Nucleic Acids Research

Survey and Summary:

Stephen E. Halford and John F. Marko

How do site-specific DNA-binding proteins find their targets?
Nucl. Acids Res. 2004 32: 3040-3052; doi:10.1093/nar/gkh624 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Articles:

Obituary
Nucl. Acids Res. 2004 32: 2975-2976; doi:10.1093/nar/gkh647 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jenny Thirlway, Ian J. Turner, Christopher T. Gibson, Laurence Gardiner, Kevin Brady, Stephanie Allen, Clive J. Roberts, and Panos Soultanas

DnaG interacts with a linker region that joins the N- and C-domains of DnaB and induces the formation of 3-fold symmetric rings
Nucl. Acids Res. 2004 32: 2977-2986; doi:10.1093/nar/gkh628 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Patricia Uguen and Shona Murphy

3'-Box-dependent processing of human pre-U1 snRNA requires a combination of RNA and protein co-factors
Nucl. Acids Res. 2004 32: 2987-2994; doi:10.1093/nar/gkh619 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Udo Moehren, Uwe Dressel, Christina A. Reeb, Sami Väisänen, Thomas W. Dunlop, Carsten Carlberg, and Aria Baniahmad

The highly conserved region of the co-repressor Sin3A functionally interacts with the co-repressor Alien
Nucl. Acids Res. 2004 32: 2995-3004; doi:10.1093/nar/gkh621 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Javier Sanchez Garcia, Leonora F. Ciufo, Xiaowen Yang, Stephen E. Kearsey, and Stuart A. MacNeill

The C-terminal zinc finger of the catalytic subunit of DNA polymerase is responsible for direct interaction with the B-subunit
Nucl. Acids Res. 2004 32: 3005-3016; doi:10.1093/nar/gkh623 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jeffrey Watson, Franklin A. Hays, and P. Shing Ho

Definitions and analysis of DNA Holliday junction geometry
Nucl. Acids Res. 2004 32: 3017-3027; doi:10.1093/nar/gkh631 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Fedor V. Karginov and Olke C. Uhlenbeck

Interaction of Escherichia coli DbpA with 23S rRNA in different functional states of the enzyme
Nucl. Acids Res. 2004 32: 3028-3032; doi:10.1093/nar/gkh640 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kishor K. Bhakat, Tapas K. Hazra, and Sankar Mitra

Acetylation of the human DNA glycosylase NEIL2 and inhibition of its activity
Nucl. Acids Res. 2004 32: 3033-3039; doi:10.1093/nar/gkh632 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Sjoerd Wanrooij, Petri Luoma, Gert van Goethem, Christine van Broeckhoven, Anu Suomalainen, and Johannes N. Spelbrink

Twinkle and POLG defects enhance age-dependent accumulation of mutations in the control region of mtDNA
Nucl. Acids Res. 2004 32: 3053-3064; doi:10.1093/nar/gkh634 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Ainslie Mitchell, Crispin R. Dass, Lun-Quan Sun, and Levon M. Khachigian

Inhibition of human breast carcinoma proliferation, migration, chemoinvasion and solid tumour growth by DNAzymes targeting the zinc finger transcription factor EGR-1
Nucl. Acids Res. 2004 32: 3065-3069; doi:10.1093/nar/gkh626 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jérôme Delaunay, Gwenn Le Mée, Nader Ezzeddine, Gilles Labesse, Christophe Terzian, Michèle Capri, and Ounissa Aït-Ahmed

The Drosophila Bruno paralogue Bru-3 specifically binds the EDEN translational repression element
Nucl. Acids Res. 2004 32: 3070-3082; doi:10.1093/nar/gkh627 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Antonio Randazzo, Veronica Esposito, Oliver Ohlenschläger, Ramadurai Ramachandran, and Luciano Mayol

NMR solution structure of a parallel LNA quadruplex
Nucl. Acids Res. 2004 32: 3083-3092; doi:10.1093/nar/gkh629 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

James E. Graham

Sequence-specific Rho–RNA interactions in transcription termination
Nucl. Acids Res. 2004 32: 3093-3100; doi:10.1093/nar/gkh630 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Fabien Darfeuille, Jens Bo Hansen, Henrik Orum, Carmelo Di Primo, and Jean-Jacques Toulmé

LNA/DNA chimeric oligomers mimic RNA aptamers targeted to the TAR RNA element of HIV-1
Nucl. Acids Res. 2004 32: 3101-3107; doi:10.1093/nar/gkh636 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Núria López-Bigas and Christos A. Ouzounis

Genome-wide identification of genes likely to be involved in human genetic disease
Nucl. Acids Res. 2004 32: 3108-3114; doi:10.1093/nar/gkh605 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Xingping Su and Lloyd M. Smith

Demonstration of a universal surface DNA computer
Nucl. Acids Res. 2004 32: 3115-3123; doi:10.1093/nar/gkh635 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Mark D. D’Ascenzo, Alan Collmer, and Gregory B. Martin

PeerGAD: a peer-review-based and community-centric web application for viewing and annotating prokaryotic genome sequences
Nucl. Acids Res. 2004 32: 3124-3135; doi:10.1093/nar/gkh615 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ana B. de la Hoz, Florencia Pratto, Rolf Misselwitz, Christian Speck, Wilhelm Weihofen, Karin Welfle, Wolfram Saenger, Heinz Welfle, and Juan C. Alonso

Recognition of DNA by protein from the broad-host range Streptococcus pyogenes plasmid pSM19035: analysis of binding to operator DNA with one to four heptad repeats
Nucl. Acids Res. 2004 32: 3136-3147; doi:10.1093/nar/gkh633 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Siddamadappa Chandrashekaran, U. H. Manjunatha, and Valakunja Nagaraja

