Nucleic Acids Research

Survey and Summary

Get checked abstract Eugene V. Koonin

Darwinian evolution in the light of genomics
Nucleic Acids Research Advance Access published on February 12, 2009
Nucl. Acids Res. 2009 37: 1011-1034; doi:10.1093/nar/gkp089 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Zhumur Ghosh, Bibekanand Mallick, and Jayprokas Chakrabarti

Cellular versus viral microRNAs in host–virus interaction
Nucleic Acids Research Advance Access published on December 18, 2008
Nucl. Acids Res. 2009 37: 1035-1048; doi:10.1093/nar/gkn1004 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Chemistry and Synthetic Biology

Get checked abstract Yasunori Mitsuoka, Tetsuya Kodama, Ryo Ohnishi, Yoshiyuki Hari, Takeshi Imanishi, and Satoshi Obika

A bridged nucleic acid, 2',4'-BNA^COC: synthesis of fully modified oligonucleotides bearing thymine, 5-methylcytosine, adenine and guanine 2',4'-BNA^COC monomers and RNA-selective nucleic-acid recognition
Nucleic Acids Research Advance Access published on January 9, 2009
Nucl. Acids Res. 2009 37: 1225-1238; doi:10.1093/nar/gkn1062 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract David A. Rusling, Guomei Peng, Natarajan Srinivasan, Keith R. Fox, and Tom Brown

DNA triplex formation with 5-dimethylaminopropargyl deoxyuridine
Nucleic Acids Research Advance Access published on January 12, 2009
Nucl. Acids Res. 2009 37: 1288-1296; doi:10.1093/nar/gkn1060 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Mayumi Takahashi, Noriaki Minakawa, and Akira Matsuda

Synthesis and characterization of 2'-modified-4'-thioRNA: a comprehensive comparison of nuclease stability
Nucleic Acids Research Advance Access published on January 16, 2009
Nucl. Acids Res. 2009 37: 1353-1362; doi:10.1093/nar/gkn1088 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Computational Biology

Get checked abstract Gil-Mi Ryu, Pamela Song, Kyu-Won Kim, Kyung-Soo Oh, Keun-Joon Park, and Jong Hun Kim

Genome-wide analysis to predict protein sequence variations that change phosphorylation sites or their corresponding kinases
Nucleic Acids Research Advance Access published on January 12, 2009
Nucl. Acids Res. 2009 37: 1297-1307; doi:10.1093/nar/gkn1008 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Gene regulation, Chromatin and Epigenetics

Get checked abstract Yasuhiro Tomaru, Misato Nakanishi, Hisashi Miura, Yasumasa Kimura, Hiroki Ohkawa, Yusuke Ohta, Yoshihide Hayashizaki, and Masanori Suzuki

Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi
Nucleic Acids Research Advance Access published on January 7, 2009
Nucl. Acids Res. 2009 37: 1049-1060; doi:10.1093/nar/gkn1028 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Yu-Chien Chen, Suewei I. Lin, Ying-Kuan Chen, Chuen-Sheue Chiang, and Gwo-Jen Liaw

The Torso signaling pathway modulates a dual transcriptional switch to regulate tailless expression
Nucleic Acids Research Advance Access published on January 7, 2009
Nucl. Acids Res. 2009 37: 1061-1072; doi:10.1093/nar/gkn1036 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Mattia Frontini, Meeraa Vijayakumar, Alexander Garvin, and Nicole Clarke

A ChIP–chip approach reveals a novel role for transcription factor IRF1 in the DNA damage response
Nucleic Acids Research Advance Access published on January 7, 2009
Nucl. Acids Res. 2009 37: 1073-1085; doi:10.1093/nar/gkn1051 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Neil P. Blackledge, Christopher J. Ott, Austin E. Gillen, and Ann Harris

An insulator element 3' to the CFTR gene binds CTCF and reveals an active chromatin hub in primary cells
Nucleic Acids Research Advance Access published on January 7, 2009
Nucl. Acids Res. 2009 37: 1086-1094; doi:10.1093/nar/gkn1056 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Peter Pelka, Jailal N. G. Ablack, Joseph Torchia, Andrew S. Turnell, Roger J. A. Grand, and Joe S. Mymryk

