Nucleic Acids Research

Computational Biology

Get checked abstract Osamu Gotoh

A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence
Nucleic Acids Research Advance Access published on March 15, 2008
Nucl. Acids Res. 2008 36: 2630-2638; doi:10.1093/nar/gkn105 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Kannan Tharakaraman, Olivier Bodenreider, David Landsman, John L. Spouge, and Leonardo Mariño-Ramírez

The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site
Nucleic Acids Research Advance Access published on March 26, 2008
Nucl. Acids Res. 2008 36: 2777-2786; doi:10.1093/nar/gkn137 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genomics

Get checked abstract Marcus B. Noyes, Xiangdong Meng, Atsuya Wakabayashi, Saurabh Sinha, Michael H. Brodsky, and Scot A. Wolfe

A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system
Nucleic Acids Research Advance Access published on March 10, 2008
Nucl. Acids Res. 2008 36: 2547-2560; doi:10.1093/nar/gkn048 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Alan K. Todd and Stephen Neidle

The relationship of potential G-quadruplex sequences in cis-upstream regions of the human genome to SP1-binding elements
Nucleic Acids Research Advance Access published on March 19, 2008
Nucl. Acids Res. 2008 36: 2700-2704; doi:10.1093/nar/gkn078 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Yaroslav Ryabov and Michael Gribskov

Spontaneous symmetry breaking in genome evolution
Nucleic Acids Research Advance Access published on March 26, 2008
Nucl. Acids Res. 2008 36: 2756-2763; doi:10.1093/nar/gkn086 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology

Get checked abstract Tomas Linder, Nina N. Rasmussen, Camilla O. Samuelsen, Emmanouella Chatzidaki, Vera Baraznenok, Jenny Beve, Peter Henriksen, Claes M. Gustafsson, and Steen Holmberg

Two conserved modules of Schizosaccharomyces pombe Mediator regulate distinct cellular pathways
Nucleic Acids Research Advance Access published on February 29, 2008
Nucl. Acids Res. 2008 36: 2489-2504; doi:10.1093/nar/gkn070 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Davide Normanno, Francesco Vanzi, and Francesco Saverio Pavone

Single-molecule manipulation reveals supercoiling-dependent modulation of lac repressor-mediated DNA looping
Nucleic Acids Research Advance Access published on February 29, 2008
Nucl. Acids Res. 2008 36: 2505-2513; doi:10.1093/nar/gkn071 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Nataliya Schostak, Konstantin Pyatkov, Elena Zelentsova, Irina Arkhipova, Dmitrii Shagin, Irina Shagina, Elena Mudrik, Anatolii Blintsov, Ivan Clark, David J. Finnegan, and Michael Evgen’ev

Molecular dissection of Penelope transposable element regulatory machinery
Nucleic Acids Research Advance Access published on March 4, 2008
Nucl. Acids Res. 2008 36: 2522-2529; doi:10.1093/nar/gkm1166 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Leonie Schulte-Uentrop, Raafat A. El-Awady, Lena Schliecker, Henning Willers, and Jochen Dahm-Daphi

Distinct roles of XRCC4 and Ku80 in non-homologous end-joining of endonuclease- and ionizing radiation-induced DNA double-strand breaks
Nucleic Acids Research Advance Access published on March 10, 2008
Nucl. Acids Res. 2008 36: 2561-2569; doi:10.1093/nar/gkn094 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Hong-Mei Zhang, Li Li, Nektaria Papadopoulou, Glenn Hodgson, Emma Evans, Matthew Galbraith, Mark Dear, Stéphanie Vougier, Janice Saxton, and Peter E. Shaw

Mitogen-induced recruitment of ERK and MSK to SRE promoter complexes by ternary complex factor Elk-1
Nucleic Acids Research Advance Access published on March 11, 2008
Nucl. Acids Res. 2008 36: 2594-2607; doi:10.1093/nar/gkn099 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Lucy Glover, Richard McCulloch, and David Horn

Sequence homology and microhomology dominate chromosomal double-strand break repair in African trypanosomes
Nucleic Acids Research Advance Access published on March 11, 2008
Nucl. Acids Res. 2008 36: 2608-2618; doi:10.1093/nar/gkn104 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract K. H. Brettingham-Moore, O. R. Sprod, X. Chen, P. Oakford, M. F. Shannon, and A. F. Holloway

