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Tare, Priyanka ; Mallick, Bratati ; Nagaraja, Valakunja (2013) Co-evolution of specific amino acid in sigma 1.2 region and nucleotide base in the discriminator to act as sensors of small molecule effectors of transcription initiation in mycobacteria Molecular Microbiology, 90 (3). pp. 569-583. ISSN 0950-382X

Tare, Priyanka ; Nagaraja, Valakunja (2013) Regulation of transcription initiation in mycobacteria Current Science, 105 (5). pp. 632-642. ISSN 0011-3891

Ahmed, W. ; Bhat, A. G. ; Leelaram, M. N. ; Menon, S. ; Nagaraja, V. (2013) Carboxyl terminal domain basic amino acids of mycobacterial topoisomerase I bind DNA to promote strand passage Nucleic Acids Research, 41 (15). pp. 7462-7471. ISSN 0305-1048

Marathe, S. A. ; Kumar, R. ; Ajitkumar, P. ; Nagaraja, V. ; Chakravortty, D. (2013) Curcumin reduces the antimicrobial activity of ciprofloxacin against Salmonella typhimurium and Salmonella typhi Journal of Antimicrobial Chemotherapy, 68 (1). pp. 139-152. ISSN 0305-7453

Vasu, K. ; Nagaraja, V. (2013) Diverse functions of restriction-modification systems in addition to cellular defense Microbiology and Molecular Biology Reviews, 77 (1). pp. 53-72. ISSN 1092-2172

Vasu, K. ; Nagamalleswari, E. ; Zahran, M. ; Imhof, P. ; Xu, S. Y. ; Zhu, Z. ; Chan, S. H. ; Nagaraja, V. (2013) Increasing cleavage specificity and activity of restriction endonuclease KpnI Nucleic Acids Research, 41 (21). pp. 9812-9824. ISSN 0305-1048

Ghosh, S. ; Indi, S. S. ; Nagaraja, V. (2013) Regulation of lipid biosynthesis, sliding motility, and biofilm formation by a membrane-anchored nucleoid-associated protein of Mycobacterium tuberculosis Journal of Bacteriology, 195 (8). pp. 1769-1778. ISSN 0021-9193

Leelaram, M. N. ; Bhat, A. G. ; Godbole, A. A. ; Bhat, R. S. ; Manjunath, R. ; Nagaraja, V. (2013) Type IA topoisomerase inhibition by clamp closure The Faseb Journal, 27 (8). pp. 3030-3038. ISSN 0892-6638

Godbole, Adwait Anand ; Leelaram, Majety Naga ; Bhat, Anuradha Gopal ; Jain, Paras ; Nagaraja, Valakunja (2012) Characterization of DNA topoisomerase I from Mycobacterium tuberculosis: DNA cleavage and religation properties and inhibition of its activity Archives of Biochemistry and Biophysics, 528 (2). pp. 197-203. ISSN 0003-9861

Mitra, Anirban ; Nagaraja, Valakunja (2012) Under-representation of intrinsic terminators across bacterial genomic islands: Rho as a principal regulator of xenogenic DNA expression Gene, 508 (2). pp. 221-228. ISSN 0378-1119

China, A. ; Mishra, S. ; Tare, P. ; Nagaraja, V. (2012) Inhibition of Mycobacterium tuberculosis RNA polymerase by binding of a gre factor homolog to the secondary channel Journal of Bacteriology, 194 (5). pp. 1009-1017. ISSN 0021-9193

Leelaram, Majety Naga ; Bhat, Anuradha Gopal ; Hegde, Shivanand Manjunath ; Manjunath, Ramanathapuram ; Nagaraja, Valakunja (2012) Inhibition of type IA topoisomerase by a monoclonal antibody through perturbation of DNA cleavage-religation equilibrium FEBS Journal, 279 (1). pp. 55-65. ISSN 1742-464X

Kumar, R. ; Riley, J. E. ; Parry, D. ; Bates, A. D. ; Nagaraja, V. (2012) Binding of two DNA molecules by type II topoisomerases for decatenation Nucleic Acids Research, 40 (21). pp. 10904-10915. ISSN 0305-1048

Nagamalleswari, Easa ; Vasu, Kommireddy ; Nagaraja, Valakunja (2012) Ca²⁺ binding to the ExDxD motif regulates the DNA cleavage specificity of a promiscuous endonuclease Biochemistry, 51 (44). pp. 8939-8949. ISSN 0006-2960

Tare, Priyanka ; China, Arnab ; Nagaraja, Valakunja (2012) Distinct and contrasting transcription initiation patterns at Mycobacterium tuberculosis promoters PLoS One, 7 (9). Article ID e43900, 12 pages. ISSN 1932-6203

Vasu, K. ; Nagamalleswari, E. ; Nagaraja, V. (2012) Promiscuous restriction is a cellular defense strategy that confers fitness advantage to bacteria Proceedings of the National Academy of Sciences of the United States of America, 109 (20). E1287-E1293. ISSN 0027-8424

Karambelkar, S. ; Swapna, G. ; Nagaraja, V. (2012) Silencing of toxic gene expression by Fis Nucleic Acids Research, 40 (10). pp. 4358-4367. ISSN 0305-1048

