrinsic terminators across bacterial genomic islands: Rho as a principal regulator of xenogenic DNA expression. Gene.  508, 221-228. PubMed  

  4. Tare, P., China, A. and  Nagaraja, V.(2012). Distinct and Contrasting Transcription Initiation Patterns at Mycobacterium tuberculosis Promoters. PLoS One.7, e43900. PubMed

  5. Marathe, S.A., Kumar, R., Ajitkumar, P., Nagaraja, V. and Chakravortty, D. (2013)  Curcumin reduces the antimicrobial activity of ciprofloxacin against Salmonella Typhimurium and Salmonella Typhi. J Antimicrob Chemother.  68, 139-152. PubMed

  6. Nagamalleswari, E., Vasu, K. and Nagaraja, V. (2012). Ca(2+) binding to ExDxD motif regulates DNA cleavage specificity of a promiscuous endonuclease. Biochemistry.  51, 8939-8949. PubMed

  7. Kumar, R., Riley, J.E., Parry, D., Bates, A.D. and  Nagaraja, V. (2012) Binding of two DNA molecules by type II topoisomerases for decatenation.  Nucl. Acids Res. 40, 10904-109015 PubMed

  8. Godbole, A.A., Leelaram, M.N., Bhat, A.G., Jain, P. and Nagaraja, V. (2012) .Characterization of DNA topoisomerase I from Mycobacterium tuberculosis: DNA cleavage and religation properties and inhibition of its activity. Arch. Biochem. Biophys.  528, 197-203. PubMed

  9. 125. China, A., Mishra,S., Tare, P. and  Nagaraja, V.(2011). Inhibition of Mycobacterium tuberculosis RNA polymerase by binding of a Gre factor homolog to secondary channel.  J Bacteriol. 194,1009-1017. PubMed

Publications 2011

  1. Swapna, G., Chakraborty, A., Kumari, V., Sen, R. and  Nagaraja V.(2011)  Mutations in β' subunit of Escherichia coli RNA polymerase perturb the activator polymerase functional interaction required for promoter clearance. Mol Microbiol. 80,1169-1185. PubMed

  2. Prabha, S., Rao, D.N. and  Nagaraja, V. (2011) Distinct Properties of Hexameric but Functionally Conserved Mycobacterium tuberculosis Transcription-Repair Coupling Factor. PLos One.6, e19131. PubMed

  3. China, A., Mishra, S. and  Nagaraja, V.(2011) A transcript cleavage factor of Mycobacterium tuberculosis important for its survival .  PLoS One. 6, e21941. PubMed

  4. Vasu, K., Saravanan, M.  and Nagaraja, V. (2011) Endonuclease active site plasticity allows DNA cleavage with diverse alkaline earth and transition metal ions. ACS Chem Biol.  6, 934-942. PubMed

  5. Leelaram, M.N., Bhat ,A.G., Hegde, S.M., Manjunath, R. and Nagaraja V.(2012) Inhibition of type IA topoisomerase by a monoclonal antibody through perturbation of DNA cleavage-religation equilibrium. FEBS J.  279, 55-65. PubMed

  6. Mitra, A., Kesarwani, A.K., Pal, D. and  Nagaraja V. (2010) WebGeSTer DB--a transcription terminator database. Nucl. Acids Res.  39, D129-D135. PubMed


Publications 2010

  1. China, A., and Nagaraja, V.(2010) Purification of RNA polymerase from mycobacteria for optimized promoter-polymerase interactions. Protein Expr Purif.  69, 235-242. PubMed

  2. Malshetty, V., Kurthkoti, K., China, A., Mullick, B., Yamunadevi, S., Sang, P.B., Srinivasan, N., Nagaraja, V., and Varshney, U.(2010) Novel insertion and deletion mutants of RpoB which render Mycobacterium smegmatis RNA polymerase recalcitrant to rifampicin mediated inhibition of transcription. Microbiology. 156, 1565-1573. PubMed

  3. China, A., Tare, P., and Nagaraja, V.(2010) Comparison of promoter specific events during transcription initiation in mycobacteria. Microbiology, 156, 1942-1952. PubMed

  4. Leelaram, M.N., Suneetha, N., Nagaraja, V., and Manjunath, R. (2010). A new ELISA plate based microtiter well assay for mycobacterial topoisomerase I for the direct screening of enzyme inhibitory monoclonal antibody supernatants. J Immunol Methods. 357, 26-32. PubMed

  5. Anandhakumar, S., Nagaraja, V. and Raichur, A.M. .(2010). Reversible polyelectrolyte capsules as carriers for protein delivery. Colloids Surf B Biointerfaces. 78, 266-274. PubMed

