Nucleic Acids Research

Computational Biology

Get checked abstract Folker Meyer, Ross Overbeek, and Alex Rodriguez

FIGfams: yet another set of protein families
Nucleic Acids Research Advance Access published on September 17, 2009
Nucl. Acids Res. 2009 37: 6643-6654; doi:10.1093/nar/gkp698 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Gene Regulation, Chromatin and Epigenetics

Get checked abstract Robert Lyzen, Maja Kochanowska, Grzegorz Wegrzyn, and Agnieszka Szalewska-Palasz

Transcription from bacteriophage pR promoter is regulated independently and antagonistically by DksA and ppGpp
Nucleic Acids Research Advance Access published on September 16, 2009
Nucl. Acids Res. 2009 37: 6655-6664; doi:10.1093/nar/gkp676 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Nóra Zsindely, Tibor Pankotai, Zsuzsanna Újfaludi, Dániel Lakatos, Orbán Komonyi, László Bodai, László Tora, and Imre M. Boros

The loss of histone H3 lysine 9 acetylation due to dSAGA-specific dAda2b mutation influences the expression of only a small subset of genes
Nucleic Acids Research Advance Access published on September 8, 2009
Nucl. Acids Res. 2009 37: 6665-6680; doi:10.1093/nar/gkp722 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Mario Dandrea, Massimo Donadelli, Chiara Costanzo, Aldo Scarpa, and Marta Palmieri

MeCP2/H3meK9 are involved in IL-6 gene silencing in pancreatic adenocarcinoma cell lines
Nucleic Acids Research Advance Access published on September 10, 2009
Nucl. Acids Res. 2009 37: 6681-6690; doi:10.1093/nar/gkp723 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Mariana Saint Just Ribeiro, Magnus L. Hansson, Mikael J. Lindberg, Anita E. Popko-Scibor, and Annika E. Wallberg

GSK3β is a negative regulator of the transcriptional coactivator MAML1
Nucleic Acids Research Advance Access published on September 8, 2009
Nucl. Acids Res. 2009 37: 6691-6700; doi:10.1093/nar/gkp724 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Adriana P. Rebelo, Sion L. Williams, and Carlos T. Moraes

In vivo methylation of mtDNA reveals the dynamics of protein–mtDNA interactions
Nucleic Acids Research Advance Access published on September 9, 2009
Nucl. Acids Res. 2009 37: 6701-6715; doi:10.1093/nar/gkp727 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Himesh Fernando, Sven Sewitz, Jeremy Darot, Simon Tavaré, Julian Leon Huppert, and Shankar Balasubramanian

Genome-wide analysis of a G-quadruplex-specific single-chain antibody that regulates gene expression
Nucleic Acids Research Advance Access published on September 10, 2009
Nucl. Acids Res. 2009 37: 6716-6722; doi:10.1093/nar/gkp740 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Supplementary Data]  

Get checked abstract Simon Haenni, Helen E. Sharpe, Maria Gravato Nobre, Kerstin Zechner, Cathy Browne, Jonathan Hodgkin, and André Furger

Regulation of transcription termination in the nematode Caenorhabditis elegans
Nucleic Acids Research Advance Access published on September 9, 2009
Nucl. Acids Res. 2009 37: 6723-6736; doi:10.1093/nar/gkp744 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genome Integrity, Repair and Replication

Get checked abstract Shay Covo, Jean-Pierre de Villartay, Penny A. Jeggo, and Zvi Livneh

Translesion DNA synthesis-assisted non-homologous end-joining of complex double-strand breaks prevents loss of DNA sequences in mammalian cells
Nucleic Acids Research Advance Access published on September 17, 2009
Nucl. Acids Res. 2009 37: 6737-6745; doi:10.1093/nar/gkp703 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Shuyi Li, Wendy W. Kuhne, Anita Kulharya, Farlyn Z. Hudson, Kyungsoo Ha, Zhen Cao, and William S. Dynan

Involvement of p54(nrb), a PSF partner protein, in DNA double-strand break repair and radioresistance
Nucleic Acids Research Advance Access published on September 16, 2009
Nucl. Acids Res. 2009 37: 6746-6753; doi:10.1093/nar/gkp741 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Sierra Colavito, Margaret Macris-Kiss, Changhyun Seong, Olive Gleeson, Eric C. Greene, Hannah L. Klein, Lumir Krejci, and Patrick Sung

Functional significance of the Rad51-Srs2 complex in Rad51 presynaptic filament disruption
Nucleic Acids Research Advance Access published on September 10, 2009
Nucl. Acids Res. 2009 37: 6754-6764; doi:10.1093/nar/gkp748 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Tuck Seng Wong, Sridharan Rajagopalan, Stefan M. Freund, Trevor J. Rutherford, Antonina Andreeva, Fiona M. Townsley, Miriana Petrovich, and Alan R. Fersht

