Nucleic Acids Research

Chemistry

Get checked abstract Akihiro Ohkubo, Rintaro Kasuya, Kazushi Sakamoto, Kenichi Miyata, Haruhiko Taguchi, Hiroshi Nagasawa, Toshifumi Tsukahara, Takuma Watanobe, Yoshiyuki Maki, Kohji Seio, and Mitsuo Sekine

‘Protected DNA Probes’ capable of strong hybridization without removal of base protecting groups
Nucleic Acids Research Advance Access published on February 13, 2008
Nucl. Acids Res. 2008 36: 1952-1964; doi:10.1093/nar/gkm927 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Computational Biology

Get checked abstract Jie Guo, Xiaomei Wu, Da-Yong Zhang, and Kui Lin

Genome-wide inference of protein interaction sites: lessons from the yeast high-quality negative protein–protein interaction dataset
Nucleic Acids Research Advance Access published on February 14, 2008
Nucl. Acids Res. 2008 36: 2002-2011; doi:10.1093/nar/gkn016 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genomics

Get checked abstract Dmitry A. Rodionov, Xiaoqing Li, Irina A. Rodionova, Chen Yang, Leonardo Sorci, Etienne Dervyn, Dariusz Martynowski, Hong Zhang, Mikhail S. Gelfand, and Andrei L. Osterman

Transcriptional regulation of NAD metabolism in bacteria: genomic reconstruction of NiaR (YrxA) regulon
Nucleic Acids Research Advance Access published on February 14, 2008
Nucl. Acids Res. 2008 36: 2032-2046; doi:10.1093/nar/gkn046 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Dmitry A. Rodionov, Jessica De Ingeniis, Chiara Mancini, Flavio Cimadamore, Hong Zhang, Andrei L. Osterman, and Nadia Raffaelli

Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulators
Nucleic Acids Research Advance Access published on February 14, 2008
Nucl. Acids Res. 2008 36: 2047-2059; doi:10.1093/nar/gkn047 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology

Get checked abstract SunMi L. Palumbo, Regan M. Memmott, Diana J. Uribe, Yulia Krotova-Khan, Laurence H. Hurley, and Scot W. Ebbinghaus

A novel G-quadruplex-forming GGA repeat region in the c-myb promoter is a critical regulator of promoter activity
Nucleic Acids Research Advance Access published on February 5, 2008
Nucl. Acids Res. 2008 36: 1755-1769; doi:10.1093/nar/gkm1069 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Wenjian Ma, Michael A. Resnick, and Dmitry A. Gordenin

Apn1 and Apn2 endonucleases prevent accumulation of repair-associated DNA breaks in budding yeast as revealed by direct chromosomal analysis
Nucleic Acids Research Advance Access published on February 11, 2008
Nucl. Acids Res. 2008 36: 1836-1846; doi:10.1093/nar/gkm1148 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Marco Lodrini, Tobias Münz, Nicolas Coudevylle, Christian Griesinger, Stefan Becker, and Edith Pfitzner

p160/SRC/NCoA coactivators form complexes via specific interaction of their PAS-B domain with the CID/AD1 domain
Nucleic Acids Research Advance Access published on February 11, 2008
Nucl. Acids Res. 2008 36: 1847-1860; doi:10.1093/nar/gkn029 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Antoine Graindorge, Olivier Le Tonquèze, Raphaël Thuret, Nicolas Pollet, H. Beverley Osborne, and Yann Audic

Identification of CUG-BP1/EDEN-BP target mRNAs in Xenopus tropicalis
Nucleic Acids Research Advance Access published on February 11, 2008
Nucl. Acids Res. 2008 36: 1861-1870; doi:10.1093/nar/gkn031 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Markus Sauer, Anne Catherine Bretz, Rasa Beinoraviciute-Kellner, Michaela Beitzinger, Christof Burek, Andreas Rosenwald, Gregory S. Harms, and Thorsten Stiewe

C-terminal diversity within the p53 family accounts for differences in DNA binding and transcriptional activity
Nucleic Acids Research Advance Access published on February 11, 2008
Nucl. Acids Res. 2008 36: 1900-1912; doi:10.1093/nar/gkn044 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Estella Sanchez-Guerrero, Valerie C. Midgley, and Levon M. Khachigian

Angiotensin II induction of PDGF-C expression is mediated by AT1 receptor-dependent Egr-1 transactivation
Nucleic Acids Research Advance Access published on February 13, 2008
Nucl. Acids Res. 2008 36: 1941-1951; doi:10.1093/nar/gkm923 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Takumi Yamagishi, Shigehisa Hirose, and Takashi Kondo