  6. Vasu, K, Saravanan, M., Rajendra, B.V. and  Nagaraja, V. (2010) Generation of a manganese specific restriction endonuclease with nicking activity. Biochemistry, 49, 8425-8433. PubMed


Publications 2009

  1. Swapna, G., Saravanan, M. and  Nagaraja, V. (2009). Conformational changes triggered by Mg2+  mediate transactivator function. Biochemistry. 48, 2347-2354. PubMed

  2. Mitra, A., Angamuthu, K., Jayashree, H.V. and Nagaraja, V. (2009). Occurrence, divergence and evolution of intrinsic terminators across eubacteria. Genomics, 94, 110 -116. PubMed

  3. Leelaram, M..N., Bhat, A.G., Suneetha, N., Nagaraja, V. and Manjunath, R.(2009). Imunological cross-reactivity of mycobacterial topoisomerase I and divergence from other bacteria. Tuberculosis, 89, 256-262. PubMed

  4. Senthilkumar, P., Dinakaran, M.,Yogeeswari, P.,Sriram,D., China,A., Nagaraja, V. and Sriram, D. (2009) Antimycobacterial activites of novel fluoroquinolones. Biomed Pharmacother. 63, 27-35. PubMed

  5. Williams, D.L., Slayden, R.A., Amin, A., Martinez, A.N., Pittman, T.L., Mira, A., Mitra, A., Nagaraja, V., Morrison, N.E., Moraes, M. and  Gillis TP.(2009). Implications of high level pseudogene transcription in Mycobacterium leprae. BMC Genomics, 10, 397. PubMed

  6. Bhat, A.G., Leelaram, M.N., Hegde, S.M. and  Nagaraja V.(2009). Deciphering the distinct role for the metal coordination motif in the catalytic activity of Mycobacterium smegmatis topoisomerase I.  J Mol Biol.,393, 788-802. PubMed

Publications 2008

  1. Vasu, K.,Saravanan, M., Bujnicki, J.M. and Nagaraja, V. (2008) Structural integrity of the Beta Beta Alpha-Metal finger motif is required for DNA binding and stable protein–DNA complex formation in R.KpnI. Biochim.  Biophys. Acta., 1784, 269-275. PubMed

  2. Dinakaran, M., Senthilkumar, P.,Yogeeswari, P.,Sriram,D., China,A. and  Nagaraja, V. (2008) Antimycobacterial activities of novel 2-(sub)-3-fluoro/nitro-5,12-dihydro-5-          oxobenzothiazolo[3,2-a]quinoline-6-carboxylic acid. Bioorg & Medicinal Chem. 16, 3408-3418. PubMed

  3. Sengupta, S. and Nagaraja, V. (2008) Studies with glutamate racemase, a DNA gyrase inhibitory protein from Mycobacterium smegmatis. FEMS Microbiol. Lett. 279, 40-47. PubMed

  4. Dinakaran, M., Senthilkumar, P.,Yogeeswari, P.,Sriram,D., China,A. and  Nagaraja, V. (2008)  Novel ofloxacin derivatives: Synthesis, antibacterial and toxicological evaluation. Bioorg & Medicinal Chem. 18, 1229-1236. PubMed

  5. Sengupta, S. and Nagaraja, V. (2008) Yac G from E.coli is a specific endogeneous inhibitor of DNA gyrase. Nucl. Acids Res. 36, 4310-4316. PubMed

  6. Murugesan, D., Palaniappan, S., Perumal, Y., Arnab, C., Nagaraja, V. and  Sriram, D. (2008) Antimycobacterial and phototoxic evaluation of novel 6-fluoro/nitro-4-oxo-7-(sub)-4H-[1,3] thiazelo [3,2-alpha] quinoline-3-carboxylic acid. Int J Antimicrob Agents 31, 337-344. PubMed

  7. Saravanan,  M., Vasu, K. and Nagaraja, V. (2008) Evolution of sequence specificity in a restriction endonuclease by a point mutation. Proc. Natl. Acad. Sci, USA. 105, 10344-10347. PubMed

  8. Senthilkumar, P., Dinakaran, M., Yogeeswari, P., Sriram, D., China, A. and Nagaraja, V.(2009)        Synthesis and antimycobacterial activities of novel 6-nitroquinolone-3-carboxylic acids.    Eur J Med Chem.  44, 345-358. PubMed

  9. Mitra, A., Angamuthu, K and Nagaraja, V (2008) Genome-wide analysis of the intrinsic terminators of transcription across the genus MycobacteriumTuberculosis, 88, 566-575.  

