Nucleic Acids Research

Chemistry

Get checked abstract Chang Geng Peng and Masad J. Damha

G-quadruplex induced stabilization by 2'-deoxy-2'-fluoro-D-arabinonucleic acids (2'F-ANA)
Nucleic Acids Research Advance Access published on July 17, 2007
Nucl. Acids Res. 2007 35: 4977-4988; doi:10.1093/nar/gkm520 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Margaret Gaskell, Balvinder Kaur, Peter B. Farmer, and Rajinder Singh

Detection of phosphodiester adducts formed by the reaction of benzo[a]pyrene diol epoxide with 2'-deoxynucleotides using collision-induced dissociation electrospray ionization tandem mass spectrometry
Nucleic Acids Research Advance Access published on July 18, 2007
Nucl. Acids Res. 2007 35: 5014-5027; doi:10.1093/nar/gkm526 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Computational Biology

Get checked abstract Göran O. Sperber, Tove Airola, Patric Jern, and Jonas Blomberg

Automated recognition of retroviral sequences in genomic data—RetroTector^©
Nucleic Acids Research Advance Access published on July 17, 2007
Nucl. Acids Res. 2007 35: 4964-4976; doi:10.1093/nar/gkm515 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Ralf Mrowka, Andreas Steege, Charlotte Kaps, Hanspeter Herzel, Bernd J. Thiele, Pontus B. Persson, and Nils Blüthgen

Dissecting the action of an evolutionary conserved non-coding region on renin promoter activity
Nucleic Acids Research Advance Access published on July 26, 2007
Nucl. Acids Res. 2007 35: 5120-5129; doi:10.1093/nar/gkm535 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Genomics

Get checked abstract Yan Zhang and Vadim N. Gladyshev

High content of proteins containing 21st and 22nd amino acids, selenocysteine and pyrrolysine, in a symbiotic deltaproteobacterium of gutless worm Olavius algarvensis
Nucleic Acids Research Advance Access published on July 11, 2007
Nucl. Acids Res. 2007 35: 4952-4963; doi:10.1093/nar/gkm514 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract P. Roback, J. Beard, D. Baumann, C. Gille, K. Henry, S. Krohn, H. Wiste, M.I. Voskuil, C. Rainville, and R. Rutherford

A predicted operon map for Mycobacterium tuberculosis
Nucleic Acids Research Advance Access published on July 25, 2007
Nucl. Acids Res. 2007 35: 5085-5095; doi:10.1093/nar/gkm518 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology

Get checked abstract Hideaki Ogiwara, Takashi Ohuchi, Ayako Ui, Shusuke Tada, Takemi Enomoto, and Masayuki Seki

Ctf18 is required for homologous recombination-mediated double-strand break repair
Nucleic Acids Research Advance Access published on July 18, 2007
Nucl. Acids Res. 2007 35: 4989-5000; doi:10.1093/nar/gkm523 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jennifer R. Schultz-Norton, Vivian A. Gabisi, Yvonne S. Ziegler, Ian X. McLeod, John R. Yates, and Ann M. Nardulli

Interaction of estrogen receptor with proliferating cell nuclear antigen
Nucleic Acids Research Advance Access published on July 18, 2007
Nucl. Acids Res. 2007 35: 5028-5038; doi:10.1093/nar/gkm533 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jay D. Kissel, Daniel M. Held, Richard W. Hardy, and Donald H. Burke

Active site binding and sequence requirements for inhibition of HIV-1 reverse transcriptase by the RT1 family of single-stranded DNA aptamers
Nucleic Acids Research Advance Access published on July 21, 2007
Nucl. Acids Res. 2007 35: 5039-5050; doi:10.1093/nar/gkm420 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Cecilia Y. Chan, Markus Kiechle, Palaniyandi Manivasakam, and Robert H. Schiestl