Determinants of a transcriptionally competent environment at the GM-CSF promoter
Nucleic Acids Research Advance Access published on March 15, 2008
Nucl. Acids Res. 2008 36: 2639-2653; doi:10.1093/nar/gkn117 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Shivanthi Samarasinghe, Mohamed Samir El-Robh, David C. Grainger, Wenke Zhang, Panos Soultanas, and Stephen J. W. Busby

Autoregulation of the Escherichia coli melR promoter: repression involves four molecules of MelR
Nucleic Acids Research Advance Access published on March 16, 2008
Nucl. Acids Res. 2008 36: 2667-2676; doi:10.1093/nar/gkn119 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Qiang Sun, Yan Zhang, Guang Yang, Xiaoping Chen, Yingai Zhang, Guojun Cao, Jian Wang, Yanxun Sun, Peng Zhang, Ming Fan, Ningsheng Shao, and Xiao Yang

Transforming growth factor-β-regulated miR-24 promotes skeletal muscle differentiation
Nucleic Acids Research Advance Access published on March 19, 2008
Nucl. Acids Res. 2008 36: 2690-2699; doi:10.1093/nar/gkn032 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Md Rowshon Alam, Vidula Dixit, Hyunmin Kang, Zi-Bo Li, Xiaoyuan Chen, JoAnn Trejo, Michael Fisher, and Rudy L. Juliano

Intracellular delivery of an anionic antisense oligonucleotide via receptor-mediated endocytosis
Nucleic Acids Research Advance Access published on March 26, 2008
Nucl. Acids Res. 2008 36: 2764-2776; doi:10.1093/nar/gkn115 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Qiang Wang, Li Zhang, Bert Lynn, and Brian C. Rymond

A BBP–Mud2p heterodimer mediates branchpoint recognition and influences splicing substrate abundance in budding yeast
Nucleic Acids Research Advance Access published on March 29, 2008
Nucl. Acids Res. 2008 36: 2787-2798; doi:10.1093/nar/gkn144 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Nucleic Acid Enzymes

Get checked abstract Iwona Mruk and Robert M. Blumenthal

Real-time kinetics of restriction–modification gene expression after entry into a new host cell
Nucleic Acids Research Advance Access published on March 11, 2008
Nucl. Acids Res. 2008 36: 2581-2593; doi:10.1093/nar/gkn097 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Brigitte Paap, David M. Wilson, III, and Betsy M. Sutherland

Human abasic endonuclease action on multilesion abasic clusters: implications for radiation-induced biological damage
Nucleic Acids Research Advance Access published on March 19, 2008
Nucl. Acids Res. 2008 36: 2717-2727; doi:10.1093/nar/gkn118 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

RNA

Get checked abstract Sébastien Muller, Fabrice Leclerc, Isabelle Behm-Ansmant, Jean-Baptiste Fourmann, Bruno Charpentier, and Christiane Branlant

Combined in silico and experimental identification of the Pyrococcus abyssi H/ACA sRNAs and their target sites in ribosomal RNAs
Nucleic Acids Research Advance Access published on February 27, 2008
Nucl. Acids Res. 2008 36: 2459-2475; doi:10.1093/nar/gkn077 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Gelina S. Kopeina, Zhanna A. Afonina, Kira V. Gromova, Vladimir A. Shirokov, Victor D. Vasiliev, and Alexander S. Spirin

Step-wise formation of eukaryotic double-row polyribosomes and circular translation of polysomal mRNA
Nucleic Acids Research Advance Access published on February 29, 2008
Nucl. Acids Res. 2008 36: 2476-2488; doi:10.1093/nar/gkm1177 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Songon An, George Barany, and Karin Musier-Forsyth

Evolution of acceptor stem tRNA recognition by class II prolyl-tRNA synthetase
Nucleic Acids Research Advance Access published on March 1, 2008
Nucl. Acids Res. 2008 36: 2514-2521; doi:10.1093/nar/gkn063 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Peter Simmonds, Ioannis Karakasiliotis, Dalan Bailey, Yasmin Chaudhry, David J. Evans, and Ian G. Goodfellow

Bioinformatic and functional analysis of RNA secondary structure elements among different genera of human and animal caliciviruses
Nucleic Acids Research Advance Access published on March 4, 2008
Nucl. Acids Res. 2008 36: 2530-2546; doi:10.1093/nar/gkn096 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Birte Reichenbach, Alexandre Maes, Falk Kalamorz, Eliane Hajnsdorf, and Boris Görke