  10. Sengupta, S., Ghosh, S. and Nagaraja, V.(2008) Moonlighting function of Glutamate Racemase from Mycobacterium tuberculosis: Racemization and DNA gyrase inhibition are two independent activities of the enzyme. Microbiology  154, 2796-2803. PubMed

  11. Dinakaran, M., Senthilkumar, P., Yogeeswari, P., China, A., Nagaraja, V. and Sriram, D.(2008) Synthesis, antimycobacterial activities and phototoxic evaluation of 5H-thiazolo[3,2-a]quinoline-4-carboxylic acid derivatives. Med Chem. 4, 482-491. PubMed

 

Publications 2007

  1. Chakraborty, A., Paul, B.D. and  Nagaraja, V. (2007) Bacteriophage Mu C protein is a new member of unusual leucine zipper-HTH class of protein.  Protein Eng, Design & Selection. 20, 1-5. PubMed

  2. Wootla, B., Dasgupta,S., Mallet, V.O., Kazatchkine, M.D., Nagaraja, V.,Friboulet, A., Kaveri, S.V. and Lacroix-Desmazes, S. (2006).  Physiopathology of catalytic antibodies; the case for factor VIII-hydrolyzing immunoglobulin G.   J. Blood Coagulation and Fibrinolysis. 17, 229-234. PubMed

  3. Saravanan, M.,Vasu,K., Kanakaraj,R., Rao, D.N. and Nagaraja, V. (2007)   R.KpnI, an HNH superfamily REase exhibites differential DNA discrimination at non-canonical sequences in the presence of Ca 2+ and Mg2+. Nucl. Acids Res. 35, 2777-2786. PubMed

  4. Kamal, A, Ahmed, S.K., Reddy, K.S., Khan, M.N.A., Rajesh V. C. R.,  Shetty , N.C.,Siddhardha ,B., Murty U. S. N.,  China, A. and  Nagaraja, V. (2007) Synthesis and biological evaluation of  benzothiazole-benzothiadiazine conjugates as antibacterial agents. Lett.  Drug Des. Discov. 4, 550-556.

  5. Saravanan, M., Vasu, K., Ghosh, S. and Nagaraja, V. (2007) Dual Role for Zn2+ in maintaining structural integrity and inducing DNA sequence specificity in a promiscuous endonuclease. J. Biol. Chem. 282, 32320-32326. PubMed

  6. Dasgupta, S., Navarrete, A.M., Delignat, S., Wootla, B., Andre, S., Nagaraja. V., Lacroix-Desmazes, S. and Kaveri, S.V. (2007) Immune response against therapeutic factor VIII in hemophilia A patients--a survey of probable risk factors. Immunol Lett. Review 110, 23-28. PubMed

  7. Senthilkumar, P., Dinakaran,M., Yogeeswari,P.,  China,A., Nagaraja,V and  Sriram,D. (2007) Synthesis and Antimycobacterial Evaluation of Newer 1-Cyclopropyl-1,4-dihydro-6-fluoro-7-(substituted secondary amino)-8-methoxy-5-(sub)-4-oxoquinoline-3-carboxylic acids. Bioorg & Medicinal Chem. 16, 2558-2569. PubMed

  8. Sriram, D., Senthilkumar, P., Dinakaran, M., Yogeeswari, P., China, A. and Nagaraja, V. (2007) Antimycobacterial activities of novel  1-(cyclopropyl/t-butyl/4-fluorophenyl)-1,4-dihydro-6-nitro-4-oxo-7-(substituted secondary amino)-1,8-naphthyridine-3-carboxylic acid. J. Med. Chem. 50, 6232-6239. PubMed

  9. Dinakaran, M., Senthilkumar, P.,Yogeeswari, P.,Sriram,D., China,A. and  Nagaraja, V. (2007) Antimycobacterial activities of novel 2-(sub)-3-fluoro/nitro-5,12-dihydro-5-   oxobenzothiazolo[3,2-a]quinoline-6-carboxylic acid. Bioorg & Medicinal Chem. 16, 3408-3418

Publications 2006

  1. Manjunatha, U.H., Madhusudhan, K., Unniraman, S., Sikder, D., Chatterjee, M., Bhaduri, T., Radha, D.R. and Nagaraja, V. (2006).  DNA topoisomerases from Mycobacterium tuberculosis and Mycobacterium smegmatis. J. Ind. Inst. Sci. 86, 751-762.