Ionizing radiation and restriction enzymes induce microhomology-mediated illegitimate recombination in Saccharomyces cerevisiae
Nucleic Acids Research Advance Access published on July 25, 2007
Nucl. Acids Res. 2007 35: 5051-5059; doi:10.1093/nar/gkm442 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Rebecca P. Wu, Derek S. Youngblood, Jed N. Hassinger, Candace E. Lovejoy, Michelle H. Nelson, Patrick L. Iversen, and Hong M. Moulton

Cell-penetrating peptides as transporters for morpholino oligomers: effects of amino acid composition on intracellular delivery and cytotoxicity
Nucleic Acids Research Advance Access published on August 1, 2007
Nucl. Acids Res. 2007 35: 5182-5191; doi:10.1093/nar/gkm478 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Anat Haviv-Chesner, Yoshifumi Kobayashi, Abram Gabriel, and Martin Kupiec

Capture of linear fragments at a double-strand break in yeast
Nucleic Acids Research Advance Access published on August 1, 2007
Nucl. Acids Res. 2007 35: 5192-5202; doi:10.1093/nar/gkm521 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Cecilie T. Freddie, Zongling Ji, Anett Marais, and Andrew D. Sharrocks

Functional interactions between the Forkhead transcription factor FOXK1 and the MADS-box protein SRF
Nucleic Acids Research Advance Access published on August 1, 2007
Nucl. Acids Res. 2007 35: 5203-5212; doi:10.1093/nar/gkm528 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Neal F. Lue and Zhaohui Li

Modeling and structure function analysis of the putative anchor site of yeast telomerase
Nucleic Acids Research Advance Access published on August 1, 2007
Nucl. Acids Res. 2007 35: 5213-5222; doi:10.1093/nar/gkm531 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jianzhong Hu, Stuart C. Sealfon, Fernand Hayot, Ciriyam Jayaprakash, Madhu Kumar, Audrey C. Pendleton, Arnaud Ganee, Ana Fernandez-Sesma, Thomas M. Moran, and James G. Wetmur

Chromosome-specific and noisy IFNB1 transcription in individual virus-infected human primary dendritic cells
Nucleic Acids Research Advance Access published on August 2, 2007
Nucl. Acids Res. 2007 35: 5232-5241; doi:10.1093/nar/gkm557 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Nucleic Acid Enzymes

Get checked abstract Syed Z. Imam, Fred E. Indig, Wen-Hsing Cheng, Satya P. Saxena, Tinna Stevnsner, Donald Kufe, and Vilhelm A. Bohr

Cockayne syndrome protein B interacts with and is phosphorylated by c-Abl tyrosine kinase
Nucleic Acids Research Advance Access published on July 11, 2007
Nucl. Acids Res. 2007 35: 4941-4951; doi:10.1093/nar/gkm386 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Michal Stros, Alena Bacíková, Eva Polanská, Jitka Stokrová, and François Strauss

HMGB1 interacts with human topoisomerase II and stimulates its catalytic activity
Nucleic Acids Research Advance Access published on July 18, 2007
Nucl. Acids Res. 2007 35: 5001-5013; doi:10.1093/nar/gkm525 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract O. Adelfinskaya, M. Terrazas, M. Froeyen, P. Marlière, K. Nauwelaerts, and P. Herdewijn

Polymerase-catalyzed synthesis of DNA from phosphoramidate conjugates of deoxynucleotides and amino acids
Nucleic Acids Research Advance Access published on July 25, 2007
Nucl. Acids Res. 2007 35: 5060-5072; doi:10.1093/nar/gkm498 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Miguel de Vega and Margarita Salas

A highly conserved Tyrosine residue of family B DNA polymerases contributes to dictate translesion synthesis past 8-oxo-7,8-dihydro-2'-deoxyguanosine
Nucleic Acids Research Advance Access published on July 25, 2007
Nucl. Acids Res. 2007 35: 5096-5107; doi:10.1093/nar/gkm545 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Emmanuele Crespan, Ulrich Hübscher, and Giovanni Maga