Secondary DNA structure formation for Hoxb9 promoter and identification of its specific binding protein
Nucleic Acids Research Advance Access published on February 14, 2008
Nucl. Acids Res. 2008 36: 1965-1975; doi:10.1093/nar/gkm1079 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Nurit Gal-Mark, Schraga Schwartz, and Gil Ast

Alternative splicing of Alu exons—two arms are better than one
Nucleic Acids Research Advance Access published on February 14, 2008
Nucl. Acids Res. 2008 36: 2012-2023; doi:10.1093/nar/gkn024 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Alfica Sehgal, Bridget T. Hughes, and Peter J. Espenshade

Oxygen-dependent, alternative promoter controls translation of tco1⁺ in fission yeast
Nucleic Acids Research Advance Access published on February 14, 2008
Nucl. Acids Res. 2008 36: 2024-2031; doi:10.1093/nar/gkn027 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Prafulla Raval, Aleksei N. Kriatchko, Sushil Kumar, and Patrick C. Swanson

Evidence for Ku70/Ku80 association with full-length RAG1
Nucleic Acids Research Advance Access published on February 14, 2008
Nucl. Acids Res. 2008 36: 2060-2072; doi:10.1093/nar/gkn049 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Amy L. Abdulovic, Brenda K. Minesinger, and Sue Jinks-Robertson

The effect of sequence context on spontaneous Pol-dependent mutagenesis in Saccharomyces cerevisiae
Nucleic Acids Research Advance Access published on February 14, 2008
Nucl. Acids Res. 2008 36: 2082-2093; doi:10.1093/nar/gkn054 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes

Get checked abstract Kelly Sheppard, Jing Yuan, Michael J. Hohn, Brian Jester, Kevin M. Devine, and Dieter Söll

From one amino acid to another: tRNA-dependent amino acid biosynthesis
Nucleic Acids Research Advance Access published on February 5, 2008
Nucl. Acids Res. 2008 36: 1813-1825; doi:10.1093/nar/gkn015 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract R. Lynn Sherrer, Joanne M. L. Ho, and Dieter Söll

Divergence of selenocysteine tRNA recognition by archaeal and eukaryotic O-phosphoseryl-tRNA^Sec kinase
Nucleic Acids Research Advance Access published on February 11, 2008
Nucl. Acids Res. 2008 36: 1871-1880; doi:10.1093/nar/gkn036 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Robert Lewis, Harald Dürr, Karl-Peter Hopfner, and Jens Michaelis

Conformational changes of a Swi2/Snf2 ATPase during its mechano-chemical cycle
Nucleic Acids Research Advance Access published on February 11, 2008
Nucl. Acids Res. 2008 36: 1881-1890; doi:10.1093/nar/gkn040 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Cyril M. Sanders

A DNA-binding activity in BPV initiator protein E1 required for melting duplex ori DNA but not processive helicase activity initiated on partially single-stranded DNA
Nucleic Acids Research Advance Access published on February 11, 2008
Nucl. Acids Res. 2008 36: 1891-1899; doi:10.1093/nar/gkn041 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Ye Yang, Shuo-Xing Dou, Hua Ren, Peng-Ye Wang, Xing-Dong Zhang, Min Qian, Bing-Yi Pan, and Xu Guang Xi

Evidence for a functional dimeric form of the PcrA helicase in DNA unwinding
Nucleic Acids Research Advance Access published on February 14, 2008
Nucl. Acids Res. 2008 36: 1976-1989; doi:10.1093/nar/gkm1174 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Kevin A. Fiala, Shanen M. Sherrer, Jessica A. Brown, and Zucai Suo

Mechanistic consequences of temperature on DNA polymerization catalyzed by a Y-family DNA polymerase
Nucleic Acids Research Advance Access published on February 14, 2008
Nucl. Acids Res. 2008 36: 1990-2001; doi:10.1093/nar/gkn004 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Lucy E. Catto, Stuart R. W. Bellamy, Susan E. Retter, and Stephen E. Halford

Dynamics and consequences of DNA looping by the FokI restriction endonuclease
Nucleic Acids Research Advance Access published on February 14, 2008
Nucl. Acids Res. 2008 36: 2073-2081; doi:10.1093/nar/gkn051 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Vera S. Brok-Volchanskaya, Farid A. Kadyrov, Dmitry E. Sivogrivov, Peter M. Kolosov, Andrey S. Sokolov, Michael G. Shlyapnikov, Valentine M. Kryukov, and Igor E. Granovsky