  2. Sriram, D., Bal, T.R., Yogeeswari, P., Radha, D.R, and  Nagaraja, V. (2006) Evaluation of antimycobacterial and DNA gyrase inhibition of fluoroquinolone derivatives.  J. Gen. Appl. Microbiol. 52, 195-200. PubMed

  3. Jain, P. and Nagaraja , V .(2006) Indispensable, functionally complementing N- and C-  terminal domains   constitute site specific topoisomerase I . J. Mol. Biol.14:  357, 1409-1421. PubMed

  4. Gupta, R, China, A., Manjunatha, U.H.,  Ponnanna, N.M. and  Nagaraja, V. (2006). A complex of DNA gyrase and RNA polymerase fosters transcription in Mycobacterium smegmatis. Biochem. Biophys. Res. Comm. 343, 1141-1145. PubMed

  5. Bheemanaik, S., Bujnicki, J.M., Nagaraja, V. and Rao, D.N. (2006) Functional Analysis of Amino acid Residues in the Dimerisation Interface of KpnI DNA Methyltransferase. Biol. Chem. 387, 515-523. PubMed

  6. Chakraborty, A., and Nagaraja, V. (2006) Dual role for transactivator protein C in activation of mom promoter of bacteriophage Mu.  J.Biol.Chem. 281, 8511-8517. PubMed

  7. Lacroix-Desmazes, S., Wootla, B.,Delignat, S.,Dasgupta,S., Nagaraja, V. Kazatchkine, M.D. and Kaveri, S.V (2006). Pathophysiology of catalytic antibodies. Immunol. Lett.103, 3-7. PubMed

  8. Kamal, A, Satyanarayana, M., Devaiah, V. Rohini, V. Yadav, J.S., Mullick, B. and  Nagaraja, V. (2006) Synthesis and Biological Evaluation of Coumarin Linked Flouro- quinolones, Phthalimides and Naphthalimides as Potential DNA gyrase Inhibitors. Lett.  Drug Des. Discov. 3, 494-502.

  9. Lacroix-Desmazes S., Wootla, B., Dasgupta, S., Delignat, S., Bayry, J., Reinbolt, J., Hoebeke, J., Saenko,E., Kazatchkine, M.D., Friboulet, A., Christophe, O., Nagaraja, V. and Kaveri, S.V. (2006)  Catalytic IgG from Patients with Hemophilia A Inactivate Therapeutic Factor VIII. J. Immunol. 177, 1355-1363. PubMed

  10. Nagaraja, V. and B.D. Paul (2006). DNA recognition by prokaryotic transcription activators. Proc.Ind. Natl. Acad. B. 71, 43-60.

  11. Sengupta, S., Shah, M. and  Nagaraja V. (2006) Glutamate Racemase from  Mycobacterium tuberculosis inhibits DNA gyrase by affecting its DNA binding. Nucl. Acids Res. 34, 5567-5576. PubMed

Publications 2005

  1. Lacroix-Desmazes S., Nagaraja, V.  et.al. (2005). High levels of catalytic antibodies correlate with favorable outcome in sepsis. Proc. Natl. Acad.Sci., USA, 102, 11, 4109-4113. PubMed

  2.  Manjunatha, U.H., Maxwell, A. and Nagaraja, V. (2005).  A monoclonal antibody that inhibits mycobacterial DNA gyrase by a novel mechanism. Nucl. Acids Res., 33, 3085-3094. PubMed

  3.  Sriram, D., Yogeeswari, P.,Basha,J.H., Radha, D.R. and Nagaraja, V. (2005). Synthesis  and antimycobacterial evaluation of 7-substituted ciprofloxacin derivatives.  Bioorg & Medicinal Chem. 13, 5774-5778. PubMed

  4. Jain, P. and Nagaraja , V. (2005) An atypical type II topoisomerase from Mycobacterium smegmatis with positive supercoiling activity. Molecular  Microbiol. 58(5), 1392-1405. PubMed

Publications 2004

  1. Smith, I., Bishai, R.W. and Nagaraja, V. (2004). Control of Mycobacterial Transcription. In.  S. Cole, D. N. McMurray, K.Eisenach, B. Gicquel, and W.R. Jacobs (ed.), Genetics Of  Mycobacteria, ASM Press, Washington.