Vasu, Kommireddy ; Saravanan, Matheshwaran ; Nagaraja, Valakunja (2011) Endonuclease active site plasticity allows DNA cleavage with diverse alkaline earth and transition metal ions ACS Chemical Biology, 6 (9). pp. 934-942. ISSN 1554-8929

Swapna, Ganduri ; Chakraborty, Atanu ; Kumari, Vandana ; Sen, Ranjan ; Nagaraja, Valakunja (2011) Mutations in β′ subunit of Escherichia coli RNA polymerase perturb the activator polymerase functional interaction required for promoter clearance Molecular Microbiology, 80 (5). pp. 1169-1185. ISSN 0950-382X

Prabha, Swayam ; Rao, Desirazu N. ; Nagaraja, Valakunja (2011) Distinct properties of hexameric but functionally conserved Mycobacterium tuberculosis transcription-repair coupling factor PLoS One, 6 (4). Article ID e19131, 15 pages. ISSN 1932-6203

China, Arnab ; Mishra, Sonakshi ; Nagaraja, Valakunja (2011) A transcript cleavage factor of Mycobacterium tuberculosis important for its survival PLoS One, 6 (7). Article ID e21941, 13 pages. ISSN 1932-6203

Vasu, Kommireddy ; Saravanan, Matheshwaran ; Rajendra, Boggavarapu V. R. N. ; Nagaraja, Valakunja (2010) Generation of a manganese specific restriction endonuclease with nicking activity Biochemistry, 49 (38). pp. 8425-8433. ISSN 0006-2960

Anandhakumar, S. ; Nagaraja, V. ; Raichur, Ashok M. (2010) Reversible polyelectrolyte capsules as carriers for protein delivery Colloids and Surfaces B: Biointerfaces, 78 (2). pp. 266-274. ISSN 0927-7765

Leelaram, Majety Naga ; Suneetha, Nunna ; Nagaraja, Valakunja ; Manjunath, Ramanathapuram (2010) A new ELISA plate based microtiter well assay for mycobacterial topoisomerase I for the direct screening of enzyme inhibitory monoclonal antibody supernatants Journal of Immunological Methods, 357 (1-2). pp. 26-32. ISSN 0022-1759

Malshetty, Vidyasagar ; Kurthkoti, Krishna ; China, Arnab ; Mallick, Bratati ; Yamunadevi, Subburaj ; Sang, Pau Biak ; Srinivasan, Narayanaswamy ; Nagaraja, Valakunja ; Varshney, Umesh (2010) Novel insertion and deletion mutants of RpoB that render mycobacterium smegmatis RNA polymerase resistant to rifampicin-mediated inhibition of transcription Microbiology, 156 (5). pp. 1565-1573. ISSN 1350-0872

China, Arnab ; Nagaraja, Valakunja (2010) Purification of RNA polymerase from mycobacteria for optimized promoter-polymerase interactions Protein Expression and Purification, 69 (2). pp. 235-242. ISSN 1046-5928

China, Arnab ; Tare, Priyanka ; Nagaraja, Valakunja (2010) Comparison of promoter specific events during transcription initiation in mycobacteria Microbiology, 156 (7). pp. 1942-1952. ISSN 1350-0872

Mitra, Anirban ; Kesarwani, Anil K. ; Pal, Debnath ; Nagaraja, Valakunja (2010) WebGeSTer DB-a transcription terminator database Nucleic Acids Research . ISSN 0305-1048

Bhat, Anuradha Gopal ; Leelaram, Majety Naga ; Hegde, Shivanand Manjunath ; Nagaraja, Valakunja (2009) Deciphering the distinct role for the metal coordination motif in the catalytic activity of Mycobacterium smegmatis topoisomerase I Journal of Molecular Biology, 3934 (4). pp. 788-802. ISSN 0022-2836

Anil Kumar, K. N. ; Basu Ray, S. ; Nagaraja, V. ; Raichur, Ashok M. (2009) Encapsulation and release of rifampicin using poly(vinyl pyrrolidone)-poly(methacrylic acid) polyelectrolyte capsules Materials Science and Engineering: C - Biomimetic and Supramolecular Systems, 29 (8). pp. 2508-2513. ISSN 0928-4931

Williams, Diana L. ; Slayden, Richard A. ; Amin, Amol ; Martinez, Alejandra N. ; Pittman, Tana L. ; Mira, Alex ; Mitra, Anirban ; Nagaraja, Valakunja ; Morrison, Norman E. ; Moraes, Milton ; Gillis, Thomas P. (2009) Implications of high level pseudogene transcription in Mycobacterium leprae BMC Genomics, 10 (397). No pp. given. ISSN 1471-2164

Mitra, Anirban ; Angamuthu, Kandavelmani ; Jayashree, Hanasoge Vasudevamurthy ; Nagaraja, Valakunja (2009) Occurrence, divergence and evolution of intrinsic terminators across Eubacteria Genomics, 94 (2). pp. 110-116. ISSN 0888-7543

Leelaram, Majety Naga ; Bhat, Anuradha Gopal ; Suneetha, Nunna ; Nagaraja, Valakunja ; Manjunath, Ramanathapuram (2009) Immunological cross-reactivity of mycobacterial topoisomerase I and divergence from other bacteria Tuberculosis, 89 (4). pp. 256-262. ISSN 1472-9792

Swapna, Ganduri ; Saravanan, Matheswaran ; Nagaraja, Valakunja (2009) Conformational changes triggered by Mg²⁺ mediate transactivator function Biochemistry, 48 (11). pp. 2347-2354. ISSN 0006-2960