Error-free bypass of 2-hydroxyadenine by human DNA polymerase with Proliferating Cell Nuclear Antigen and Replication Protein A in different sequence contexts
Nucleic Acids Research Advance Access published on July 30, 2007
Nucl. Acids Res. 2007 35: 5173-5181; doi:10.1093/nar/gkm568 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Kate L. Fox, Stefanie J. Dowideit, Alice L. Erwin, Yogitha N. Srikhanta, Arnold L. Smith, and Michael P. Jennings

Haemophilus influenzae phasevarions have evolved from type III DNA restriction systems into epigenetic regulators of gene expression
Nucleic Acids Research Advance Access published on August 2, 2007
Nucl. Acids Res. 2007 35: 5242-5252; doi:10.1093/nar/gkm571 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Supplementary Data]  

RNA

Get checked abstract Ekaterini C. Kouvela, George V. Gerbanas, Maria A. Xaplanteri, Alexandros D. Petropoulos, George P. Dinos, and Dimitrios L. Kalpaxis

Changes in the conformation of 5S rRNA cause alterations in principal functions of the ribosomal nanomachine
Nucleic Acids Research Advance Access published on July 25, 2007
Nucl. Acids Res. 2007 35: 5108-5119; doi:10.1093/nar/gkm546 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Melanie Amort, Brigitte Wotzel, Kamilla Bakowska-Zywicka, Matthias D. Erlacher, Ronald Micura, and Norbert Polacek

An intact ribose moiety at A2602 of 23S rRNA is key to trigger peptidyl-tRNA hydrolysis during translation termination
Nucleic Acids Research Advance Access published on July 26, 2007
Nucl. Acids Res. 2007 35: 5130-5140; doi:10.1093/nar/gkm539 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract S. Henriet, L. Sinck, G. Bec, R. J. Gorelick, R. Marquet, and J.-C. Paillart

Vif is a RNA chaperone that could temporally regulate RNA dimerization and the early steps of HIV-1 reverse transcription
Nucleic Acids Research Advance Access published on July 26, 2007
Nucl. Acids Res. 2007 35: 5141-5153; doi:10.1093/nar/gkm542 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Daniela Castanotto, Kumi Sakurai, Robert Lingeman, Haitang Li, Louise Shively, Lars Aagaard, Harris Soifer, Anne Gatignol, Arthur Riggs, and John J. Rossi

Combinatorial delivery of small interfering RNAs reduces RNAi efficacy by selective incorporation into RISC
Nucleic Acids Research Advance Access published on July 26, 2007
Nucl. Acids Res. 2007 35: 5154-5164; doi:10.1093/nar/gkm543 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Marcel Ooms, Truus E. M. Abbink, Chi Pham, and Ben Berkhout

Circularization of the HIV-1 RNA genome
Nucleic Acids Research Advance Access published on August 7, 2007
Nucl. Acids Res. 2007 35: 5253-5261; doi:10.1093/nar/gkm564 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jonas Noeske, Harald Schwalbe, and Jens Wöhnert

Metal-ion binding and metal-ion induced folding of the adenine-sensing riboswitch aptamer domain
Nucleic Acids Research Advance Access published on August 7, 2007
Nucl. Acids Res. 2007 35: 5262-5273; doi:10.1093/nar/gkm565 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Structural Biology

Get checked abstract Jixun Dai, Megan Carver, Chandanamali Punchihewa, Roger A. Jones, and Danzhou Yang

Structure of the Hybrid-2 type intramolecular human telomeric G-quadruplex in K⁺ solution: insights into structure polymorphism of the human telomeric sequence
Nucleic Acids Research Advance Access published on July 10, 2007
Nucl. Acids Res. 2007 35: 4927-4940; doi:10.1093/nar/gkm522 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Kazuhiko Yamasaki, Toshihiko Akiba, Tomoko Yamasaki, and Kazuaki Harata