  2. Chandrashekaran, S.,Manjunatha, U.H. and Nagaraja, V. (2004).  KpnI restriction endonuclease and methyltransferase exhibite contrasting mode of sequence  recognition. Nucl.Acids Res. 32, 3148-3155. PubMed

  3. Chandrashekaran, S., Saravanan, M., Radha D.R. and Nagaraja V. (2004) .Ca2+ mediated site-specific DNA cleavage and suppression of promiscuous activity of KpnI restriction endonuclease J.Biol.Chem., 279, 49736-49740. PubMed

  4. Saravanan, M., Bujnicki J.M. Cymerman, I.A., Rao, D.N and Nagaraja, V.  (2004) Type II restriction endonuclease R. KpnI is a member of the HNH nuclease superfamily. Nucl. Acids Res., 32,6129-6135. PubMed

Publications 2003

  1. Paul, B.D., Kanhere, A., Chakraborty, A., Bansal, M. and Nagaraja, V. (2003). Identification of the domains for DNA binding and transactivation function of C protein from bacteriophage Mu.  Proteins: structure function and genetics. 52, 272-282. PubMed

  2. Roberts, R.J., Nagaraja, V. et al. (2003). A nomenclature and classification for restriction enzymes and DNA methyltransferases. Nucl. Acids. Res. 31, 1805-1812. PubMed

  3. Bheemanaik. S., Chandrashekaran. S., Nagaraja. V,.,and Rao, D.N. (2003). Kinetic and catalytic properties of dimeric KpnI DNA methyltransferase. J. Biol.Chem. 278, 7863-7874. PubMed

  4. Unniraman, S., and Nagaraja V. (2003).  Catechol dioxygenase is an insensitive reporter for  transcription in Mycobacterium smegmatis.  Biotechniques. 35, 256-262. PubMed

  5. Saravanan, S., Elango, K., Chandrashekaran, S., Anand, N. and Nagaraja, V. (2003).  A new type II restriction endonuclease, OfoI from nonheterocystous cyanobacterium Oscillatoria foreaui. Curr. Sci. 85, 188-191.

  6. Chatterji, M., Sengupta, S. and Nagaraja, V. (2003). Chromosomally encoded gyrase inhibitor GyrI protects against diverse DNA damaging agents. Arch. Microbiol. 180, 339-346. PubMed

  7. Nagaraja, V. (2003). Regulation of DNA topology and DNA topoisomerases in mycobacteria.   Curr. Sci., 86, 135-140.

Publications 2002

  1. Unniraman, S., Prakash, R. and Nagaraja V. (2002). Conserved economics of transcription terminators in eubacteria. Nucl. Acids Res. 30, 675-684. PubMed

  2. Chatterji, M. and Nagaraja V. (2002). Gyri, a counter defensive strategy against proteinaeous inhibitors of DNA gyrase. EMBO Reports.  3, 261-267. PubMed

  3. Manjunatha, U.H., Dalal, M., Chatterji, M., Radha, D.R., Visweswariah, S.S. and Nagaraja V. (2002). Functional characterization of Mycobacterium smegmatis DNA gyrase: a potent decatenase. Nucl. Acids Res. 30, 2144-2153. PubMed

  4. Nagaraja, V., Sikder, D. and Jain, P. (2002). DNA topoisomerase 1 from mycobacteria . a potential drug targets. Curr. Pharmaceutical Design. 8, 1995-2007. PubMed

  5. Unniraman, S., Chatterji, M. and Nagaraja, V. (2002). DNA gyrase genes in Mycobacterium tuberculosis: A single operon driven by multiple promoters. J. Bacteriology. 184, 5449-5456. PubMed

  6. Kalate R.N., Kulkarni, B.D. and Nagaraja, V. (2002). Analysis of DNA curvature distribution in mycobacterial promoters using theoretical models. Biophys. Chem. 99, 77-97. PubMed

  7. Unniraman, S., Chatterji, M. and Nagaraja, V. (2002). A hairpin near the 5. end stablises the DNA gyrase mRNA in Mycobacterium smegmatis. Nucl. Acids Res. 30, 5376-5381. PubMed

  8. Jain, P. and Nagaraja, V. (2002). An orphan gyrB in M. smegmatis genome uncovered by comparative genomics. J. Genet. 81, 105-110. PubMed

Publications 2001

  1.  Manjunatha, U.H., Somesh, B.P., Nagaraja V. and Visweswariah S.S.(2001). A mycobacterium smegmatis gyrase B specific monoclonal antibody reveals association of gyrase A and B subunits in the cell. FEMS Microbiol. Lett. 194, 87-92. PubMed

  2. Unniraman, S. and Nagaraja, V. (2001). Axial distortion as a sensor for supercoil changes: A hypothesis for the homeostatic regulation of DNA gyrase in E. coli. J. Genet. 80, 119-124.  PubMed

  3. Basak, S., Olsen, L., Hattman, S. and Nagaraja, V. (2001). Intrinsic DNA distortion of the bacteriophage Mu. Mom P1 promoter is a negative regulator of its transcription. J. Biol. Chem. 276, 19836-19844. PubMed