Transcriptional control by adenovirus E1A conserved region 3 via p300/CBP
Nucleic Acids Research Advance Access published on January 7, 2009
Nucl. Acids Res. 2009 37: 1095-1106; doi:10.1093/nar/gkn1057 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genomics

Get checked abstract Karl J. Clark, Daniel F. Carlson, Michael J. Leaver, Linda K. Foster, and Scott C. Fahrenkrug

Passport, a native Tc1 transposon from flatfish, is functionally active in vertebrate cells
Nucleic Acids Research Advance Access published on January 9, 2009
Nucl. Acids Res. 2009 37: 1239-1247; doi:10.1093/nar/gkn1025 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Mickael Throude, Stéphanie Bolot, Mickael Bosio, Caroline Pont, Xavier Sarda, Umar Masood Quraishi, Fabienne Bourgis, Philippe Lessard, Peter Rogowsky, Alain Ghesquiere, Alain Murigneux, Gilles Charmet, Pascual Perez, and Jérôme Salse

Structure and expression analysis of rice paleo duplications
Nucleic Acids Research Advance Access published on January 9, 2009
Nucl. Acids Res. 2009 37: 1248-1259; doi:10.1093/nar/gkn1048 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Monica C. Sleumer, Mikhail Bilenky, An He, Gordon Robertson, Nina Thiessen, and Steven J. M. Jones

Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements
Nucleic Acids Research Advance Access published on January 16, 2009
Nucl. Acids Res. 2009 37: 1323-1334; doi:10.1093/nar/gkn1041 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Supplementary Data]  

Molecular Biology

Get checked abstract Jingyun Zhang, Micah J. McCauley, L. James Maher, III, Mark C. Williams, and N. E. Israeloff

Mechanism of DNA flexibility enhancement by HMGB proteins
Nucleic Acids Research Advance Access published on January 7, 2009
Nucl. Acids Res. 2009 37: 1107-1114; doi:10.1093/nar/gkn1011 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Yasuhiro Hara, Yoshiaki Onishi, Katsutaka Oishi, Koyomi Miyazaki, Akiyoshi Fukamizu, and Norio Ishida

Molecular characterization of Mybbp1a as a co-repressor on the Period2 promoter
Nucleic Acids Research Advance Access published on January 7, 2009
Nucl. Acids Res. 2009 37: 1115-1126; doi:10.1093/nar/gkn1013 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Claudia Schneider, Eileen Leung, Jeremy Brown, and David Tollervey

The N-terminal PIN domain of the exosome subunit Rrp44 harbors endonuclease activity and tethers Rrp44 to the yeast core exosome
Nucleic Acids Research Advance Access published on January 7, 2009
Nucl. Acids Res. 2009 37: 1127-1140; doi:10.1093/nar/gkn1020 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Elena Babaylova, Dmitri Graifer, Alexey Malygin, Joachim Stahl, Ivan Shatsky, and Galina Karpova

Positioning of subdomain IIId and apical loop of domain II of the hepatitis C IRES on the human 40S ribosome
Nucleic Acids Research Advance Access published on January 7, 2009
Nucl. Acids Res. 2009 37: 1141-1151; doi:10.1093/nar/gkn1026 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Laura J. Ng, Jennifer E. Cropley, Hilda A. Pickett, Roger R. Reddel, and Catherine M. Suter

Telomerase activity is associated with an increase in DNA methylation at the proximal subtelomere and a reduction in telomeric transcription
Nucleic Acids Research Advance Access published on January 7, 2009
Nucl. Acids Res. 2009 37: 1152-1159; doi:10.1093/nar/gkn1030 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Niresh Hariparsad, Xiaoyan Chu, Jocelyn Yabut, Paul Labhart, Dylan P. Hartley, Xudong Dai, and Raymond Evers

Identification of pregnane-X receptor target genes and coactivator and corepressor binding to promoter elements in human hepatocytes
Nucleic Acids Research Advance Access published on January 7, 2009
Nucl. Acids Res. 2009 37: 1160-1173; doi:10.1093/nar/gkn1047 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Warawan Eiamphungporn, Sumarin Soonsanga, Jin-Won Lee, and John D. Helmann