The small RNA GlmY acts upstream of the sRNA GlmZ in the activation of glmS expression and is subject to regulation by polyadenylation in Escherichia coli
Nucleic Acids Research Advance Access published on March 11, 2008
Nucl. Acids Res. 2008 36: 2570-2580; doi:10.1093/nar/gkn091 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Pei-Yu Liao, Prateek Gupta, Alexey N. Petrov, Jonathan D. Dinman, and Kelvin H. Lee

A new kinetic model reveals the synergistic effect of E-, P- and A-sites on +1 ribosomal frameshifting
Nucleic Acids Research Advance Access published on March 15, 2008
Nucl. Acids Res. 2008 36: 2619-2629; doi:10.1093/nar/gkn100 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jiro Kondo and Eric Westhof

The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates
Nucleic Acids Research Advance Access published on March 16, 2008
Nucl. Acids Res. 2008 36: 2654-2666; doi:10.1093/nar/gkn112 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Christoph Jöchl, Mathieu Rederstorff, Jana Hertel, Peter F. Stadler, Ivo L. Hofacker, Markus Schrettl, Hubertus Haas, and Alexander Hüttenhofer

Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis
Nucleic Acids Research Advance Access published on March 16, 2008
Nucl. Acids Res. 2008 36: 2677-2689; doi:10.1093/nar/gkn123 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Ranjit Prasad Bahadur, Martin Zacharias, and Joël Janin

Dissecting protein–RNA recognition sites
Nucleic Acids Research Advance Access published on March 19, 2008
Nucl. Acids Res. 2008 36: 2705-2716; doi:10.1093/nar/gkn102 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Peng Yao, Bin Zhu, Sophie Jaeger, Gilbert Eriani, and En-Duo Wang

Recognition of tRNA^Leu by Aquifex aeolicus leucyl-tRNA synthetase during the aminoacylation and editing steps
Nucleic Acids Research Advance Access published on March 26, 2008
Nucl. Acids Res. 2008 36: 2728-2738; doi:10.1093/nar/gkn028 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology

Get checked abstract Sunggeon Ko, Sung-Hoon Jun, Hansol Bae, Jung-Sue Byun, Woong Han, Heeyoung Park, Seong Wook Yang, Sam-Yong Park, Young Ho Jeon, Chaejoon Cheong, Woo Taek Kim, Weontae Lee, and Hyun-Soo Cho

Structure of the DNA-binding domain of NgTRF1 reveals unique features of plant telomere-binding proteins
Nucleic Acids Research Advance Access published on March 26, 2008
Nucl. Acids Res. 2008 36: 2739-2755; doi:10.1093/nar/gkn030 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Kevin B. Turner, Robert G. Brinson, Hye Young Yi-Brunozzi, Jason W. Rausch, Jennifer T. Miller, Stuart F.J. Le Grice, John P. Marino, and Daniele Fabris

Structural probing of the HIV-1 polypurine tract RNA:DNA hybrid using classic nucleic acid ligands
Nucleic Acids Research Advance Access published on April 9, 2008
Nucl. Acids Res. 2008 36: 2799-2810; doi:10.1093/nar/gkn129 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online

Get checked abstract Olle Ericsson, Jonas Jarvius, Edith Schallmeiner, Mathias Howell, Rachel Yuan Nong, Hendrik Reuter, Meinhard Hahn, Johan Stenberg, Mats Nilsson, and Ulf Landegren

A dual-tag microarray platform for high-performance nucleic acid and protein analyses
Nucleic Acids Research Advance Access published on March 16, 2008
Nucl. Acids Res. 2008 36: e45; doi:10.1093/nar/gkn106 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Liesbeth van Oeffelen, Pierre Cornelis, Wouter Van Delm, Fedor De Ridder, Bart De Moor, and Yves Moreau

Detecting cis-regulatory binding sites for cooperatively binding proteins
Nucleic Acids Research Advance Access published on April 9, 2008
Nucl. Acids Res. 2008 36: e46; doi:10.1093/nar/gkn140 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Giulio Pavesi, Federico Zambelli, Corrado Caggese, and Graziano Pesole

Exalign: a new method for comparative analysis of exon–intron gene structures
Nucleic Acids Research Advance Access published on April 8, 2008
Nucl. Acids Res. 2008 36: e47; doi:10.1093/nar/gkn153 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

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