Senthilkumar, Palaniappan ; Dinakaran, Murugesan ; Yogeeswari, Perumal ; China, Arnab ; Nagaraja, V. ; Sriram, Dharmarajan (2009) Antimycobacterial activities of novel fluoroquinolones Biomedicine & Pharmacotherapy, 63 (1). pp. 27-35. ISSN 0753-3322

Senthilkumar, Palaniappan ; Dinakaran, Murugesan ; Yogeeswari, Perumal ; Sriram, Dharmarajan ; China, Arnab ; Nagaraja, Valakunja (2009) Synthesis and antimycobacterial activities of novel 6-nitroquinolone-3-carboxylic acids European Journal of Medicinal Chemistry, 44 (1). pp. 345-358. ISSN 0223-5234

Mitra, A. ; Angamuthu, K. ; Nagaraja, V. (2008) Genome-wide analysis of the intrinsic terminators of transcription across the genus Mycobacterium Tuberculosis, 88 (6). pp. 566-575. ISSN 1472-9792

Dinakaran, Murugesan ; Senthilkumar, Palaniappan ; Yogeeswari, Perumal ; China, Arnab ; Nagaraja, Valakunja ; Sriram, Dharmarajan (2008) Synthesis, antimycobacterial activities and phototoxic evaluation of 5H-thiazolo[3,2-a]quinoline-4-carboxylic acid derivatives Medicinal Chemistry, 4 (5). pp. 482-491. ISSN 1573-4064

Saravanan, Matheshwaran ; Vasu, Kommireddy ; Nagaraja, Valakunja (2008) Evolution of sequence specificity in a restriction endonuclease by a point mutation Proceedings of the National Academy of Sciences of the United States of America, 105 (30). pp. 10344-10347. ISSN 0027-8424

Murugesan, Dinakaran ; Palaniappan, Senthilkumar ; Perumal, Yogeeswari ; Arnab, China ; Valakunja, Nagaraja ; Sriram, Dharmarajan (2008) Antimycobacterial and phototoxic evaluation of novel 6-fluoro/nitro-4-oxo-7-(sub)-4H-[1,3]thiazeto[3,2-a]quinoline-3-carboxylic acid International Journal of Antimicrobial Agents, 31 (4). pp. 337-344. ISSN 0924-8579

Dinakaran, Murugesan ; Senthilkumar, Palaniappan ; Yogeeswari, Perumal ; China, Arnab ; Nagaraja, Valakunja ; Sriram, Dharmarajan (2008) Antimycobacterial activities of novel 2-(sub)-3-fluoro/nitro-5,12-dihydro-5-oxobenzothiazolo[3,2-a]quinoline-6-carboxylic acid Bioorganic & Medicinal Chemistry, 16 (6). pp. 3408-3418. ISSN 0968-0896

Senthilkumar, Palaniappan ; Dinakaran, Murugesan ; Banerjee, Debjani ; Devakaram, Ruth Vandana ; Yogeeswari, Perumal ; China, Arnab ; Nagaraja, Valakunja ; Sriram, Dharmarajan (2008) 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 Bioorganic & Medicinal Chemistry, 16 (5). pp. 2558-2569. ISSN 0968-0896

Dinakaran, Murugesan ; Senthilkumar, Palaniappan ; Yogeeswari, Perumal ; China, Arnab ; Nagaraja, Valakunja ; Sriram, Dharmarajan (2008) Novel ofloxacin derivatives: synthesis, antimycobacterial and toxicological evaluation Bioorganic & Medicinal Chemistry Letters, 18 (3). pp. 1229-1236. ISSN 0960-894X

Sengupta, Sugopa ; Nagaraja, Valakunja (2008) Inhibition of DNA gyrase activity by Mycobacterium smegmatis MurI FEMS Microbiology Letters, 279 (1). pp. 40-47. ISSN 0378-1097

Vasu, Kommireddy ; Saravanan, Matheshwaran ; Bujnicki, Janusz M. ; Nagaraja, Valakunja (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 Biochimica et Biophysica Acta: Proteins & Proteomics, 1784 (2). pp. 269-275. ISSN 1570-9639

Sengupta, Sugopa ; Ghosh, Soumitra ; Nagaraja, Valakunja (2008) Moonlighting function of glutamate racemase from Mycobacterium tuberculosis: racemization and DNA gyrase inhibition are two independent activities of the enzyme Microbiology, 154 (9). pp. 2796-2803. ISSN 1350-0872

Sengupta, Sugopa ; Nagaraja, Valakunja (2008) YacG from Escherichia coli is a specific endogenous inhibitor of DNA gyrase Nucleic Acids Research, 36 (13). pp. 4310-4316. ISSN 0305-1048

Kamal, Ahmed ; Ahmed, S. K. ; Reddy, K. S. ; Khan, M. N. ; Shetty, Rajesh V. C. R. N. C. ; Siddhardha, B. ; Murty, U. S. N. ; China, A. ; Nagaraja, V. (2007) Synthesis and biological evaluation of a new series of benzothiazole-benzothiadiazine conjugates as antibacterial agents Letters in Drug Design and Discovery, 4 (8). pp. 550-556. ISSN 1570-1808