Oxidation of a single active site suffices for the functional inactivation of the dimeric Bacillus subtilis OhrR repressor in vitro
Nucleic Acids Research Advance Access published on January 7, 2009
Nucl. Acids Res. 2009 37: 1174-1181; doi:10.1093/nar/gkn1052 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Graziano Lolli

Binding to DNA of the RNA-polymerase II C-terminal domain allows discrimination between Cdk7 and Cdk9 phosphorylation
Nucleic Acids Research Advance Access published on January 9, 2009
Nucl. Acids Res. 2009 37: 1260-1268; doi:10.1093/nar/gkn1061 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Nucleic Acid Enzymes

Get checked abstract L. Peter Sarin, Minna M. Poranen, N. Marika Lehti, Janne J. Ravantti, Minni R. L. Koivunen, Antti P. Aalto, Alberdina A. van Dijk, David I. Stuart, Jonathan M. Grimes, and Dennis H. Bamford

Insights into the pre-initiation events of bacteriophage 6 RNA-dependent RNA polymerase: towards the assembly of a productive binary complex
Nucleic Acids Research Advance Access published on January 7, 2009
Nucl. Acids Res. 2009 37: 1182-1192; doi:10.1093/nar/gkn1035 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Olivier Delelis, Isabelle Malet, Li Na, Luba Tchertanov, Vincent Calvez, Anne-Genevieve Marcelin, Frederic Subra, Eric Deprez, and Jean-François Mouscadet

The G140S mutation in HIV integrases from raltegravir-resistant patients rescues catalytic defect due to the resistance Q148H mutation
Nucleic Acids Research Advance Access published on January 7, 2009
Nucl. Acids Res. 2009 37: 1193-1201; doi:10.1093/nar/gkn1050 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

RNA

Get checked abstract Taraka Dale, Richard P. Fahlman, Mikolaj Olejniczak, and Olke C. Uhlenbeck

Specificity of the ribosomal A site for aminoacyl-tRNAs
Nucleic Acids Research Advance Access published on January 7, 2009
Nucl. Acids Res. 2009 37: 1202-1210; doi:10.1093/nar/gkn1040 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Mounia Bensaid, Mireille Melko, Elias G. Bechara, Laetitia Davidovic, Antonio Berretta, Maria Vincenza Catania, Jozef Gecz, Enzo Lalli, and Barbara Bardoni

FRAXE-associated mental retardation protein (FMR2) is an RNA-binding protein with high affinity for G-quartet RNA forming structure
Nucleic Acids Research Advance Access published on January 9, 2009
Nucl. Acids Res. 2009 37: 1269-1279; doi:10.1093/nar/gkn1058 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Sébastien Muller, Alan Urban, Arnaud Hecker, Fabrice Leclerc, Christiane Branlant, and Yuri Motorin

Deficiency of the tRNA^Tyr:35-synthase aPus7 in Archaea of the Sulfolobales order might be rescued by the H/ACA sRNA-guided machinery
Nucleic Acids Research Advance Access published on January 12, 2009
Nucl. Acids Res. 2009 37: 1308-1322; doi:10.1093/nar/gkn1037 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Supplementary Data]  

Get checked abstract Akiko Noma, Yuriko Sakaguchi, and Tsutomu Suzuki

Mechanistic characterization of the sulfur-relay system for eukaryotic 2-thiouridine biogenesis at tRNA wobble positions
Nucleic Acids Research Advance Access published on January 16, 2009
Nucl. Acids Res. 2009 37: 1335-1352; doi:10.1093/nar/gkn1023 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology

Get checked abstract Muthiah Kumaraswami, Jason T. Schuman, Susan M. Seo, Glenn W. Kaatz, and Richard G. Brennan

Structural and biochemical characterization of MepR, a multidrug binding transcription regulator of the Staphylococcus aureus multidrug efflux pump MepA
Nucleic Acids Research Advance Access published on January 7, 2009
Nucl. Acids Res. 2009 37: 1211-1224; doi:10.1093/nar/gkn1046 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Patrick A. Holt, Patricia Ragazzon, Lucjan Strekowski, Jonathan B. Chaires, and John O. Trent

