Nucleic Acids Research

Chemistry:

Zunyi Yang, Daniel Hutter, Pinpin Sheng, A. Michael Sismour, and Steven A. Benner

Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern
Nucleic Acids Research Advance Access published on October 29, 2006
Nucl. Acids Res. 2006 34: 6095-6101; doi:10.1093/nar/gkl633 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Computational Biology:

B. Jayaram, Kumkum Bhushan, Sandhya R. Shenoy, Pooja Narang, Surojit Bose, Praveen Agrawal, Debashish Sahu, and Vidhu Pandey

Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2006 34: 6195-6204; doi:10.1093/nar/gkl789 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Huiyu Xia, Jianning Bi, and Yanda Li

Identification of alternative 5'/3' splice sites based on the mechanism of splice site competition
Nucleic Acids Research Advance Access published on November 10, 2006
Nucl. Acids Res. 2006 34: 6305-6313; doi:10.1093/nar/gkl900 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Genomics:

Jeffrey M. Goodenbour and Tao Pan

Diversity of tRNA genes in eukaryotes
Nucleic Acids Research Advance Access published on November 6, 2006
Nucl. Acids Res. 2006 34: 6137-6146; doi:10.1093/nar/gkl725 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Molecular Biology:

Jorge Lopez-Garcia, Manikandan Periyasamy, Ross S. Thomas, Mark Christian, Maria Leao, Parmjit Jat, Karin B. Kindle, David M. Heery, Malcolm G. Parker, Lakjaya Buluwela, Tahereh Kamalati, and Simak Ali

ZNF366 is an estrogen receptor corepressor that acts through CtBP and histone deacetylases
Nucleic Acids Research Advance Access published on November 3, 2006
Nucl. Acids Res. 2006 34: 6126-6136; doi:10.1093/nar/gkl875 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Yanhua Gong, Jiping Yue, Xudong Wu, Xu Wang, Jianyan Wen, Lifang Lu, Xiaozhong Peng, Boqin Qiang, and Jiangang Yuan

NSPc1 is a cell growth regulator that acts as a transcriptional repressor of p21Waf1/Cip1 via the RARE element
Nucleic Acids Research Advance Access published on November 6, 2006
Nucl. Acids Res. 2006 34: 6158-6169; doi:10.1093/nar/gkl834 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Minli Wang, Weizhong Wu, Wenqi Wu, Bustanur Rosidi, Lihua Zhang, Huichen Wang, and George Iliakis

PARP-1 and Ku compete for repair of DNA double strand breaks by distinct NHEJ pathways
Nucleic Acids Research Advance Access published on November 6, 2006
Nucl. Acids Res. 2006 34: 6170-6182; doi:10.1093/nar/gkl840 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Michael S. Y. Huen, Xin-tian Li, Lin-Yu Lu, Rory M. Watt, De-Pei Liu, and Jian-Dong Huang

The involvement of replication in single stranded oligonucleotide-mediated gene repair
Nucleic Acids Research Advance Access published on November 6, 2006
Nucl. Acids Res. 2006 34: 6183-6194; doi:10.1093/nar/gkl852 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yasuko Kamisugi, Katja Schlink, Stefan A. Rensing, Gabriele Schween, Mark von Stackelberg, Andrew C. Cuming, Ralf Reski, and David J. Cove

The mechanism of gene targeting in Physcomitrella patens: homologous recombination, concatenation and multiple integration
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2006 34: 6205-6214; doi:10.1093/nar/gkl832 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

S. Desfarges, J. San Filippo, M. Fournier, C. Calmels, A. Caumont-Sarcos, S. Litvak, P. Sung, and V. Parissi

Chromosomal integration of LTR-flanked DNA in yeast expressing HIV-1 integrase: down regulation by RAD51
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2006 34: 6215-6224; doi:10.1093/nar/gkl843 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Abhijit Shukla, Pratibha Bajwa, and Sukesh R. Bhaumik

SAGA-associated Sgf73p facilitates formation of the preinitiation complex assembly at the promoters either in a HAT-dependent or independent manner in vivo
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2006 34: 6225-6232; doi:10.1093/nar/gkl844 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Todd Blevins, Rajendran Rajeswaran, Padubidri V. Shivaprasad, Daria Beknazariants, Azeddine Si-Ammour, Hyun-Sook Park, Franck Vazquez, Dominique Robertson, Frederick Meins, Jr, Thomas Hohn, and Mikhail M. Pooggin

Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2006 34: 6233-6246; doi:10.1093/nar/gkl886 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Olga Moreno-Moreno, Mònica Torras-Llort, and Fernando Azorín

Proteolysis restricts localization of CID, the centromere-specific histone H3 variant of Drosophila, to centromeres
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2006 34: 6247-6255; doi:10.1093/nar/gkl902 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Qianghua Hu, Jing-Fang Lu, Rong Luo, Subrata Sen, and Sankar N. Maity

Inhibition of CBF/NF-Y mediated transcription activation arrests cells at G₂/M phase and suppresses expression of genes activated at G₂/M phase of the cell cycle
Nucleic Acids Research Advance Access published on November 10, 2006
Nucl. Acids Res. 2006 34: 6272-6285; doi:10.1093/nar/gkl801 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Jin-zhong Chen, Chao-neng Ji, Guan-lan Xu, Rong-yan Pang, Ji-hua Yao, Huan-zhang Zhu, Jing-lun Xue, and William Jia

DAXX interacts with phage C31 integrase and inhibits recombination
Nucleic Acids Research Advance Access published on November 10, 2006
Nucl. Acids Res. 2006 34: 6298-6304; doi:10.1093/nar/gkl890 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yan Sun, Lihua Ding, Hao Zhang, Juqiang Han, Xiao Yang, Jinghua Yan, Yunfeng Zhu, Jiezhi Li, Haifeng Song, and Qinong Ye

Potentiation of Smad-mediated transcriptional activation by the RNA-binding protein RBPMS
Nucleic Acids Research Advance Access published on November 11, 2006
Nucl. Acids Res. 2006 34: 6314-6326; doi:10.1093/nar/gkl914 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Shun-Fu Tseng, Jing-Jer Lin, and Shu-Chun Teng

The telomerase-recruitment domain of the telomere binding protein Cdc13 is regulated by Mec1p/Tel1p-dependent phosphorylation
Nucleic Acids Research Advance Access published on November 15, 2006
Nucl. Acids Res. 2006 34: 6327-6336; doi:10.1093/nar/gkl786 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Ephraim S. Tang and Alberto Martin

NHEJ-deficient DT40 cells have increased levels of immunoglobulin gene conversion: evidence for a double strand break intermediate
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2006 34: 6345-6351; doi:10.1093/nar/gkl830 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Paul M. Rindler, Rhonda M. Clark, Laura M. Pollard, Irene De Biase, and Sanjay I. Bidichandani

Replication in mammalian cells recapitulates the locus-specific differences in somatic instability of genomic GAA triplet-repeats
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2006 34: 6352-6361; doi:10.1093/nar/gkl846 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nirupam Roy Choudhury, Punjab Singh Malik, Dharmendra Kumar Singh, Mohammad Nurul Islam, Kosalai Kaliappan, and Sunil Kumar Mukherjee

The oligomeric Rep protein of Mungbean yellow mosaic India virus (MYMIV) is a likely replicative helicase
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2006 34: 6362-6377; doi:10.1093/nar/gkl903 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Nucleic Acid Enzymes:

Tracy L. Diamond and Frederic D. Bushman

Role of metal ions in catalysis by HIV integrase analyzed using a quantitative PCR disintegration assay
Nucleic Acids Research Advance Access published on November 3, 2006
Nucl. Acids Res. 2006 34: 6116-6125; doi:10.1093/nar/gkl862 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Agneyo Ganguly, Benu Brata Das, Nilkantha Sen, Amit Roy, Somdeb Bose Dasgupta, and Hemanta K. Majumder

‘LeishMan’ topoisomerase I: an ideal chimera for unraveling the role of the small subunit of unusual bi-subunit topoisomerase I from Leishmania donovani
Nucleic Acids Research Advance Access published on November 10, 2006
Nucl. Acids Res. 2006 34: 6286-6297; doi:10.1093/nar/gkl829 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Gyri Teien Haugland, Jae-Ho Shin, Nils-Kåre Birkeland, and Zvi Kelman

Stimulation of MCM helicase activity by a Cdc6 protein in the archaeon Thermoplasma acidophilum
Nucleic Acids Research Advance Access published on November 15, 2006
Nucl. Acids Res. 2006 34: 6337-6344; doi:10.1093/nar/gkl864 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

RNA:

Tetsuhiro Ogawa, Sakura Inoue, Shunsuke Yajima, Makoto Hidaka, and Haruhiko Masaki