Biophysical characterizations of human mitochondrial transcription factor A and its binding to tumor suppressor p53
Nucleic Acids Research Advance Access published on September 15, 2009
Nucl. Acids Res. 2009 37: 6765-6783; doi:10.1093/nar/gkp750 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genomics

Get checked abstract Zhuo Du, Yiqiang Zhao, and Ning Li

Genome-wide colonization of gene regulatory elements by G4 DNA motifs
Nucleic Acids Research Advance Access published on September 16, 2009
Nucl. Acids Res. 2009 37: 6784-6798; doi:10.1093/nar/gkp710 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Yang Huang, Eugene V. Koonin, David J. Lipman, and Teresa M. Przytycka

Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage
Nucleic Acids Research Advance Access published on September 10, 2009
Nucl. Acids Res. 2009 37: 6799-6810; doi:10.1093/nar/gkp712 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Supplementary Data]  

Molecular Biology

Get checked abstract Kangkan Halder, Markus Wieland, and Jörg S. Hartig

Predictable suppression of gene expression by 5'-UTR-based RNA quadruplexes
Nucleic Acids Research Advance Access published on September 9, 2009
Nucl. Acids Res. 2009 37: 6811-6817; doi:10.1093/nar/gkp696 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jenny L. Barton, David H. J. Bunka, Stuart E. Knowling, Pascal Lefevre, Alan J. Warren, Constanze Bonifer, and Peter G. Stockley

Characterization of RNA aptamers that disrupt the RUNX1–CBFβ/DNA complex
Nucleic Acids Research Advance Access published on September 9, 2009
Nucl. Acids Res. 2009 37: 6818-6830; doi:10.1093/nar/gkp728 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Martin Sanchez, Markus Drechsler, Holger Stark, and Georg Lipps

DNA translocation activity of the multifunctional replication protein ORF904 from the archaeal plasmid pRN1
Nucleic Acids Research Advance Access published on September 17, 2009
Nucl. Acids Res. 2009 37: 6831-6848; doi:10.1093/nar/gkp742 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes

Get checked abstract Paola Fiorani, Cinzia Tesauro, Giordano Mancini, Giovanni Chillemi, Ilda D'A;nnessa, Grazia Graziani, Lucio Tentori, Alessia Muzi, and Alessandro Desideri

Evidence of the crucial role of the linker domain on the catalytic activity of human topoisomerase I by experimental and simulative characterization of the Lys681Ala mutant
Nucleic Acids Research Advance Access published on September 18, 2009
Nucl. Acids Res. 2009 37: 6849-6858; doi:10.1093/nar/gkp669 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Robert K. Neely, Gintautas Tamulaitis, Kai Chen, Marta Kubala, Virginijus Siksnys, and Anita C. Jones

Time-resolved fluorescence studies of nucleotide flipping by restriction enzymes
Nucleic Acids Research Advance Access published on September 8, 2009
Nucl. Acids Res. 2009 37: 6859-6870; doi:10.1093/nar/gkp688 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jordan Jarjour, Hoku West-Foyle, Michael T. Certo, Christopher G. Hubert, Lindsey Doyle, Melissa M. Getz, Barry L. Stoddard, and Andrew M. Scharenberg

High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display
Nucleic Acids Research Advance Access published on September 8, 2009
Nucl. Acids Res. 2009 37: 6871-6880; doi:10.1093/nar/gkp726 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA

Get checked abstract Marie Messmer, Joern Pütz, Takeo Suzuki, Tsutomu Suzuki, Claude Sauter, Marie Sissler, and Florentz Catherine

Tertiary network in mammalian mitochondrial tRNA^Asp revealed by solution probing and phylogeny
Nucleic Acids Research Advance Access published on September 18, 2009
Nucl. Acids Res. 2009 37: 6881-6895; doi:10.1093/nar/gkp697 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Anna L. Ludwig, Christopher Raske, Flora Tassone, Dolores Garcia-Arocena, John W. Hershey, and Paul J. Hagerman

Translation of the FMR1 mRNA is not influenced by AGG interruptions
Nucleic Acids Research Advance Access published on September 14, 2009
Nucl. Acids Res. 2009 37: 6896-6904; doi:10.1093/nar/gkp713 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Michal Barak, Erez Y. Levanon, Eli Eisenberg, Nurit Paz, Gideon Rechavi, George M. Church, and Ramit Mehr

Evidence for large diversity in the human transcriptome created by Alu RNA editing
Nucleic Acids Research Advance Access published on September 8, 2009
Nucl. Acids Res. 2009 37: 6905-6915; doi:10.1093/nar/gkp729 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Mats Ensterö, Chammiran Daniel, Helene Wahlstedt, François Major, and Marie Öhman

Recognition and coupling of A-to-I edited sites are determined by the tertiary structure of the RNA
Nucleic Acids Research Advance Access published on September 8, 2009
Nucl. Acids Res. 2009 37: 6916-6926; doi:10.1093/nar/gkp731 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Timothy A. Vickers, Walt F. Lima, Hongjiang Wu, Josh G. Nichols, Peter S. Linsley, and Stanley T. Crooke

