Nucleic Acids Research

Chemistry and Synthetic Biology

Get checked abstract Shawn M. Douglas, Adam H. Marblestone, Surat Teerapittayanon, Alejandro Vazquez, George M. Church, and William M. Shih

Rapid prototyping of 3D DNA-origami shapes with caDNAno
Nucleic Acids Research Advance Access published on June 16, 2009
Nucl. Acids Res. 2009 37: 5001-5006; doi:10.1093/nar/gkp436 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Computational Biology

Get checked abstract K. S. Shavkunov, I. S. Masulis, M. N. Tutukina, A. A. Deev, and O. N. Ozoline

Gains and unexpected lessons from genome-scale promoter mapping
Nucleic Acids Research Advance Access published on June 15, 2009
Nucl. Acids Res. 2009 37: 4919-4931; doi:10.1093/nar/gkp490 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Gene Regulation, Chromatin and Epigenetics

Get checked abstract Debashree Basu, Garima Khare, Shashi Singh, Anil Tyagi, Sanjeev Khosla, and Shekhar C. Mande

A novel nucleoid-associated protein of Mycobacterium tuberculosis is a sequence homolog of GroEL
Nucleic Acids Research Advance Access published on June 15, 2009
Nucl. Acids Res. 2009 37: 4944-4954; doi:10.1093/nar/gkp502 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Asmaa M. Baker, Qiang Fu, William Hayward, Stuart M. Lindsay, and Terace M. Fletcher

The Myb/SANT domain of the telomere-binding protein TRF2 alters chromatin structure
Nucleic Acids Research Advance Access published on June 16, 2009
Nucl. Acids Res. 2009 37: 5019-5031; doi:10.1093/nar/gkp515 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Annette N. D. Scharf, Teresa K. Barth, and Axel Imhof

Establishment of Histone Modifications after Chromatin Assembly
Nucleic Acids Research Advance Access published on June 18, 2009
Nucl. Acids Res. 2009 37: 5032-5040; doi:10.1093/nar/gkp518 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Federica Ferri, Haniaa Bouzinba-Segard, Guillaume Velasco, Florent Hubé, and Claire Francastel

Non-coding murine centromeric transcripts associate with and potentiate Aurora B kinase
Nucleic Acids Research Advance Access published on June 19, 2009
Nucl. Acids Res. 2009 37: 5071-5080; doi:10.1093/nar/gkp529 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Patricia C. Burrows, Nicolas Joly, B. Tracy Nixon, and Martin Buck

Comparative analysis of activator-E⁵⁴ complexes formed with nucleotide-metal fluoride analogues
Nucleic Acids Research Advance Access published on June 24, 2009
Nucl. Acids Res. 2009 37: 5138-5150; doi:10.1093/nar/gkp541 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Rui Zhou, Limin Han, Guodong Li, and Tanjun Tong

Senescence delay and repression of p16^INK4a by Lsh via recruitment of histone deacetylases in human diploid fibroblasts
Nucleic Acids Research Advance Access published on June 26, 2009
Nucl. Acids Res. 2009 37: 5183-5196; doi:10.1093/nar/gkp533 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genome Integrity, Repair and Replication

Get checked abstract Neta Agmon, Shiri Pur, Batia Liefshitz, and Martin Kupiec

Analysis of repair mechanism choice during homologous recombination
Nucleic Acids Research Advance Access published on June 23, 2009
Nucl. Acids Res. 2009 37: 5081-5092; doi:10.1093/nar/gkp495 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Songmin Ying, Katie Myers, Sarah Bottomley, Thomas Helleday, and Helen E. Bryant

BRCA2-dependent homologous recombination is required for repair of Arsenite-induced replication lesions in mammalian cells
Nucleic Acids Research Advance Access published on June 23, 2009
Nucl. Acids Res. 2009 37: 5105-5113; doi:10.1093/nar/gkp538 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Genomics

Get checked abstract Silvio Bicciato, Roberta Spinelli, Mattia Zampieri, Eleonora Mangano, Francesco Ferrari, Luca Beltrame, Ingrid Cifola, Clelia Peano, Aldo Solari, and Cristina Battaglia

A computational procedure to identify significant overlap of differentially expressed and genomic imbalanced regions in cancer datasets
Nucleic Acids Research Advance Access published on June 19, 2009
Nucl. Acids Res. 2009 37: 5057-5070; doi:10.1093/nar/gkp520 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology

Get checked abstract Virginia Castilla-Llorente, Wilfried J. J. Meijer, and Margarita Salas

Differential Spo0A-mediated effects on transcription and replication of the related Bacillus subtilis phages Nf and 29 explain their different behaviours in vivo
Nucleic Acids Research Advance Access published on June 15, 2009
Nucl. Acids Res. 2009 37: 4955-4964; doi:10.1093/nar/gkp504 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Supplementary Data]  