Sriram, Dharmarajan ; Senthilkumar, Palaniappan ; Dinakaran, Murugesan ; Yogeeswari, Perumal ; China, Arnab ; Nagaraja, Valakunja (2007) Antimycobacterial activities of novel 1-(cyclopropyl/tert-butyl/4-fluorophenyl)-1,4-dihydro- 6-nitro-4-oxo-7-(substituted secondary amino)-1,8-naphthyridine-3-carboxylic acid Journal of Medicinal Chemistry, 50 (24). pp. 6232-6239. ISSN 0022-2623

Saravanan, Matheshwaran ; Vasu, Kommireddy ; Ghosh, Soumitra ; Nagaraja, Valakunja (2007) Dual role for Zn²⁺ in maintaining structural integrity and inducing DNA sequence specificity in a promiscuous endonuclease Journal of Biological Chemistry, 282 (44). pp. 32320-32326. ISSN 0021-9258

Chakraborty, Atanu ; Paul, Bindu Diana ; Nagaraja, Valakunja (2007) Bacteriophage Mu C protein is a new member of unusual leucine zipper-HTH class of proteins Protein Engineering Design & Selection, 20 (1). pp. 1-5. ISSN 1741-0126

Dasgupta, Suryasarathi ; Navarrete, Ana-Maria ; Delignat, Sandrine ; Wootla, Bharath ; Andre, Sebastien ; Nagaraja, Valakunja ; Lacroix-Desmazes, Sebastien ; Kaveri, Srinivas V. (2007) Immune response against therapeutic factor VIII in hemophilia A patients-a survey of probable risk factors Immunology Letters, 110 (1). pp. 23-28. ISSN 0165-2478

Saravanan, Matheshwaran ; Vasu, Kommireddy ; Kanakaraj, Radhakrishnan ; Rao, Desirazu Narasimha ; Nagaraja, Valakunja (2007) R.KpnI, an HNH superfamily REase, exhibits differential discrimination at non-canonical sequences in the presence of Ca²⁺ and Mg²⁺ Nucleic Acids Research, 35 (8). pp. 2777-2786. ISSN 0305-1048

Lacroix-Desmazes, Sebastien ; Wootla, Bharath ; Dasgupta, Suryasarathi ; Delignat, Sandrine ; Bayry, Jagadeesh ; Reinbolt, Joseph ; Hoebeke, Johan ; Saenko, Evgueni ; Kazatchkine, Michel D. ; Friboulet, Alain ; Christophe, Olivier ; Nagaraja, Valakunja ; Kaveri, Srini V. (2006) Catalytic IgG from patients with hemophilia A inactivate therapeutic factor VIII Journal of Immunology, 177 (2). pp. 1355-1363. ISSN 0022-1767

Wootla, Bharath ; Dasgupta, Suryasarathi ; Mallet, Vincent ; Kazatchkine, Michel D. ; Nagaraja, Valakunja ; Friboulet, Alain ; Kaveri, Srinivas V. ; Lacroix-Desmazes, Sebastien (2006) Physiopathology of catalytic antibodies: the case for factor VIII-hydrolyzing immunoglobulin G Blood Coagulation and Fibrinolysis, 17 (4). pp. 229-234. ISSN 0957-5235

Gupta, Richa ; China, Arnab ; Manjunatha, Ujjini H. ; Ponnanna, N. M. ; Nagaraja, Valakunja (2006) A complex of DNA gyrase and RNA polymerase fosters transcription in Mycobacterium smegmatis Biochemical and Biophysical Research Communications, 343 (4). pp. 1141-1145. ISSN 0006-291X

Bheemanaik, Shivakumara ; Bujnicki, Janusz M. ; Nagaraja, Valakunja ; Rao, Desirazu N. (2006) Functional analysis of amino acid residues at the dimerisation interface of KpnI DNA methyltransferase Biological Chemistry, 387 (5). pp. 515-523. ISSN 1431-6730

Jain, Paras ; Nagaraja, Valakunja (2006) Indispensable, functionally complementing N and C-terminal domains constitute site-specific topoisomerase I Journal of Molecular Biology, 357 (5). pp. 1409-1421. ISSN 0022-2836

Chakraborty, Atanu ; Nagaraja, Valakunja (2006) Dual role for transactivator protein C in activation of mom promoter of bacteriophage Mu Journal of Biological Chemistry, 281 (13). pp. 8511-8517. ISSN 0021-9258

Lacroix-Desmazes, Sebastien ; Wootla, Bharath ; Delignat, Sandrine ; Dasgupta, Suryasarathi ; Nagaraja, Valakunja ; Kazatchkine, Michel D. ; Kaveri, Srini V. (2006) Pathophysiology of catalytic antibodies Immunology Letters, 103 (1). pp. 3-7. ISSN 0165-2478

Sriram, Dharmarajan ; Bal, Tanushree Ratan ; Yogeeswari, Perumal ; Radha, Deshpande R. ; Nagaraja, Valakunja (2006) Evaluation of antimycobacterial and DNA gyrase inhibition of fluoroquinolone derivatives Journal of General and Applied Microbiology, 52 (4). pp. 195-200. ISSN 0022-1260

Sengupta, Sugopa ; Shah, Meera ; Nagaraja, Valakunja (2006) Glutamate racemase from Mycobacterium tuberculosis inhibits DNA gyrase by affecting its DNA-binding Nucleic Acids Research, 34 (19). pp. 5567-5576. ISSN 0305-1048

