Nucleic Acids Research

Survey and Summary:

Monica Riley, Takashi Abe, Martha B. Arnaud, Mary K.B. Berlyn, Frederick R. Blattner, Roy R. Chaudhuri, Jeremy D. Glasner, Takashi Horiuchi, Ingrid M. Keseler, Takehide Kosuge, Hirotada Mori, Nicole T. Perna, Guy Plunkett, III, Kenneth E. Rudd, Margrethe H. Serres, Gavin H. Thomas, Nicholas R. Thomson, David Wishart, and Barry L. Wanner

Escherichia coli K-12: a cooperatively developed annotation snapshot—2005
Nucl. Acids Res. 2006 34: 1-9; doi:10.1093/nar/gkj405 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Articles:

Heike Uhlmann-Schiffler, Carolin Jalal, and Hans Stahl

Ddx42p—a human DEAD box protein with RNA chaperone activities
Nucl. Acids Res. 2006 34: 10-22; doi:10.1093/nar/gkj403 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Martin Akerman and Yael Mandel-Gutfreund

Alternative splicing regulation at tandem 3' splice sites
Nucl. Acids Res. 2006 34: 23-31; doi:10.1093/nar/gkj408 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Nicolas Lévy, Adeline Martz, Anne Bresson, Catherine Spenlehauer, Gilbert de Murcia, and Josiane Ménissier-de Murcia

XRCC1 is phosphorylated by DNA-dependent protein kinase in response to DNA damage
Nucl. Acids Res. 2006 34: 32-41; doi:10.1093/nar/gkj409 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Valérie Goldschmidt, Joël Didierjean, Bernard Ehresmann, Chantal Ehresmann, Catherine Isel, and Roland Marquet

Mg²⁺ dependency of HIV-1 reverse transcription, inhibition by nucleoside analogues and resistance
Nucl. Acids Res. 2006 34: 42-52; doi:10.1093/nar/gkj411 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

David Vallenet, Laurent Labarre, Zoé Rouy, Valérie Barbe, Stéphanie Bocs, Stéphane Cruveiller, Aurélie Lajus, Géraldine Pascal, Claude Scarpelli, and Claudine Médigue

MaGe: a microbial genome annotation system supported by synteny results
Nucl. Acids Res. 2006 34: 53-65; doi:10.1093/nar/gkj406 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Ivan Erill, Susana Campoy, Gerard Mazon, and Jordi Barbé

Dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain
Nucl. Acids Res. 2006 34: 66-77; doi:10.1093/nar/gkj412 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Klavs R. Hansen, Pablo Tejero Ibarra, and Geneviève Thon

Evolutionary-conserved telomere-linked helicase genes of fission yeast are repressed by silencing factors, RNAi components and the telomere-binding protein Taz1
Nucl. Acids Res. 2006 34: 78-88; doi:10.1093/nar/gkj415 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Hal P. Bogerd, Heather L. Wiegand, Brian P. Doehle, Kira K. Lueders, and Bryan R. Cullen

APOBEC3A and APOBEC3B are potent inhibitors of LTR-retrotransposon function in human cells
Nucl. Acids Res. 2006 34: 89-95; doi:10.1093/nar/gkj416 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Iris Cheung, Michael Schertzer, Ann Rose, and Peter M. Lansdorp

High incidence of rapid telomere loss in telomerase-deficient Caenorhabditis elegans
Nucl. Acids Res. 2006 34: 96-103; doi:10.1093/nar/gkj417 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Hana Faiger, Marina Ivanchenko, Ilana Cohen, and Tali E. Haran

TBP flanking sequences: asymmetry of binding, long-range effects and consensus sequences
Nucl. Acids Res. 2006 34: 104-119; doi:10.1093/nar/gkj414 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Gema López-Torrejón, María I. Martínez-Jiménez, and Silvia Ayora

Role of LrpC from Bacillus subtilis in DNA transactions during DNA repair and recombination
Nucl. Acids Res. 2006 34: 120-129; doi:10.1093/nar/gkj418 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jeffrey J. DeStefano and Jason V. Cristofaro

Selection of primer-template sequences that bind human immunodeficiency virus reverse transcriptase with high affinity
Nucl. Acids Res. 2006 34: 130-139; doi:10.1093/nar/gkj426 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Lauren Seiple, Pawel Jaruga, Miral Dizdaroglu, and James T. Stivers

Linking uracil base excision repair and 5-fluorouracil toxicity in yeast
Nucl. Acids Res. 2006 34: 140-151; doi:10.1093/nar/gkj430 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Mary K. Smalley and Scott K. Silverman

Fluorescence of covalently attached pyrene as a general RNA folding probe
Nucl. Acids Res. 2006 34: 152-166; doi:10.1093/nar/gkj420 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Bram van den Broek, Francesco Vanzi, Davide Normanno, Francesco S. Pavone, and Gijs J.L. Wuite

Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI
Nucl. Acids Res. 2006 34: 167-174; doi:10.1093/nar/gkj432 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ishtiaq Ahmad, Daniel C. Hoessli, Evelyne Walker-Nasir, Saleem M. Rafik, Abdul R. Shakoori, and Nasir-ud-Din

Oct-2 DNA binding transcription factor: functional consequences of phosphorylation and glycosylation
Nucl. Acids Res. 2006 34: 175-184; doi:10.1093/nar/gkj401 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Maureen A. Sartor, Aaron M. Zorn, Jennifer A. Schwanekamp, Danielle Halbleib, Saikumar Karyala, Michael L. Howell, Gary E. Dean, Mario Medvedovic, and Craig R. Tomlinson

A new method to remove hybridization bias for interspecies comparison of global gene expression profiles uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus
Nucl. Acids Res. 2006 34: 185-200; doi:10.1093/nar/gkj413 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Xiaoqiu Huang, Shiaw-Pyng Yang, Asif T. Chinwalla, LaDeana W. Hillier, Patrick Minx, Elaine R. Mardis, and Richard K. Wilson

Application of a superword array in genome assembly
Nucl. Acids Res. 2006 34: 201-205; doi:10.1093/nar/gkj419 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Joaquim Jaumot, Ramon Eritja, Romà Tauler, and Raimundo Gargallo

Resolution of a structural competition involving dimeric G-quadruplex and its C-rich complementary strand
Nucl. Acids Res. 2006 34: 206-216; doi:10.1093/nar/gkj421 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Ju-Ming Wang, Chiung-Yuan Ko, Lei-Chin Chen, Wen-Lin Wang, and Wen-Chang Chang

Functional role of NF-IL6ß and its sumoylation and acetylation modifications in promoter activation of cyclooxygenase 2 gene
Nucl. Acids Res. 2006 34: 217-231; doi:10.1093/nar/gkj422 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Bénédicte Trouiller, Didier G. Schaefer, Florence Charlot, and Fabien Nogué

MSH2 is essential for the preservation of genome integrity and prevents homeologous recombination in the moss Physcomitrella patens
Nucl. Acids Res. 2006 34: 232-242; doi:10.1093/nar/gkj423 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Luisa Costessi, Giulia Devescovi, Francisco E. Baralle, and Andrés F. Muro

Brain-specific promoter and polyadenylation sites of the ß-adducin pre-mRNA generate an unusually long 3'-UTR
Nucl. Acids Res. 2006 34: 243-253; doi:10.1093/nar/gkj425 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Sung-Hun Bae, Sang Hoon Yun, Dawei Sun, Heon M. Lim, and Byong-Seok Choi

Structural and dynamic basis of a supercoiling-responsive DNA element
Nucl. Acids Res. 2006 34: 254-261; doi:10.1093/nar/gkj428 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Livia Merendino, Karl Perron, Michèle Rahire, Isabelle Howald, Jean-David Rochaix, and Michel Goldschmidt-Clermont

A novel multifunctional factor involved in trans-splicing of chloroplast introns in Chlamydomonas
Nucl. Acids Res. 2006 34: 262-274; doi:10.1093/nar/gkj429 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Michael J. Law, Michael E. Linde, Eric J. Chambers, Chris Oubridge, Phinikoula S. Katsamba, Lennart Nilsson, Ian S. Haworth, and Ite A. Laird-Offringa

The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA
Nucl. Acids Res. 2006 34: 275-285; doi:10.1093/nar/gkj436 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Isabelle Ernens, Sarah J. Goodfellow, Fiona Innes, Niall S. Kenneth, Louise E. Derblay, Robert J. White, and Pamela H. Scott

Hypoxic stress suppresses RNA polymerase III recruitment and tRNA gene transcription in cardiomyocytes
Nucl. Acids Res. 2006 34: 286-294; doi:10.1093/nar/gkj402 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Meltem Muftuoglu, Sudha Sharma, Tina Thorslund, Tinna Stevnsner, Martin M. Soerensen, Robert M. Brosh, Jr, and Vilhelm A. Bohr

Cockayne syndrome group B protein has novel strand annealing and exchange activities
Nucl. Acids Res. 2006 34: 295-304; doi:10.1093/nar/gkj410 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Chad Haynes and Lilia M. Iakoucheva

Serine/arginine-rich splicing factors belong to a class of intrinsically disordered proteins
Nucl. Acids Res. 2006 34: 305-312; doi:10.1093/nar/gkj424 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tatsuhiko Shimizu, Koichiro Manabe, Shinya Yoshikawa, Yusuke Kawasaki, and Shigenori Iwai

Preferential formation of (5S,6R)-thymine glycol for oligodeoxyribonucleotide synthesis and analysis of drug binding to thymine glycol-containing DNA
Nucl. Acids Res. 2006 34: 313-321; doi:10.1093/nar/gkj443 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Derek W. Bartlett and Mark E. Davis