  4. Sikder D., Unniraman S., Bhaduri T. and Nagaraja V. (2001). Functional cooperation between topoisomerase 1 and single strand DNA binding protein. J. Mol. Biol. 306, 669-679. PubMed

  5. Chatterji, M., Mahadevan S, Unniraman S. and Nagaraja V. (2001). Effect of different class of inhibitors on DNA gyrase from Mycobacterium smegmatis. J. Antimicrob. Chemotherapy. 48, 479-485. PubMed

  6. Sikder, D. and Nagaraja, V. (2001). A novel bipartite mode of binding of M. smegmatis topoisomerase 1 to its recognition sequence. J. Mol. Biol. 312, 347-357. PubMed

  7. Unniraman, S., Prakash, R. and Nagaraja, V. (2001) Alternate paradigm for intrinsic transcription termination in eubacteria. J. Biol. Chem. 276, 41850-41855. PubMed

  8. Basak, S. and Nagaraja, V. (2001). A versatile in vivo footprinting technique using 1, 10-phenanthroline-copper complex to study important cellular processes. Nucl. Acids Res. 29, e105. PubMed

  9. Basak, S. and Nagaraja, V. (2001). DNA unwinding mechanism for the transcriptional activation of momP1 promoter by the transactivator protein C of bacteriophage Mu. J. Biol. Chem. 276, 46941-46945. PubMed

Publications 2000

  1. Parbhane, R., Unniraman, S., Tambe, S.S., Nagaraja V. and Kulkarni, B.D. (2000). Optimum DNA curvature using a hybrid approach involving an artificial neural network and genetic algorithm. J. Biomolec. Structure Dynamics. 17, 665-672. PubMed

  2. Nagaraja, V., Basak, S., Paul, B.D. and Radha, D.R. (2000). Structure-function and mechanistic studies with transcription activator protein C : A new mechanism for transcription activation. SERC Research Highlights, Department of Science and Technology, Govt. of India. 

  3. Sikder, D. and Nagaraja,  V. (2000). Determination of the recgonition sequence of M. smegmatis topoisomerase 1 on mycobacterial genomic sequences. Nucl. Acids Res. 28, 1830-1837. PubMed

  4. Chatterji, M., Unniraman, S, Maxwell, A. and Nagaraja V. (2000). The additional 165 amino acids in the B protein of Escherichia coli DNA gyrase have an important role in DNA binding. J. Biol. Chem. 275, 22888-22894. PubMed

  5. Manjunatha, U.H., Madhusudan, K., Visweswariah, S.S. and Nagaraja, V. (2000). Structural heterogeneity in DNA gyrases from gram-positive and gram-negative bacteria. Curr. Sci. 79, 968-974.

  6. Bhaduri, T., Basak, S., Sikder, D. and Nagaraja, V. (2000). Inhibition of mycobacterium smegmatis topoisomerase I by specific oligonucleotides. FEBS Lett. 486, 126-130. PubMed

  7. Manujantha, U.H., Mahadevan, S., Visweswariah, S.S. and Nagaraja, V. (2001). Monoclonal antibodies to mycobacterial DNA gyrase A inhibit DNA supercoiling activity. Eur. J. Biochem. 268, 2038-2046. PubMed

Publications 1999

  1. Janscak, P., MacWilliams, M., Sandmeir, U., Nagaraja, V. and Bickle, T.A. (1999). DNA translocation blockage, a general mechanism of cleavage site selection by type 1 restriction enzymes, EMBO J, 18, 2638-2647. PubMed

  2. Chandrashekaran,   S.,   Shankar,   A.B.,   Babu,   P.,   Paul,   B.D.  and   Nagaraja,    V. (1999). Identification   and   characterization  of  a type  II   restriction   endonuclease, Str1   from Streptomyces thermodiastaticus. Curr. Sci. 77, 273-276. 

  3. Chandrashekaran,  S.,   Babu,   P.   and  Nagaraja.  V.  (1999). Characterization of DNA binding activities of over-expressed KpnI restrictin endonuclease and modification methylase. J. Biosci. 24, 269-277. 

  4. Unniraman,  S.  and  Nagaraja,  V. (1999).  Regulation  of  the gyrase  operon  in  Mycobacterium smegmatis   :   A distinct mechanism of relaxation stimulated   transcription. Genes to Cells 4, 697-706. PubMed

  5. Chandrashekaran, S., Babu, P. and Nagaraja, V. (1999). Bas1, a type II restriction endonuclease from Bacillus species J. Biochem. Mol. Biol. & Biophys. 3, 225-229.  