Jain, Paras ; Nagaraja, Valakunja (2005) An atypical type II topoisomerase from Mycobacterium smegmatis with positive supercoiling activity Molecular Microbiology, 58 (5). pp. 1392-1405. ISSN 0950-382X

Sriram, Dharmarajan ; Yogeeswari, Perumal ; Basha, Jafar Sadik ; Radha, Deshpande R. ; Nagaraja, Valakunja (2005) Synthesis and antimycobacterial evaluation of various 7-substituted ciprofloxacin derivatives Bioorganic & Medicinal Chemistry, 13 (20). pp. 5774-5778. ISSN 0968-0896

Lacroix-Desmazes, Sebastien ; Bayry, Jagadeesh ; Kaveri, Srini V. ; Hayon-Sonsino, David ; Thorenoor, Nithyananda ; Charpentier, Julien ; Luyt, Charles-Edouard ; Mira, Jean-Paul ; Nagaraja, Valakunja ; Kazatchkine, Michel D. ; Dhainaut, Jean-Francois ; Mallet, Vincent O. (2005) High levels of catalytic antibodies correlate with favorable outcome in sepsis Proceedings of the National Academy of Sciences of the United States of America, 102 (11). pp. 4109-4113. ISSN 0027-8424

Manjunatha, Ujjini H. ; Maxwell, Anthony ; Nagaraja, Valakunja (2005) A monoclonal antibody that inhibits mycobacterial DNA gyrase by a novel mechanism Nucleic Acids Research, 33 (10). pp. 3085-3094. ISSN 0305-1048

Chandrashekaran, Siddamadappa ; Saravanan, Matheshwaran ; Radha, Deshpande R. ; Nagaraja, Valakunja (2004) Ca²⁺-mediated site-specific DNA cleavage and suppression of promiscuous activity of KpnI restriction endonuclease Journal of Biological Chemistry, 279 (48). pp. 49736-49740. ISSN 0021-9258

Nagaraja, V. (2004) Regulation of DNA topology in mycobacteria Current Science, 86 (1). pp. 135-140. ISSN 0011-3891

Chandrashekaran, Siddamadappa ; Manjunatha, U. H. ; Nagaraja, Valakunja (2004) KpnI restriction endonuclease and methyltransferase exhibit contrasting mode of sequence recognition Nucleic Acids Research, 32 (10). pp. 3148-3155. ISSN 0305-1048

Saravanan, Matheshwaran ; Bujnicki, Janusz M. ; Cymerman, Iwona A. ; Rao, Desirazu Narasimha ; Nagaraja, Valakunja (2004) Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily Nucleic Acids Research, 32 (20). pp. 6129-6135. ISSN 0305-1048

Paul, Bindu Diana ; Kanhere, Aditi ; Chakraborty, Atanu ; Bansal, Manju ; Nagaraja, Valakunja (2003) Identification of the domains for DNA binding and transactivation function of C protein from bacteriophage Mu Proteins: Structure, Function, and Bioinformatics, 52 (2). pp. 272-282. ISSN 0887-3585

Saravanan, Matheshwaran ; Elango, Kathirvel ; Chandrashekaran, Siddamadappa ; Anand, Narayanaswamy ; Nagaraja, Valakunja (2003) A new type II restriction endonuclease, OfoI from nonheterocystous cyanobacterium Oscillatoria foreaui Current Science, 85 (2). pp. 188-191. ISSN 0011-3891

Bheemanaik, Shivakumar ; Chandrashekaran, Siddamadappa ; Nagaraja, Valakunja ; Rao, Desirazu Narasimha (2003) Kinetic and catalytic properties of dimeric KpnI DNA methyltransferase Journal of Biological Chemistry, 278 (10). pp. 7863-7874. ISSN 0021-9258

Chatterji, Monalisa ; Sengupta, Sugopa ; Nagaraja, Valakunja (2003) Chromosomally encoded gyrase inhibitor GyrI protects Escherichia coli against DNA-damaging agents Archives of Microbiology, 180 (5). pp. 339-346. ISSN 0302-8933

Roberts, Richard J. ; Belfort, Marlene ; Bestor, Timothy ; Bhagwat, Ashok S. ; Bickle, Thomas A. ; Bitinaite, Jurate ; Blumentha, Robert M. ; Degtyarev, Sergey Kh. ; Dryden, David T. F. ; Dybvig, Kevin ; Firman, Keith ; Gromova, Elizaveta S. ; Gumport, Richard I. ; Halford, Stephen E. ; Hattman, Stanley ; Heitman, Joseph ; Hornby, David P. ; Janulaitis, Arvydas ; Jeltsch, Albert ; Josephsen, Jytte ; Kiss, Antal ; Klaenhammer, Todd R. ; Kobayashi, Ichizo ; Kong, Huimin ; Kruger, Detlev H. ; Lacks, Sanford ; Marinus, Martin G. ; Miyahara, Michiko ; Morgan, Richard D. ; Murray, Noreen E. ; Nagaraja, Valakunja ; Piekarowicz, Andrzej ; Pingoud, Alfred ; Raleigh, Elisabeth ; Rao, Desirazu N. ; Reich, Norbert ; Repin, Vladimir E. ; Selker, Eric U. ; Shaw, Pang-Chui ; Stein, Daniel C. ; Stoddard, Barry L. ; Szybalski, Waclaw ; Trautner, Thomas A. ; Van Etten, James L. ; Vitor, Jorge M. B. ; Wilson, Geoffrey G. ; Xu, Shuang-yong (2003) A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes Nucleic Acids Research, 31 (7). pp. 1805-1812. ISSN 0305-1048