Insights into the kinetics of siRNA-mediated gene silencing from live-cell and live-animal bioluminescent imaging
Nucl. Acids Res. 2006 34: 322-333; doi:10.1093/nar/gkj439 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Christina Lorenz, Nicolas Piganeau, and Renée Schroeder

Stabilities of HIV-1 DIS type RNA loop–loop interactions in vitro and in vivo
Nucl. Acids Res. 2006 34: 334-342; doi:10.1093/nar/gkj435 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Fabien Kieken, Françoise Paquet, Fabienne Brulé, Jacques Paoletti, and Gérard Lancelot

A new NMR solution structure of the SL1 HIV-1_Lai loop–loop dimer
Nucl. Acids Res. 2006 34: 343-352; doi:10.1093/nar/gkj427 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tilman Heise, Gunhild Sommer, Kerstin Reumann, Imke Meyer, Hans Will, and Heiner Schaal

The hepatitis B virus PRE contains a splicing regulatory element
Nucl. Acids Res. 2006 34: 353-363; doi:10.1093/nar/gkj440 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tiziana Angrisano, Francesca Lembo, Raffaela Pero, Francesco Natale, Alfredo Fusco, Vittorio E. Avvedimento, Carmelo B. Bruni, and Lorenzo Chiariotti

TACC3 mediates the association of MBD2 with histone acetyltransferases and relieves transcriptional repression of methylated promoters
Nucl. Acids Res. 2006 34: 364-372; doi:10.1093/nar/gkj400 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ruben H. Hovhannisyan, Claude C. Warzecha, and Russ P. Carstens

Characterization of sequences and mechanisms through which ISE/ISS-3 regulates FGFR2 splicing
Nucl. Acids Res. 2006 34: 373-385; doi:10.1093/nar/gkj407 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Birgit Klinkert, Ingolf Elles, and Jörg Nickelsen

Translation of chloroplast psbD mRNA in Chlamydomonas is controlled by a secondary RNA structure blocking the AUG start codon
Nucl. Acids Res. 2006 34: 386-394; doi:10.1093/nar/gkj433 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Corrigendum:

Lei Zhang, Thomas Hurek, and Barbara Reinhold-Hurek

Position of the fluorescent label is a crucial factor determining signal intensity in microarray hybridizations
Nucl. Acids Res. 2006 34: 395; doi:10.1093/nar/gkj404 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Min Li, Yu-Cheng Lin, Chao-Chin Wu, and Hsiao-Sheng Liu

Enhancing the efficiency of a polymerase chain reaction using gold nanoparticles
Nucl. Acids Res. 2006 34: 396; doi:10.1093/nar/gkj457 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Pilar Servert, Javier Garcia-Castro, Vicente Díaz, Daniel Lucas, Manuel A. Gonzalez, Carlos Martínez-A, and Antonio Bernad

Inducible model for ß-six-mediated site-specific recombination in mammalian cells
Nucl. Acids Res. 2006 34: e1; doi:10.1093/nar/gnj001 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Joel D. Nelson, Oleg Denisenko, Pavel Sova, and Karol Bomsztyk

Fast chromatin immunoprecipitation assay
Nucl. Acids Res. 2006 34: e2; doi:10.1093/nar/gnj004 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Hong-Yu Ou, Ling-Ling Chen, James Lonnen, Roy R. Chaudhuri, Ali Bin Thani, Rebecca Smith, Natalie J. Garton, Jay Hinton, Mark Pallen, Michael R. Barer, and Kumar Rajakumar

A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria
Nucl. Acids Res. 2006 34: e3; doi:10.1093/nar/gnj005 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Heping Liu, Hong Wang, Zhiyang Shi, Hua Wang, Chaoyong Yang, Spering Silke, Weihong Tan, and Zuhong Lu

TaqMan probe array for quantitative detection of DNA targets
Nucl. Acids Res. 2006 34: e4; doi:10.1093/nar/gnj006 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Chana Palmer, Elisabeth M. Bik, Michael B. Eisen, Paul B. Eckburg, Theodore R. Sana, Paul K. Wolber, David A. Relman, and Patrick O. Brown

Rapid quantitative profiling of complex microbial populations
Nucl. Acids Res. 2006 34: e5; doi:10.1093/nar/gnj007 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Alexey V. Antonov, Igor V. Tetko, and Hans W. Mewes

A systematic approach to infer biological relevance and biases of gene network structures
Nucl. Acids Res. 2006 34: e6; doi:10.1093/nar/gnj002 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Norihito Muranaka, Takahiro Hohsaka, and Masahiko Sisido

Four-base codon mediated mRNA display to construct peptide libraries that contain multiple nonnatural amino acids
Nucl. Acids Res. 2006 34: e7; doi:10.1093/nar/gnj003 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

To see an article, click its [Full Text] or [PDF] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.