Hattman S., Newman L., Krishnamurthy H.M and Nagaraja V
1991. Com, the phage
Mu
mom
translational activator, is a
binding
protein
that
binds specifically to its cognate mRNA.
Proc. Natl. Acad. Sci. USA. 88, 10027-10031.
Balke V., Nagaraja V., Gindlesperger T and Hattman S. 1992.
Functionally distinct RNA polymerase binding sites in the phage
mom promoter
region.
Nucleic Acids Res. 20, 2777-2784.
zinc
Mu
Nagaraja V. 1993. Control of transcription initiation. J. Biosci.
18, 13-25.
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.
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.
Madhusudan K., Ramesh V and Nagaraja V. 1994. Cloning
and
sequence analysis of DNA gyrase genes from Mycobacterium
tuberculosis. Current Science.
66, 664-667.
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.
Bhaduri T., and Nagaraja V. 1994. DNA Topoisomerase I from
Mycobacterium smegmatis, Ind. J. Biochem. Biophys. 31, 339-343.
Ahmed S.A.,
S.M.
1994.
193-197.
Ramesh V., Nagaraja V., Parish J.H and Hadi
Mode of binding of quercetin to DNA. Mutagenesis 9
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.
Nair T.M., Kulkarni B.D and Nagaraja V. 1995. Differential
binding of
RNA polymerase to the wild type Mu mom promoter and
C independent mutant: A theoretical analysis. Biophys. Chem. 53
241-245.
its
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.
Madhusudan K. and Nagaraja V. 1995. Mycobacterium smegmatis
DNA gyrase: cloning and overexpression in Escherichia coli. Microbiol.
141, 3029-3037.
Madhusudan K. and Nagaraja V. 1996. Alignment and Phylogenetic
analysis of Type II DNA topoisomerases. J. Biosci. 21, 613-629.
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.
Ramesh V. and Nagaraja V. 1996. Sequence-specific DNA binding of
the phage Mu C protein:
Footprinting analysis reveals altered
conformation upon protein binding. J. Mol. Biol. 260, 22-33
DNA
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.
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.
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. Biochemistry, 37, 3831-3838.
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.
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.
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.
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.
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.
Janscak P, MacWilliams M, Sandmeir U., Nagaraja V and Bickle TA.
1999. DNA translocation blockage, a general mechanism of cleavage site
selection by type 1 restriction enzymes, EMBO J, 18, 2638-2647.
Chandrashekaran
S.,
Shankar
A.B.,
Babu
P.,
Paul
B.D.
and
Nagaraja
V. 1999. Identification
and
characterization
type II
restriction
endonuclease, Str1
from Streptomyces
thermodiastaticus. Current Science. 77, 273-276.
Chandrashekaran
S.,
Babu
P.
and
Nagaraja
V.
1999.
of
a
Molecular
cloning
of
KpnI restriction-modification system :
hyperexpression of KpnI endonuclease. J. Biosci. 24, 269-277.
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.
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.
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.
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.
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.
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.
Manjunatha U.H., Madhusudan K., Visweswariah S.S. and Nagaraja V.
(2000). Structural heterogeneity in DNA gyrases from gram-positive and
gram-negative bacteria. Current Science 79, 968-974.
Bhaduri T., Basak S., Sikder D. and Nagaraja V. (2000). Inhibition
of mycobacterium smegmatis topoisomerase I by specific oligonucleotides.
FEBS Lett. 486, 126-130.
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.
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.
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.
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.
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.
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.
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.
Unniraman S, Prakash R and Nagaraja V. (2001) Alternate paradigm
for intrinsic transcription termination in eubacteria. J. Biol. Chem. 276,
41850-41855.
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.
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.
Unniraman, S., Prakash, R. and Nagaraja V. (2002). Conserved
economics of transcription terminators in eubacteria. Nucl. Acids Res. 30,
675-684.
Chatterji, M. and Nagaraja V. (2002). Gyri, a counter defensive
strategy against proteinaeous inhibitors of DNA gyrase. EMBO Reports.
261-267.
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.
Nagaraja V, Sikder D. and Jain P. (2002). DNA topoisomerase 1 from
mycobacteria . a potential drug targets. Curr. Pharmaceutical Design. 8,
1995-2007.
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.
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.
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.
Jain P. and Nagaraja, V. (2002). An orphan gyrB in M. smegmatis
genome uncovered by comparative genomics. J. Genet. 81, 105-110.
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.
Roberts, R.J., Nagaraja, V. et al. (2003). A nomenclature and
classification for restriction enzymes and DNA methyltransferases. Nucl.
Acids. Res. 31, 1805-1812.
Shivakumara B., Chandrashekaran S., Nagaraja V.,and Rao, D.N.
(2003). Kinetic and catalytic properties of dimeric KpnI DNA
methyltransferase. J. Biol.Chem. 278, 7863-7874.
Unniraman, S., and Nagaraja V. (2003). Catechol dioxygenase is an
insensitive reporter for transcription in Mycobacterium smegmatis.
Biotechniques. 35, 256-262.
Saravanan, S., Elango, K., Chandrashekaran, S., Anand, N. and
Nagaraja, V. (2003). A new type II restriction endonuclease, OfoI from
nonheterocystous cyanobacterium Oscillatoria foreaui. Current Science 85,
188-191.
Chatterji, M., Sengupta, S. and Nagaraja, V. (2003). Chromosomally
encoded gyrase inhibitor GyrI protects against diverse DNA damaging
agents. Arch. Microbiol. 180, 339-346.
Nagaraja, V. (2003). Regulation of DNA topology and DNA
topoisomerases in mycobacteria. Current Science 86, 135-140.
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.
Chandrashekaran, S.,Manjunatha, U.H. and Nagaraja, V. (2004).
KpnI restriction endonuclease and methyltransferase exhibite contrasting
mode of sequence recognition. Nucl.Acids Res. (In Press).