Publications 1998

  1. De,  A.,  Ramesh, V., Mahadevan, S. and Nagaraja, V. (1998).  Mg++  mediated  sequence specific  binding of transcriptional activator protein C of Bacteriophage Mu to  DNA. Biochem., 37, 3831-3838. PubMed

  2. Chandrasekaran,  S.,  Paul, B.D. and  Nagaraja, V. (1998). Design of novel regulatory circuit for the expression of restriction endonucleases. Biol. Chem, 379,  579-582. PubMed

  3. Bhaduri,   T.,  Sikder,  D.  and  Nagaraja,  V.  (1998).  Sequence specific interaction  of Mycobacterium  smegmatis topoisomerase I with duplex DNA. Nucl. Acids  Res.  26, 1668-1674. PubMed

  4. Bhaduri,  T.,  Bagui , T.K.,  Sikder, D. and Nagaraja,  V.  (1998). DNA  topoisomerase  1  from Mycobacterium smegmatis. An enzyme with distinct features. J. Biol. Chem. 273, 13925-13932. PubMed

  5. Mahadevan, S., Bhaduri, T., Radha, D.R., Sikder, D., Unniraman, S., Manjunatha, U.H., Chatterji, M. and Nagaraja, V. (1998). Drug development.Tuberculosis: identification of new molecular targets. In .Tuberculosis Research: into the 21st Century., Tuberculosis Research Centre, Chennai, India.  

  6. Basak, S. and Nagaraja, V. (1998). Transcriptional activator C protein mediated unwinding of DNA as a possible mechanism of mom gene transactivation. J. Mol. Biol.  284, 893-902. PubMed

Publications 1997

  1. Paul,  B.D.,  Ramesh,  V.  and Nagaraja, V. (1997).  An  artificial regulatory  circuit  for stable  expression  of  DNA binding proteins in T7  expression  system.   Gene.  190, 11-15. PubMed

  2. De,  A., Paul, B.D., Ramesh, V. and Nagaraja, V.  (1997). Use of protein A gene  fusions for  the  analysis of structure-function relationship of the transactivator  protein  C of  Bacteriophage Mu.  Protein Engineering.10, 935-941. PubMed

Publications 1996

  1. Madhusudan,  K.  and  Nagaraja, V. (1996). Alignment and  Phylogenetic analysis  of Type II DNA topoisomerases. J. Biosci. 21, 613-629.

  2. Nair, T. M., Madhusudan, K., Nagaraja, V., Kulkarni, B.D., Majumder, H.K. and Singh, R.   (1996).  Theoretical  permutation  gel electrophoretic  analysis  of  a  curved  DNA  fragment located in circular permutation. Electrophoresis.  17, 633-641. PubMed

  3. Ramesh, V. and Nagaraja, V. (1996).  Sequence-specific DNA binding of the phage Mu C  protein:   Footprinting  analysis reveals altered  DNA  conformation  upon  protein  binding.  J. Mol. Biol. 260, 22-33. PubMed

Publications 1995

  1. Nair,  T.M.,  Kulkarni,  B.D  and  Nagaraja,  V.  (1995).  Differential binding  of   RNA polymerase  to  the  wild type Mu mom promoter and  its  C  independent  mutant:  A theoretical analysis. Biophys.  Chem. 53 241-245. PubMed

  2. Hemavathy, K.C and Nagaraja, V. (1995). DNA methylation in mycobacteria:  Absence of methylation  at GATC (Dam) and CCA/TGG (Dcm) sequences. FEMS Immunol. Med. Microbiol. 11, 291-296. PubMed

  3. Madhusudan,  K.  and  Nagaraja, V. (1995).  Mycobacterium  smegmatis DNA  gyrase: cloning and overexpression in Escherichia coli. Microbiol. 141, 3029-3037. PubMed

Publications 1994

  1. Ramesh,  V.,  De,  A  and  Nagaraja, V. (1994).  Overproduction  and  Purification  of  C protein,  the  late gene  transcription activator from phage  Mu.  Protein  Expression and Purification. 5,  379-384. PubMed

  2. Ramesh,   V.,   De,   A.  and  Nagaraja,  V.   (1994).   Engineering hyper- expression   of Bacteriophage  Mu  C  protein by removal of secondary  structure  at  the  translation initiation region. Protein Engineering. 7, 1053-1057. PubMed

  3. Madhusudan, K., Ramesh, V. and Nagaraja, V. (1994). Cloning    and sequence  analysis of  DNA  gyrase  genes  from  Mycobacterium  tuberculosis.  Curr.  Sci.   66,  664-667