Get checked abstract A. Scoumanne, J. Zhang, and X. Chen

PRMT5 is required for cell-cycle progression and p53 tumor suppressor function
Nucleic Acids Research Advance Access published on June 15, 2009
Nucl. Acids Res. 2009 37: 4965-4976; doi:10.1093/nar/gkp516 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Kunio Kikuchi, Makiha Fukuda, Tomoya Ito, Mitsuko Inoue, Takahide Yokoi, Suenori Chiku, Toutai Mitsuyama, Kiyoshi Asai, Tetsuro Hirose, and Yasunori Aizawa

Transcripts of unknown function in multiple-signaling pathways involved in human stem cell differentiation
Nucleic Acids Research Advance Access published on June 16, 2009
Nucl. Acids Res. 2009 37: 4987-5000; doi:10.1093/nar/gkp426 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Yingpu Yu, Assen Marintchev, Victoria G. Kolupaeva, Anett Unbehaun, Tatyana Veryasova, Shao-Chiang Lai, Peng Hong, Gerhard Wagner, Christopher U. T. Hellen, and Tatyana V. Pestova

Position of eukaryotic translation initiation factor eIF1A on the 40S ribosomal subunit mapped by directed hydroxyl radical probing
Nucleic Acids Research Advance Access published on June 26, 2009
Nucl. Acids Res. 2009 37: 5167-5182; doi:10.1093/nar/gkp519 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes

Get checked abstract Ming Fang, Wencke-Maria Zeisberg, Ciaran Condon, Vasily Ogryzko, Antoine Danchin, and Undine Mechold

Degradation of nanoRNA is performed by multiple redundant RNases in Bacillus subtilis
Nucleic Acids Research Advance Access published on June 24, 2009
Nucl. Acids Res. 2009 37: 5114-5125; doi:10.1093/nar/gkp527 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Richard D. Morgan, Elizabeth A. Dwinell, Tanya K. Bhatia, Elizabeth M. Lang, and Yvette A. Luyten

The MmeI family: type II restriction–modification enzymes that employ single-strand modification for host protection
Nucleic Acids Research Advance Access published on July 3, 2009
Nucl. Acids Res. 2009 37: 5208-5221; doi:10.1093/nar/gkp534 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Richard D. Morgan and Yvette A. Luyten

Rational engineering of type II restriction endonuclease DNA binding and cleavage specificity
Nucleic Acids Research Advance Access published on June 30, 2009
Nucl. Acids Res. 2009 37: 5222-5233; doi:10.1093/nar/gkp535 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA

Get checked abstract Craig L. Zirbel, Judit E. Sponer, Jiri Sponer, Jesse Stombaugh, and Neocles B. Leontis

Classification and energetics of the base-phosphate interactions in RNA
Nucleic Acids Research Advance Access published on June 14, 2009
Nucl. Acids Res. 2009 37: 4898-4918; doi:10.1093/nar/gkp468 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Emiliano P. Ricci, Fabrice Mure, Henri Gruffat, Didier Decimo, Cahora Medina-Palazon, Théophile Ohlmann, and Evelyne Manet

Translation of intronless RNAs is strongly stimulated by the Epstein–Barr virus mRNA export factor EB2
Nucleic Acids Research Advance Access published on June 15, 2009
Nucl. Acids Res. 2009 37: 4932-4943; doi:10.1093/nar/gkp497 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Nitin Nitin, Won Jong Rhee, and Gang Bao

Translation inhibition reveals interaction of 2'-deoxy and 2'-O-methyl molecular beacons with mRNA targets in living cells
Nucleic Acids Research Advance Access published on June 15, 2009
Nucl. Acids Res. 2009 37: 4977-4986; doi:10.1093/nar/gkp517 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Simon Haenni, Erwin Studer, Gabriela Schumann Burkard, and Isabel Roditi

Bidirectional silencing of RNA polymerase I transcription by a strand switch region in Trypanosoma brucei
Nucleic Acids Research Advance Access published on June 16, 2009
Nucl. Acids Res. 2009 37: 5007-5018; doi:10.1093/nar/gkp513 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Christian D. Sadik, Malte Bachmann, Josef Pfeilschifter, and Heiko Mühl

Activation of interferon regulatory factor-3 via toll-like receptor 3 and immunomodulatory functions detected in A549 lung epithelial cells exposed to misplaced U1-snRNA
Nucleic Acids Research Advance Access published on June 18, 2009
Nucl. Acids Res. 2009 37: 5041-5056; doi:10.1093/nar/gkp525 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Felix Grewe, Prisca Viehoever, Bernd Weisshaar, and Volker Knoop

A trans-splicing group I intron and tRNA-hyperediting in the mitochondrial genome of the lycophyte Isoetes engelmannii
Nucleic Acids Research Advance Access published on June 23, 2009
Nucl. Acids Res. 2009 37: 5093-5104; doi:10.1093/nar/gkp532 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Regis Marty, Christophe N. N’soukpoé-Kossi, David M. Charbonneau, Laurent Kreplak, and Heidar-Ali Tajmir-Riahi

Structural characterization of cationic lipid–tRNA complexes
Nucleic Acids Research Advance Access published on June 26, 2009
Nucl. Acids Res. 2009 37: 5197-5207; doi:10.1093/nar/gkp543 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Structural Biology