Sequence-specific recognition of colicin E5, a tRNA-targeting ribonuclease
Nucleic Acids Research Advance Access published on September 8, 2006
Nucl. Acids Res. 2006 34: 6065-6073; doi:10.1093/nar/gkl629 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Marc Bailly, Stamatina Giannouli, Mickael Blaise, Constantinos Stathopoulos, Daniel Kern, and Hubert Dominique Becker

A single tRNA base pair mediates bacterial tRNA-dependent biosynthesis of asparagine
Nucleic Acids Research Advance Access published on October 29, 2006
Nucl. Acids Res. 2006 34: 6083-6094; doi:10.1093/nar/gkl622 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Oliver Schilling, Christina Herzberg, Tina Hertrich, Hanna Vörsmann, Dirk Jessen, Sebastian Hübner, Fritz Titgemeyer, and Jörg Stülke

Keeping signals straight in transcription regulation: specificity determinants for the interaction of a family of conserved bacterial RNA–protein couples
Nucleic Acids Research Advance Access published on October 29, 2006
Nucl. Acids Res. 2006 34: 6102-6115; doi:10.1093/nar/gkl733 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sándor Kertész, Zoltán Kerényi, Zsuzsanna Mérai, Imre Bartos, Tamás Pálfy, Endre Barta, and Dániel Silhavy

Both introns and long 3'-UTRs operate as cis-acting elements to trigger nonsense-mediated decay in plants
Nucleic Acids Research Advance Access published on November 6, 2006
Nucl. Acids Res. 2006 34: 6147-6157; doi:10.1093/nar/gkl737 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Junlin Qi, Shihuang Su, M. Elaine McGuffin, and William Mattox

Concentration dependent selection of targets by an SR splicing regulator results in tissue-specific RNA processing
Nucleic Acids Research Advance Access published on November 10, 2006
Nucl. Acids Res. 2006 34: 6256-6263; doi:10.1093/nar/gkl755 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tomohiro Kubo, Tadashi Wada, Yuki Yamaguchi, Akira Shimizu, and Hiroshi Handa

Knock-down of 25 kDa subunit of cleavage factor Im in Hela cells alters alternative polyadenylation within 3'-UTRs
Nucleic Acids Research Advance Access published on November 10, 2006
Nucl. Acids Res. 2006 34: 6264-6271; doi:10.1093/nar/gkl794 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Structural Biology:

Shunsuke Yajima, Sakura Inoue, Tetsuhiro Ogawa, Takamasa Nonaka, Kanju Ohsawa, and Haruhiko Masaki

Structural basis for sequence-dependent recognition of colicin E5 tRNase by mimicking the mRNA–tRNA interaction
Nucleic Acids Research Advance Access published on November 11, 2006
Nucl. Acids Res. 2006 34: 6074-6082; doi:10.1093/nar/gkl729 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Claudia H. Hartmann and Christoph A. Klein

Gene expression profiling of single cells on large-scale oligonucleotide arrays
Nucleic Acids Research Advance Access published on October 27, 2006
Nucl. Acids Res. 2006 34: e143; doi:10.1093/nar/gkl740 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Hsin-Chih Yeh, Christopher M. Puleo, Teck Chuan Lim, Yi-Ping Ho, Paul E. Giza, Ru Chih C. Huang, and Tza-Huei Wang

A microfluidic-FCS platform for investigation on the dissociation of Sp1-DNA complex by doxorubicin
Nucleic Acids Research Advance Access published on November 15, 2006
Nucl. Acids Res. 2006 34: e144; doi:10.1093/nar/gkl787 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

L. Chasteen, J. Ayriss, P. Pavlik, and A. R. M. Bradbury

Eliminating helper phage from phage display
Nucleic Acids Research Advance Access published on November 6, 2006
Nucl. Acids Res. 2006 34: e145; doi:10.1093/nar/gkl772 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Hongkai Ji, Steven A. Vokes, and Wing H. Wong

A comparative analysis of genome-wide chromatin immunoprecipitation data for mammalian transcription factors
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2006 34: e146; doi:10.1093/nar/gkl803 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Marieke Aarts, Marleen Dekker, Sandra de Vries, Anja van der Wal, and Hein te Riele

Generation of a mouse mutant by oligonucleotide-mediated gene modification in ES cells
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2006 34: e147; doi:10.1093/nar/gkl896 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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