Jain, P. ; Nagaraja, V. (2002) An orphangyr B in the Mycobacterium smegmatis genome uncovered by comparative genomics Journal of Genetics, 81 (3). pp. 105-110. ISSN 0022-1333

Unniraman, Shyam ; Chatterji, Monalisa ; Nagaraja, Valakunja (2002) DNA gyrase genes in mycobacterium tuberculosis: a single operon driven by multiple promoters Journal of Bacteriology, 184 (19). pp. 5449-5456. ISSN 0021-9193

Kalate, Rupali N. ; Kulkarni, B. D. ; Nagaraja, V. (2002) Analysis of DNA curvature distribution in mycobacterial promoters using theoretical models Biophysical Chemistry, 99 (1). pp. 77-97. ISSN 0301-4622

Unniraman, Shyam ; Prakash, Ranjana ; Nagaraja, Valakunja (2002) Conserved economics of transcription termination in eubacteria Nucleic Acids Research, 30 (3). pp. 675-684. ISSN 0305-1048

Manjunatha, U. H. ; Dalal, M. ; Chatterji, M. ; Radha, D. R. ; Visweswariah, S. S. ; Nagaraja, V. (2002) Functional characterisation of mycobacterial DNA gyrase: an efficient decatenase Nucleic Acids Research, 30 (10). pp. 2144-2153. ISSN 0305-1048

Chatterji, Monalisa ; Nagaraja, Valakunja (2002) GyrI: a counter-defensive strategy against proteinaceous inhibitors of DNA gyrase EMBO reports, 3 (3). pp. 261-267. ISSN 1469-221X

Unniraman, Shyam ; Chatterji, Monalisa ; Nagaraja, Valakunja (2002) A hairpin near the 5' end stabilises the DNA gyrase mRNA in Mycobacterium smegmatis Nucleic Acids Research, 30 (24). pp. 5376-5381. ISSN 0305-1048

Basak, Shashwati ; Nagaraja, Valakunja (2001) DNA unwinding mechanism for the transcriptional activation of momP1 promoter by the transactivator protein C of bacteriophage Mu Journal of Biological Chemistry, 276 (50). pp. 46941-46945. ISSN 0021-9258

Unniraman, Shyam ; Nagaraja, Valakunja (2001) Axial distortion as a sensor of supercoil changes: a molecular model for the homeostatic regulation of DNA gyrase Journal of Genetics, 80 (3). pp. 119-124. ISSN 0022-1333

Unniraman, Shyam ; Prakash, Ranjana ; Nagaraja, Valakunja (2001) Alternate paradigm for intrinsic transcription termination in eubacteria Journal of Biological Chemistry, 276 (45). pp. 41850-41855. ISSN 0021-9258

Sikder, Devanjan ; Nagaraja, Valakunja (2001) A novel bipartite mode of binding of M. smegmatis topoisomerase I to its recognition sequence Journal of Molecular Biology, 312 (2). pp. 347-357. ISSN 0022-2836

Basak, Shashwati ; Olsen, Lars ; Hattman, Stanley ; Nagaraja, Valakunja (2001) Intrinsic DNA distortion of the bacteriophage MumomP1 promoter is a negative regulator of its transcription: a novel mode of regulation of toxic gene expression Journal of Biological Chemistry, 276 (23). pp. 19836-19844. ISSN 0021-9258

Manjunatha, U. H. ; Mahadevan, S. ; Visweswariah, Sandhya S. ; Nagaraja, V. (2001) Monoclonal antibodies to mycobacterial DNA gyrase A inhibit DNA supercoiling activity European Journal of Biochemistry, 268 (7). pp. 2038-2046. ISSN 0014-2956

Sikder, Devanjan ; Unniraman, Shyam ; Bhaduri, Tisha ; Nagaraja, Valakunja (2001) Functional cooperation between topoisomerase I and single strand DNA-binding protein Journal of Molecular Biology, 306 (4). pp. 669-679. ISSN 0022-2836

Manjunatha, U. H. ; Somesh, B. P. ; Nagaraja, V. ; Visweswariah, S. S. (2001) A Mycobacterium smegmatis gyrase B specific monoclonal antibody reveals association of gyrase A and B subunits in the cell FEMS Microbiology Letters, 194 (1). pp. 87-92. ISSN 0378-1097

Chatterji, Monalisa ; Unniraman, Shyam ; Mahadevan, Sethuraman ; Nagaraja, Valakunja (2001) Effect of different classes of inhibitors on DNA gyrase from Mycobacterium smegmatis Journal of Antimicrobial Chemotherapy, 48 (4). pp. 479-485. ISSN 0305-7453

Basak, Shashwati ; Nagaraja, V. (2001) A versatile in vivo footprinting technique using 1,10-phenanthroline-copper complex to study important cellular processes Nucleic Acids Research, 29 (21). e105_1-e105_6. ISSN 0305-1048

Bhaduri, Tisha ; Basak, Shashwati ; Sikder, Devanjan ; Nagaraja, V. (2000) Inhibition of Mycobacterium smegmatis topoisomerase I by specific oligonucleotides FEBS Letters, 486 (2). pp. 126-130. ISSN 0014-5793