Discovery of novel triple helical DNA intercalators by an integrated virtual and actual screening platform
Nucleic Acids Research Advance Access published on January 9, 2009
Nucl. Acids Res. 2009 37: 1280-1287; doi:10.1093/nar/gkn1043 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Methods Online

Get checked abstract M. C. Díaz de la Loza and R. E. Wellinger

A novel approach for organelle-specific DNA damage targeting reveals different susceptibility of mitochondrial DNA to the anticancer drugs camptothecin and topotecan
Nucleic Acids Research Advance Access published on January 16, 2009
Nucl. Acids Res. 2009 37: e26; doi:10.1093/nar/gkn1087 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Nathan A. Tanner, Joseph J. Loparo, Samir M. Hamdan, Slobodan Jergic, Nicholas E. Dixon, and Antoine M. van Oijen

Real-time single-molecule observation of rolling-circle DNA replication
Nucleic Acids Research Advance Access published on January 20, 2009
Nucl. Acids Res. 2009 37: e27; doi:10.1093/nar/gkp006 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Grigory G. Borisenko, Marina A. Zaitseva, Andrey N. Chuvilin, and Galina E. Pozmogova

DNA modification of live cell surface
Nucleic Acids Research Advance Access published on January 21, 2009
Nucl. Acids Res. 2009 37: e28; doi:10.1093/nar/gkn1034 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Alberto Apostolico, Giovanni Ciriello, Concettina Guerra, Christine E. Heitsch, Chiaolong Hsiao, and Loren Dean Williams

Finding 3D motifs in ribosomal RNA structures
Nucleic Acids Research Advance Access published on January 21, 2009
Nucl. Acids Res. 2009 37: e29; doi:10.1093/nar/gkn1044 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Susan Zimnik, Matthias Gaestel, and Rainer Niedenthal

Mutually exclusive STAT1 modifications identified by Ubc9/substrate dimerization-dependent SUMOylation
Nucleic Acids Research Advance Access published on January 27, 2009
Nucl. Acids Res. 2009 37: e30; doi:10.1093/nar/gkp020 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Siripan Limsirichaikul, Atsuko Niimi, Heather Fawcett, Alan Lehmann, Shunichi Yamashita, and Tomoo Ogi

A rapid non-radioactive technique for measurement of repair synthesis in primary human fibroblasts by incorporation of ethynyl deoxyuridine (EdU)
Nucleic Acids Research Advance Access published on January 29, 2009
Nucl. Acids Res. 2009 37: e31; doi:10.1093/nar/gkp023 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Matthew R. Baker, Tamara Zarubica, H. Tonie Wright, and Jason P. Rife

Scintillation proximity assay for measurement of RNA methylation
Nucleic Acids Research Advance Access published on January 30, 2009
Nucl. Acids Res. 2009 37: e32; doi:10.1093/nar/gkn1038 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Wilfried Weber, Stefan Luzi, Maria Karlsson, Carlota Diaz Sanchez-Bustamante, Urs Frey, Andreas Hierlemann, and Martin Fussenegger

A synthetic mammalian electro-genetic transcription circuit
Nucleic Acids Research Advance Access published on February 3, 2009
Nucl. Acids Res. 2009 37: e33; doi:10.1093/nar/gkp014 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Melanie I. Trombly, Hong Su, and Xiaozhong Wang

A genetic screen for components of the mammalian RNA interference pathway in Bloom-deficient mouse embryonic stem cells
Nucleic Acids Research Advance Access published on February 17, 2009
Nucl. Acids Res. 2009 37: e34; doi:10.1093/nar/gkp019 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Front-Matter/Back-Matter

Nucleic Acids Research: VOLUME 37 ISSUE 4 2009
Nucl. Acids Res. 2009 37: i; doi:10.1093/nar/gkp170 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acids Research
Nucl. Acids Res. 2009 37: ii; doi:10.1093/nar/gkp169 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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Nucl. Acids Res. 2009 37: iii; doi:10.1093/nar/gkp171 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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