KpnI restriction endonuclease and methyltransferase exhibit contrasting mode of sequence recognition
Nucl. Acids Res. 2004 32: 3148-3155; doi:10.1093/nar/gkh638 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

George H. Silva and Marlene Belfort

Analysis of the LAGLIDADG interface of the monomeric homing endonuclease I-DmoI
Nucl. Acids Res. 2004 32: 3156-3168; doi:10.1093/nar/gkh618 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Koshi Kinoshita, Yasuo Kikuchi, Yukie Sasakura, Masashi Suzuki, Yoshiaki Fujii-Kuriyama, and Kazuhiro Sogawa

Altered DNA binding specificity of Arnt by selection of partner bHLH–PAS proteins
Nucl. Acids Res. 2004 32: 3169-3179; doi:10.1093/nar/gkh637 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kiyohito Murai, Yoshihisa Naruse, Yosef Shaul, Yasutoshi Agata, and Nozomu Mori

Direct interaction of NRSF with TBP: chromatin reorganization and core promoter repression for neuron-specific gene transcription
Nucl. Acids Res. 2004 32: 3180-3189; doi:10.1093/nar/gkh550 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Syam P. Anand and Saleem A. Khan

Structure-specific DNA binding and bipolar helicase activities of PcrA
Nucl. Acids Res. 2004 32: 3190-3197; doi:10.1093/nar/gkh641 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yohei Tominaga, Yasuhiro Ushijima, Daisuke Tsuchimoto, Masaki Mishima, Masahiro Shirakawa, Seiki Hirano, Kunihiko Sakumi, and Yusaku Nakabeppu

MUTYH prevents OGG1 or APEX1 from inappropriately processing its substrate or reaction product with its C-terminal domain
Nucl. Acids Res. 2004 32: 3198-3211; doi:10.1093/nar/gkh642 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

S. Hani Najafi-Shoushtari, Günter Mayer, and Michael Famulok

Sensing complex regulatory networks by conformationally controlled hairpin ribozymes
Nucl. Acids Res. 2004 32: 3212-3219; doi:10.1093/nar/gkh643 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Dale M. Cameron, Jill Thompson, Steven T. Gregory, Paul E. March, and Albert E. Dahlberg

Thiostrepton-resistant mutants of Thermus thermophilus
Nucl. Acids Res. 2004 32: 3220-3227; doi:10.1093/nar/gkh644 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Bin Wu, Frederic Girard, Bernd van Buuren, Jürgen Schleucher, Marco Tessari, and Sybren Wijmenga

Global structure of a DNA three-way junction by solution NMR: towards prediction of 3H fold
Nucl. Acids Res. 2004 32: 3228-3239; doi:10.1093/nar/gkh645 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Lyudmila I. Rachek, Valentina I. Grishko, Mikhail F. Alexeyev, Viktoriya V. Pastukh, Susan P. LeDoux, and Glenn L. Wilson

Endonuclease III and endonuclease VIII conditionally targeted into mitochondria enhance mitochondrial DNA repair and cell survival following oxidative stress
Nucl. Acids Res. 2004 32: 3240-3247; doi:10.1093/nar/gkh648 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Sarah L. Donahue and Colin Campbell

A Rad50-dependent pathway of DNA repair is deficient in Fanconi anemia fibroblasts
Nucl. Acids Res. 2004 32: 3248-3257; doi:10.1093/nar/gkh649 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Giulio Pavesi, Giancarlo Mauri, Marco Stefani, and Graziano Pesole

RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences
Nucl. Acids Res. 2004 32: 3258-3269; doi:10.1093/nar/gkh650 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

NAR Methods Online:

Yipeng Wang, Steven Ringquist, Ann H. Cho, Gaelle Rondeau, and John Welsh

High-throughput polyribosome fractionation
Nucl. Acids Res. 2004 32: e79; doi:10.1093/nar/gnh077 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

P. Kumar, Jyoti Choithani, and K. C. Gupta

Construction of oligonucleotide arrays on a glass surface using a heterobifunctional reagent, N-(2-trifluoroethanesulfonatoethyl)-N-(methyl)-triethoxysilylpropyl-3-amine (NTMTA)
Nucl. Acids Res. 2004 32: e80; doi:10.1093/nar/gnh075 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Brian A. Williams, Richele M. Gwirtz, and Barbara J. Wold

Genomic DNA as a cohybridization standard for mammalian microarray measurements
Nucl. Acids Res. 2004 32: e81; doi:10.1093/nar/gnh078 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Julie K. A. Kasarjian, Masumi Hidaka, Takashi Horiuchi, Masatake Iida, and Junichi Ryu

The recognition and modification sites for the bacterial type I restriction systems KpnAI, StySEAI, StySENI and StySGI
Nucl. Acids Res. 2004 32: e82; doi:10.1093/nar/gnh079 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Brandon Ason and William S. Reznikoff

A high-throughput assay for Tn5 Tnp-induced DNA cleavage
Nucl. Acids Res. 2004 32: e83; doi:10.1093/nar/gnh080 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hae-Kap Cheong, Eunha Hwang, Chulhyun Lee, Byong-Seok Choi, and Chaejoon Cheong

Rapid preparation of RNA samples for NMR spectroscopy and X-ray crystallography
Nucl. Acids Res. 2004 32: e84; doi:10.1093/nar/gnh081 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Xavier Coumoul, Wenmei Li, Rui-Hong Wang, and Chuxia Deng

Inducible suppression of Fgfr2 and Survivin in ES cells using a combination of the RNA interference (RNAi) and the Cre–LoxP system
Nucl. Acids Res. 2004 32: e85; doi:10.1093/nar/gnh083 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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