Manjunatha, U. H. ; Madhusudan, K. ; Visweswariah, S. S. ; Nagaraja, V. (2000) Structural heterogeneity in DNA gyrases from Gram-positive and Gram-negative bacteria Current Science, 79 (7). pp. 968-974. ISSN 0011-3891

Chatterji, Monalisa ; Unniraman, Shyam ; Maxwell, Anthony ; Nagaraja, Valakunja (2000) The additional 165 amino acids in the B protein of Escherichia coli DNA gyrase have an important role in DNA binding Journal of Biological Chemistry, 275 (30). pp. 22888-22894. ISSN 0021-9258

Sikder, Devanjan ; Nagaraja, Valakunja (2000) Determination of the recognition sequence of Mycobacterium smegmatis topoisomerase I on mycobacterial genomic sequences Nucleic Acids Research, 28 (8). pp. 1830-1837. ISSN 0305-1048

Unniraman, Shyam ; Nagaraja, Valakunja (1999) Regulation of DNA gyrase operon in Mycobacterium smegmatis: a distinct mechanism of relaxation stimulated transcription Genes to Cells, 4 (12). pp. 697-706. ISSN 1356-9597

Chandrashekaran, Siddamadappa ; Babu, Padmanabhan ; Nagaraja, Valakunja (1999) Characterization of DNA binding activities of over-expressed KpnI restriction endonuclease and modification methylase Journal of Biosciences, 24 (3). pp. 269-277. ISSN 0250-5991

Chandrashekaran, Siddamadappa ; Shankar, Aparna Bhavani ; Babu, Padmanabhan ; Paul, Bindu Diana ; Nagaraja, Valakunja (1999) Identification and characterization of a type II restriction endonuclease, Str1 from Streptomyces thermodiastaticus Current Science, 77 (2). pp. 273-276. ISSN 0011-3891

Janscak, Pavel ; MacWilliams, Maria P. ; Sandmeier, Ursula ; Nagaraja, Valakunja ; Bickle, Thomas A. (1999) DNA translocation blockage, a general mechanism of cleavage site selection by type I restriction enzymes EMBO Journal, 18 (9). pp. 2638-2647. ISSN 0261-4189

Chandrashekaran, Siddamadappa ; Babu, Padmanabhan ; Nagaraja, Valakunja (1999) Purification and characterization of restriction endonuclease BasI from Bacillus species The Journal of Biochemistry, Molecular Biology and Biophysics, 3 . pp. 225-229. ISSN 1025-8140

Basak, Shashwati ; Nagaraja, Valakunja (1998) Transcriptional activator C protein-mediated unwinding of DNA as a possible mechanism for mom gene activation Journal of Molecular Biology, 284 (4). pp. 893-902. ISSN 0022-2836

Bhaduri, Tisha ; Bagui, Tapan Kumar ; Sikder, Devanjan ; Nagaraja, Valakunja (1998) DNA topoisomerase I from Mycobacterium smegmatis: an enzyme with distinct features Journal of Biological Chemistry, 273 (22). pp. 13925-13932. ISSN 0021-9258

Chandrashekharan, Siddamadappa ; Paul, Bindu Diana ; Nagaraja, Valakunja (1998) Design of a novel regulatory circuit for expression of restriction endonucleases Biological Chemistry, 379 . pp. 579-582. ISSN 1431-6730

De, Amitabha ; Ramesh, V. ; Mahadevan, S. ; Nagaraja, V. (1998) Mg²⁺ mediated sequence-specific binding of transcriptional activator protein C of bacteriophage Mu to DNA Biochemistry, 37 (11). pp. 3831-3838. ISSN 0006-2960

Bhaduri, Tisha ; Sikder, Devanjan ; Nagaraja, Valakunja (1998) Sequence specific interaction of Mycobacterium smegmatis topoisomerase I with duplex DNA Nucleic Acids Research, 26 (7). pp. 1668-1674. ISSN 0305-1048

De, A. ; Paul, B. D. ; Ramesh, V. ; 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 Design & Selection, 10 (8). pp. 935-941. ISSN 1741-0126

Paul, Bindu D. ; Ramesh, Vaidyanathan ; Nagaraja, Valakunja (1997) An artificial regulatory circuit for stable expression of DNA-binding proteins in a T7 expression system Gene, 190 (1). pp. 11-15. ISSN 0378-1119

Madhusudan, K. ; Nagaraja, V. (1996) Alignment and phylogenetic analysis of type II DNA topoisomerases Journal of Biosciences, 21 (5). pp. 613-629. ISSN 0250-5991

Ramesh, V. ; Nagaraja, V. (1996) Sequence-specific DNA binding of the phage Mu C protein: footprinting analysis reveals altered DNA conformation upon protein binding Journal of Molecular Biology, 260 (1). pp. 22-23. ISSN 0022-2836

Nair, T. Murlidharan ; Madhusudan, K. ; Nagaraja, V. ; Kulkarni, B. D. ; Majumdar, H. K. ; Singh, Rajan (1996) Theoretical permutation gel electrophoretic analysis of a curved DNA fragment located in circular permutation Electrophoresis, 17 (4). pp. 633-641. ISSN 0173-0835