Phage T4 SegB protein is a homing endonuclease required for the preferred inheritance of T4 tRNA gene region occurring in co-infection with a related phage
Nucleic Acids Research Advance Access published on February 16, 2008
Nucl. Acids Res. 2008 36: 2094-2105; doi:10.1093/nar/gkn053 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

RNA

Get checked abstract Elzbieta Kierzek, Ryszard Kierzek, Walter N. Moss, Shawn M. Christensen, Thomas H. Eickbush, and Douglas H. Turner

Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function
Nucleic Acids Research Advance Access published on February 5, 2008
Nucl. Acids Res. 2008 36: 1770-1782; doi:10.1093/nar/gkm1085 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Tomohiro Miyoshi and Toshio Uchiumi

Functional interaction between bases C1049 in domain II and G2751 in domain VI of 23S rRNA in Escherichia coli ribosomes
Nucleic Acids Research Advance Access published on February 5, 2008
Nucl. Acids Res. 2008 36: 1783-1791; doi:10.1093/nar/gkm1171 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Nurit Mirkin, Danae Fonseca, Samia Mohammed, Murat A. Cevher, James L. Manley, and Frida E. Kleiman

The 3' processing factor CstF functions in the DNA repair response
Nucleic Acids Research Advance Access published on February 5, 2008
Nucl. Acids Res. 2008 36: 1792-1804; doi:10.1093/nar/gkn005 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Gilly Padalon-Brauch, Ruth Hershberg, Maya Elgrably-Weiss, Kobi Baruch, Ilan Rosenshine, Hanah Margalit, and Shoshy Altuvia

Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence
Nucleic Acids Research Advance Access published on February 11, 2008
Nucl. Acids Res. 2008 36: 1913-1927; doi:10.1093/nar/gkn050 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology

Get checked abstract Akimasa Matsugami, Takako Ohyama, Masashi Inada, Naonori Inoue, Noriaki Minakawa, Akira Matsuda, and Masato Katahira

Unexpected A-form formation of 4'-thioDNA in solution, revealed by NMR, and the implications as to the mechanism of nuclease resistance
Nucleic Acids Research Advance Access published on February 5, 2008
Nucl. Acids Res. 2008 36: 1805-1812; doi:10.1093/nar/gkn011 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Arturas Meskauskas, Johnathan R. Russ, and Jonathan D. Dinman

Structure/function analysis of yeast ribosomal protein L2
Nucleic Acids Research Advance Access published on February 7, 2008
Nucl. Acids Res. 2008 36: 1826-1835; doi:10.1093/nar/gkn034 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jan Ferner, Alessandra Villa, Elke Duchardt, Elisabeth Widjajakusuma, Jens Wöhnert, Gerhard Stock, and Harald Schwalbe

NMR and MD studies of the temperature-dependent dynamics of RNA YNMG-tetraloops
Nucleic Acids Research Advance Access published on February 13, 2008
Nucl. Acids Res. 2008 36: 1928-1940; doi:10.1093/nar/gkm1183 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Erratum

Christiaan Klijn, Henne Holstege, Jeroen de Ridder, Xiaoling Liu, Marcel Reinders, Jos Jonkers, and Lodewyk Wessels

Identification of cancer genes using a statistical framework for multi-experiment analysis of non-discretized array CGH data
Nucl. Acids Res. 2008 36: 2106; doi:10.1093/nar/gkn092 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online

Get checked abstract Stuart Macgregor, Zhen Zhen Zhao, Anjali Henders, Nicholas G. Martin, Grant W. Montgomery, and Peter M. Visscher

Highly cost-efficient genome-wide association studies using DNA pools and dense SNP arrays
Nucleic Acids Research Advance Access published on February 14, 2008
Nucl. Acids Res. 2008 36: e35; doi:10.1093/nar/gkm1060 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jianwei Jeffery Li, Yizhuo Chu, Benjamin Yi-Hung Lee, and Xiaoliang Sunney Xie

Enzymatic signal amplification of molecular beacons for sensitive DNA detection
Nucleic Acids Research Advance Access published on February 27, 2008
Nucl. Acids Res. 2008 36: e36; doi:10.1093/nar/gkn033 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Dietmar Dirnberger, Monika Messerschmid, and Ralf Baumeister

An optimized split-ubiquitin cDNA-library screening system to identify novel interactors of the human Frizzled 1 receptor
Nucleic Acids Research Advance Access published on March 4, 2008
Nucl. Acids Res. 2008 36: e37; doi:10.1093/nar/gkm1163 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

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