  4. Madhusudan,  K.,  Ramesh, V. and Nagaraja, V. 1994. Molecular cloning of  gyrA  and gyrB  genes from Mycobacterium   tuberculosis: Analysis of  Nucleotide  sequence.   Biochem. Mol. Biol. International. 33, 651-660. PubMed

  5. Bhaduri,  T.,  and  Nagaraja,  V. (1994). DNA  Topoisomerase  I  from Mycobacterium smegmatis.  Ind. J. Biochem. Biophys. 31, 339-343. PubMed

  6. Ahmed,  S.A.,   Ramesh, V.,  Nagaraja V.,  Parish, J.H  and Hadi,  S.M.   (1994).   Mode  of  binding  of quercetin to DNA. Mutagenesis  9193-9197. PubMed

  7. Nair,  T.M., Madhusudan, K., Nagaraja, V., Kulkarni, B.D., Majumder, H.K  and  Singh, R.  (1994).   On the mobility behaviour of a curved DNA fragment located  in  circular permutation. FEBS Lett. 351, 321-324. PubMed

Publications 1989-1993

  1. Nagaraja, V. (1993). Control of transcription initiation. J. Biosci.18, 13-25.  

  2. Balke,  V., Nagaraja, V., Gindlesperger, T and Hattman, S.  (1992). Functionally  distinct RNA  polymerase binding sites in  the phage  Mu  mom  promoter   region.   Nucl. Acids Res. 20,  2777-2784. PubMed

  3. Hattman,  S.,  Newman,  L.,  Krishnamurthy,  H.M. and  Nagaraja,  V. (1991).  Com,  the phage   Mu   mom   translational  activator,  is  a  zinc binding   protein    that   binds specifically to its cognate mRNA. Proc. Natl. Acad. Sci. USA. 88, 10027-10031. PubMed

  4. Nagaraja,  V., Hecht, G. and Hattman, S. (1988).  The Phage Mu  late gene  transcription activator,  C,  is a site-specific DNA  binding  protein.  Biochem.  Pharm. 37, 1809-1811. PubMed

  5. Nagaraja,    V.    and    Gopinathan,   K.P.   (1987).    Transcriptional    specificity    after mycobacteriphage I3 infection.  J. Biosci.  11, 167-179.  

  6. Nagaraja,  V., Suri, B., Shepherd, J.C.W  and Bickle, T.A. (1986).  New variation on  old theme:  Type  I  restriction  enzymes  and   their  recognition  sequences.   In   "Gene Manipulation  and  expression" (Glass R.E. and Spizek J., editors),  Croom  Helm,  London, pp.62-78.

Publications 1980-1988

  1. Nagaraja,  V., Stieger, M., Nagar, C., Hadi, S.M and Bickle,  T.A. (1985).  The  nucleotide sequence  recognised  by the Escherichia  coli D type I restriction  and  modification enzyme. Nucl  Acids. Res. 13, 389-399. PubMed

  2. Nagaraja,  V., Shepherd, J.C.W., Pripfl, T and Bickle, T.A. (1985).  Two type  I  restriction enzymes  from Salmonella species. Purification and DNA recognition  sequences.  J. Mol. Biol. 182, 579-587. PubMed

  3. Nagaraja, V., Shepherd, J.C.W and Bickle, T.A. (1985)  A Hybrid recognition sequence in a recombinant restriction enzyme and the evolution of DNA sequence specificity.  Nature ,  316, 371-372. PubMed

  4. Gopinathan, K.P., Sadhu, C and Nagaraja, V. (1984). Interaction between phage and  host chromosomes.Curr. Trends in Life Sci. 12, 89-96.  

  5. Suri,  B.,  Nagaraja,  V and Bickle, T.A. (1984). Bacterial DNA  modification.  In:  Curr. Top. Microbiol. Immunol. 108, 1-9. PubMed

  6. Nagaraja,  V.  (1981). Interaction of Mycobacteriophage I3 with its host  M.  smegmatis 

  7. Nagaraja, V. and Gopinathan, K.P. (1981). Involvement of DNA gyrase in the replication and transcription of Mycobacteriophage I3 DNA. FEBS Lett. 127, 57-62. PubMed

  8. Nagaraja ,    V.     and    Gopinathan    K.P.    (1981).    Macromolecular     synthesis     in Mycobacteriophage I3 infected cells. Molec. Biol. Reps. 8, 11-15. PubMed

  9. Nagaraja,   V.   and   Gopinathan,   K.P.   (1980).   Requirement   for   calcium   ions    in Mycobacteriophage   I3  DNA  injection  and  propagation.  Arch.  Microbiol.   124, 249-254. PubMed