Madhusudan, K. ; Nagaraja, V. (1995) Mycobacterium smegmatis DNA gyrase: cloning and overexpression in Escherichia coli Microbiology, 141 (12). pp. 3029-3037. ISSN 1350-0872

Hemavathy, Kirugaval C. ; Nagaraja, Valakunja (1995) DNA methylation in mycobacteria: absence of methylation at GATC (Dam) and CCA/TGG (Dcm) sequences FEMS Immunology and Medical Microbiology, 11 (4). pp. 291-296. ISSN 0928-8244

Nair, T. Murlidharan ; Kulkarni, B. D. ; Nagaraja, V. (1995) Differential binding of RNA polymerase to the wild type Mu mom promoter and its C independent mutant: a theoretical analysis Biophysical Chemistry, 53 (3). pp. 241-245. ISSN 0301-4622

Nair, T. Murlidharan ; Madhusudan, K. ; Nagaraja, V. ; Kulkarni, B. D. ; Majumdar, H. K. ; Singh, Rajan (1994) On the mobility behavior of a curved DNA fragment located in circular permutations FEBS Letters, 351 (3). pp. 321-324. ISSN 0014-5793

Ramesh, V. ; De, A. ; Nagaraja, V. (1994) Overproduction and purification of C protein, the late gene transcription activator from phage Mu Protein Expression and Purification, 5 (4). pp. 379-384. ISSN 1046-5928

Madhusudan, K. ; Ramesh, V. ; Nagaraja, V. (1994) Molecular cloningof gyrA and gyrB genes from Mycobacterium tuberculosis: analysis of Nucleotide sequence Biochemistry and Molecular Biology International, 33 (4). pp. 651-660. ISSN 1039-9712

Madhusudan, K. ; Ramesh, V. ; Nagaraja, V. (1994) Cloning and sequence analysis of DNA gyrase genes from Mycobacterium tuberculosis Current Science, 66 (9). pp. 664-667. ISSN 0011-3891

Ramesh, V. ; De, Amitabha ; Nagaraja, V. (1994) Engineering hyperexpression of bacteriophage Mu C protein by removal of secondary structure at the translation initiation region Protein Engineering Design & Selection, 7 (8). pp. 1053-1057. ISSN 1741-0126

Said Ahmed, M. ; Ramesh, V. ; Nagaraja, V. ; Parish, J. H. ; Hadi, S. M. (1994) Mode of binding of quercetin to DNA Mutagenesis, 9 (3). pp. 193-197. ISSN 0267-8357

Nagaraja, V. (1993) Control of transcription initiation Journal of Biosciences, 18 (1). pp. 13-25. ISSN 0250-5991

Balke, Virginia ; Nagaraja, Valakunja ; Gindlesperger, Tracy ; Hattman, Stanley (1992) Functionally distinct RNA polymerase binding sites in the phage Mu mom promoter region Nucleic Acids Research, 20 (11). pp. 2777-2784. ISSN 0305-1048

Hattman, Stanley ; Newman, Laurel ; Krishna Murthy, H. M. ; Nagaraja, V. (1991) Com, the phage Mu mom translational activator, is a zinc-binding protein that binds specifically to its cognate mRNA Proceedings of the National Academy of Sciences of the United States of America, 88 (22). pp. 10027-10031. ISSN 0027-8424

Nagaraja, Valakunja ; Hecht, Gregory ; Hattman, Stanley (1988) The phage Mu 'late' gene transcription activator, C, is a site-specific DNA binding protein Biochemical Pharmacology, 37 (9). pp. 1809-1810. ISSN 0006-2952

Nagaraja, V. ; Gopinathan, K. P. (1987) Transcriptional specificity after mycobacteriophage I3 infection Journal of Biosciences, 11 (1-4). pp. 167-179. ISSN 0250-5991

Nagaraja, Valakunja ; Shepherd, John C. W. ; Bickle, Thomas A. (1985) A hybrid recognition sequence in a recombinant restriction enzyme and the evolution of DNA sequence specificity Nature, 316 (6026). pp. 371-372. ISSN 0028-0836

Nagaraja, Valakunja ; Shepherd, John C. W. ; Pripfl, Therese ; Bickle, Thomas A. (1985) Two type I restriction enzymes from Salmonella species: purification and DNA recognition sequences Journal of Molecular Biology, 182 (4). pp. 579-587. ISSN 0022-2836

Nagaraja, Valakunja ; Stieger, Martin ; Nager, Christoph ; Hadi, Sheikh M. ; Bickle, Thomas A. (1985) The nucleotide sequence recognised by the Escherichia coli D type I restriction and modification enzyme Nucleic Acids Research, 13 (2). pp. 389-399. ISSN 0305-1048

Nagaraja, V. ; Gopinathan, K. P. (1981) Involvement of DNA gyrase in the replication and transcription of mycobacteriophage 13 DNA FEBS Letters, 127 (1). pp. 57-62. ISSN 0014-5793

Nagaraja, V. ; Gopinathan, K. P. (1981) Macromolecular synthesis in mycobacteriophage I3 infected cells Molecular Biology Reports, 8 (1). pp. 11-15. ISSN 0301-4851

Nagaraja, V. ; Gopinathan, K. P. (1980) Requirement for calcium ions in mycobacteriophage I3 DNA injection and propagation Archives of Microbiology, 124 (2-3). pp. 249-254. ISSN 0302-8933