Structural basis for recognition of the matrix attachment region of DNA by transcription factor SATB1
Nucleic Acids Research Advance Access published on July 25, 2007
Nucl. Acids Res. 2007 35: 5073-5084; doi:10.1093/nar/gkm504 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Jiande Gu, Yaoming Xie, and Henry F. Schaefer, III

Electron attachment to DNA single strands: gas phase and aqueous solution
Nucleic Acids Research Advance Access published on July 27, 2007
Nucl. Acids Res. 2007 35: 5165-5172; doi:10.1093/nar/gkm135 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Yannis Burnier, Cedric Weber, Alessandro Flammini, and Andrzej Stasiak

Local selection rules that can determine specific pathways of DNA unknotting by type II DNA topoisomerases
Nucleic Acids Research Advance Access published on August 1, 2007
Nucl. Acids Res. 2007 35: 5223-5231; doi:10.1093/nar/gkm532 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online

Get checked abstract Olivier Loudig, Ekaterina Milova, Margaret Brandwein-Gensler, Aldo Massimi, Thomas J. Belbin, Geoffrey Childs, Robert H. Singer, Thomas Rohan, and Michael B. Prystowsky

Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)
Nucleic Acids Research Advance Access published on July 17, 2007
Nucl. Acids Res. 2007 35: e94; doi:10.1093/nar/gkm510 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Eva Kühn-Hölsken, Olexandr Dybkov, Björn Sander, Reinhard Lührmann, and Henning Urlaub

Improved identification of enriched peptide–RNA cross-links from ribonucleoprotein particles (RNPs) by mass spectrometry
Nucleic Acids Research Advance Access published on July 25, 2007
Nucl. Acids Res. 2007 35: e95; doi:10.1093/nar/gkm540 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jie Liu, Shuli Kang, Chuanning Tang, Lynda B.M. Ellis, and Tongbin Li

Meta-prediction of protein subcellular localization with reduced voting
Nucleic Acids Research Advance Access published on August 1, 2007
Nucl. Acids Res. 2007 35: e96; doi:10.1093/nar/gkm562 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Matthias Meyer, Udo Stenzel, Sean Myles, Kay Prüfer, and Michael Hofreiter

Targeted high-throughput sequencing of tagged nucleic acid samples
Nucleic Acids Research Advance Access published on August 1, 2007
Nucl. Acids Res. 2007 35: e97; doi:10.1093/nar/gkm566 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Michele M.P. Lufino, Roberto Manservigi, and Richard Wade-Martins

An S/MAR-based infectious episomal genomic DNA expression vector provides long-term regulated functional complementation of LDLR deficiency
Nucleic Acids Research Advance Access published on August 2, 2007
Nucl. Acids Res. 2007 35: e98; doi:10.1093/nar/gkm570 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Thomas E. Royce, Joel S. Rozowsky, and Mark B. Gerstein

Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification
Nucleic Acids Research Advance Access published on August 7, 2007
Nucl. Acids Res. 2007 35: e99; doi:10.1093/nar/gkm549 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Kenji Fukui, Yoshio Takahata, Noriko Nakagawa, Seiki Kuramitsu, and Ryoji Masui

Analysis of a nuclease activity of catalytic domain of Thermus thermophilus MutS2 by high-accuracy mass spectrometry
Nucleic Acids Research Advance Access published on August 7, 2007
Nucl. Acids Res. 2007 35: e100; doi:10.1093/nar/gkm575 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Corrigendum

Na Lin, Jun Yan, Zhen Huang, Craig Altier, Minyong Li, Nicholas Carraco, Mitsu Suyemoto, Lynette Johnston, Siming Wang, Qian Wang, Hao Fang, Julianne Caton-Williams, and Binghe Wang

Design and synthesis of boronic-acid-labeled thymidine triphosphate for incorporation into DNA
Nucl. Acids Res. 2007 35: 5274; doi:10.1093/nar/gkm399 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

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