Off-target and a portion of target-specific siRNA mediated mRNA degradation is Ago2 ‘Slicer’ independent and can be mediated by Ago1
Nucleic Acids Research Advance Access published on September 18, 2009
Nucl. Acids Res. 2009 37: 6927-6941; doi:10.1093/nar/gkp735 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Keng-Ming Chang and Tamara L. Hendrickson

Recognition of tRNA^Gln by Helicobacter pylori GluRS2—a tRNA^Gln-specific glutamyl-tRNA synthetase
Nucleic Acids Research Advance Access published on September 15, 2009
Nucl. Acids Res. 2009 37: 6942-6949; doi:10.1093/nar/gkp754 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Ning Xu, Sofia Gkountela, Khalid Saeed, and Göran Akusjärvi

The 5'-end heterogeneity of adenovirus virus-associated RNAI contributes to the asymmetric guide strand incorporation into the RNA-induced silencing complex
Nucleic Acids Research Advance Access published on September 15, 2009
Nucl. Acids Res. 2009 37: 6950-6959; doi:10.1093/nar/gkp764 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology

Get checked abstract Nguyen To Uyen, Suk-Youl Park, Ji-Woo Choi, Hyun-Ju Lee, Kosuke Nishi, and Jeong-Sun Kim

The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and translocation activity
Nucleic Acids Research Advance Access published on July 22, 2009
Nucl. Acids Res. 2009 37: 6960-6969; doi:10.1093/nar/gkp603 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Lisheng Ni, Slade O. Jensen, Nam Ky Tonthat, Tracey Berg, Stephen M. Kwong, Fiona H. X. Guan, Melissa H. Brown, Ronald A. Skurray, Neville Firth, and Maria A. Schumacher

The Staphylococcus aureus pSK41 plasmid-encoded ArtA protein is a master regulator of plasmid transmission genes and contains a RHH motif used in alternate DNA-binding modes
Nucleic Acids Research Advance Access published on September 16, 2009
Nucl. Acids Res. 2009 37: 6970-6983; doi:10.1093/nar/gkp756 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Synthetic Biology and Chemistry

Get checked abstract Daniel G. Gibson

Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides
Nucleic Acids Research Advance Access published on September 10, 2009
Nucl. Acids Res. 2009 37: 6984-6990; doi:10.1093/nar/gkp687 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Methods Online

Get checked abstract Arjang Hassibi, Haris Vikalo, José Luis Riechmann, and Babak Hassibi

Real-time DNA microarray analysis
Nucleic Acids Research Advance Access published on August 31, 2009
Nucl. Acids Res. 2009 37: e132; doi:10.1093/nar/gkp675 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Nelly Said, Renate Rieder, Robert Hurwitz, Jochen Deckert, Henning Urlaub, and Jörg Vogel

In vivo expression and purification of aptamer-tagged small RNA regulators
Nucleic Acids Research Advance Access published on September 2, 2009
Nucl. Acids Res. 2009 37: e133; doi:10.1093/nar/gkp719 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Stéphanie Fallot, Raouia Ben Naya, Corinne Hieblot, Philippe Mondon, Eric Lacazette, Khalil Bouayadi, Abdelhakim Kharrat, Christian Touriol, and Hervé Prats

Alternative-splicing-based bicistronic vectors for ratio-controlled protein expression and application to recombinant antibody production
Nucleic Acids Research Advance Access published on September 3, 2009
Nucl. Acids Res. 2009 37: e134; doi:10.1093/nar/gkp716 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Satoshi Yamasaki, Tohru Terada, Kentaro Shimizu, Hidetoshi Kono, and Akinori Sarai

A generalized conformational energy function of DNA derived from molecular dynamics simulations
Nucleic Acids Research Advance Access published on September 3, 2009
Nucl. Acids Res. 2009 37: e135; doi:10.1093/nar/gkp718 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Kipom Kim and Omar A. Saleh

A high-resolution magnetic tweezer for single-molecule measurements
Nucleic Acids Research Advance Access published on September 3, 2009
Nucl. Acids Res. 2009 37: e136; doi:10.1093/nar/gkp725 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Lu Ping Tan, Erwin Seinen, Gerben Duns, Debora de Jong, Ody C. M. Sibon, Sibrand Poppema, Bart-Jan Kroesen, Klaas Kok, and Anke van den Berg

A high throughput experimental approach to identify miRNA targets in human cells
Nucleic Acids Research Advance Access published on September 4, 2009
Nucl. Acids Res. 2009 37: e137; doi:10.1093/nar/gkp715 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Front-Matter/Back-Matter

Nucleic Acids Research: VOLUME 37 ISSUE 20 2009
Nucl. Acids Res. 2009 37: i; doi:10.1093/nar/gkp1111 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acids Research
Nucl. Acids Res. 2009 37: ii; doi:10.1093/nar/gkp1110 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Subscriptions
Nucl. Acids Res. 2009 37: iii; doi:10.1093/nar/gkp1112 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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