Get checked abstract Stephen A. McMahon, Gareth A. Roberts, Kenneth A. Johnson, Laurie P. Cooper, Huanting Liu, John H. White, Lester G. Carter, Bansi Sanghvi, Muse Oke, Malcolm D. Walkinshaw, Garry W. Blakely, James H. Naismith, and David T. F. Dryden

Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance
Nucleic Acids Research Advance Access published on June 8, 2009
Nucl. Acids Res. 2009 37: 4887-4897; doi:10.1093/nar/gkp478 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract María Luisa Martínez-Robles, Guillaume Witz, Pablo Hernández, Jorge B. Schvartzman, Andrzej Stasiak, and Dora B. Krimer

Interplay of DNA supercoiling and catenation during the segregation of sister duplexes
Nucleic Acids Research Advance Access published on June 24, 2009
Nucl. Acids Res. 2009 37: 5126-5137; doi:10.1093/nar/gkp530 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Kengo Tsuda, Kanako Kuwasako, Mari Takahashi, Tatsuhiko Someya, Makoto Inoue, Takaho Terada, Naohiro Kobayashi, Mikako Shirouzu, Takanori Kigawa, Akiko Tanaka, Sumio Sugano, Peter Güntert, Yutaka Muto, and Shigeyuki Yokoyama

Structural basis for the sequence-specific RNA-recognition mechanism of human CUG-BP1 RRM3
Nucleic Acids Research Advance Access published on June 24, 2009
Nucl. Acids Res. 2009 37: 5151-5166; doi:10.1093/nar/gkp546 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Methods Online

Get checked abstract Guojun Li, Qin Ma, Haibao Tang, Andrew H. Paterson, and Ying Xu

QUBIC: a qualitative biclustering algorithm for analyses of gene expression data
Nucleic Acids Research Advance Access published on June 9, 2009
Nucl. Acids Res. 2009 37: e101; doi:10.1093/nar/gkp491 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Stanislaw K. Jozwiakowski and Bernard A. Connolly

Plasmid-based lacZ assay for DNA polymerase fidelity: application to archaeal family-B DNA polymerase
Nucleic Acids Research Advance Access published on June 10, 2009
Nucl. Acids Res. 2009 37: e102; doi:10.1093/nar/gkp494 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Nobutaka Nakashima and Tomohiro Tamura

Conditional gene silencing of multiple genes with antisense RNAs and generation of a mutator strain of Escherichia coli
Nucleic Acids Research Advance Access published on June 10, 2009
Nucl. Acids Res. 2009 37: e103; doi:10.1093/nar/gkp498 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Nicolas Philippe, Anthony Boureux, Laurent Bréhélin, Jorma Tarhio, Thérèse Commes, and Éric Rivals

Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity
Nucleic Acids Research Advance Access published on June 16, 2009
Nucl. Acids Res. 2009 37: e104; doi:10.1093/nar/gkp492 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jochen B. Geigl, Anna C. Obenauf, Julie Waldispuehl-Geigl, Eva M. Hoffmann, Martina Auer, Martina Hörmann, Maria Fischer, Zlatko Trajanoski, Michael A. Schenk, Lars O. Baumbusch, and Michael R. Speicher

Identification of small gains and losses in single cells after whole genome amplification on tiling oligo arrays
Nucleic Acids Research Advance Access published on June 18, 2009
Nucl. Acids Res. 2009 37: e105; doi:10.1093/nar/gkp526 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Retraction

Rubin Cheng, Cuicui Miao, Qianhong Gong, Yuchao Gu, Xinzhi Lu, Feng Han, and Wengong Yu

Specific gene silencing by artificial trans-encoded small noncoding RNAs in bacteria
Nucleic Acids Research Advance Access published on July 16, 2009
Nucl. Acids Res. 2009 37: 5234; doi:10.1093/nar/gkp607 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Corrigenda

Diane P. Genereux, Winslow C. Johnson, Alice F. Burden, Reinhard Stöger, and Charles D. Laird

Errors in the bisulfite conversion of DNA: modulating inappropriate- and failed-conversion frequencies
Nucleic Acids Research Advance Access published on August 4, 2009
Nucl. Acids Res. 2009 37: 5235; doi:10.1093/nar/gkp637 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Na Li, Yuxuan Wang, Arti Pothukuchy, Angel Syrett, Naeem Husain, Siddharth Gopalakrisha, Pradeepa Kosaraju, and Andrew D. Ellington

Aptamers that recognize drug-resistant HIV-1 reverse transcriptase
Nucl. Acids Res. 2009 37: 5236; doi:10.1093/nar/gkp663 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Front-Matter/Back-Matter

Nucleic Acids Research: VOLUME 37 ISSUE 15 2009
Nucl. Acids Res. 2009 37: i; doi:10.1093/nar/gkp738 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acids Research
Nucl. Acids Res. 2009 37: ii; doi:10.1093/nar/gkp737 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Subscriptions
Nucl. Acids Res. 2009 37: iii; doi:10.1093/nar/gkp739 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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