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Volume 35(15);  August 2007
Molecular Biology
Ctf18 is required for homologous recombination-mediated double-strand break repair
Hideaki Ogiwara, Takashi Ohuchi, Ayako Ui, Shusuke Tada, Takemi Enomoto, and Masayuki Seki
Nucleic Acids Res. 2007 August; 35(15): 4989–5000. Published online 2007 July 18. doi: 10.1093/nar/gkm523.
PMCID: PMC1976461
Interaction of estrogen receptor α with proliferating cell nuclear antigen
Jennifer R. Schultz-Norton, Vivian A. Gabisi, Yvonne S. Ziegler, Ian X. McLeod, John R. Yates, and Ann M. Nardulli
Nucleic Acids Res. 2007 August; 35(15): 5028–5038. Published online 2007 July 18. doi: 10.1093/nar/gkm533.
PMCID: PMC1976446
Active site binding and sequence requirements for inhibition of HIV-1 reverse transcriptase by the RT1 family of single-stranded DNA aptamers
Jay D. Kissel, Daniel M. Held, Richard W. Hardy, and Donald H. Burke
Nucleic Acids Res. 2007 August; 35(15): 5039–5050. Published online 2007 July 21. doi: 10.1093/nar/gkm420.
PMCID: PMC1976467
Ionizing radiation and restriction enzymes induce microhomology-mediated illegitimate recombination in Saccharomyces cerevisiae
Cecilia Y. Chan, Markus Kiechle, Palaniyandi Manivasakam, and Robert H. Schiestl
Nucleic Acids Res. 2007 August; 35(15): 5051–5059. Published online 2007 July 25. doi: 10.1093/nar/gkm442.
PMCID: PMC1976441
Cell-penetrating peptides as transporters for morpholino oligomers: effects of amino acid composition on intracellular delivery and cytotoxicity
Rebecca P. Wu, Derek S. Youngblood, Jed N. Hassinger, Candace E. Lovejoy, Michelle H. Nelson, Patrick L. Iversen, and Hong M. Moulton
Nucleic Acids Res. 2007 August; 35(15): 5182–5191. Published online 2007 August 1. doi: 10.1093/nar/gkm478.
PMCID: PMC1976451
Capture of linear fragments at a double-strand break in yeast
Anat Haviv-Chesner, Yoshifumi Kobayashi, Abram Gabriel, and Martin Kupiec
Nucleic Acids Res. 2007 August; 35(15): 5192–5202. Published online 2007 August 1. doi: 10.1093/nar/gkm521.
PMCID: PMC1976456
Functional interactions between the Forkhead transcription factor FOXK1 and the MADS-box protein SRF
Cecilie T. Freddie, Zongling Ji, Anett Marais, and Andrew D. Sharrocks
Nucleic Acids Res. 2007 August; 35(15): 5203–5212. Published online 2007 August 1. doi: 10.1093/nar/gkm528.
PMCID: PMC1976435
Modeling and structure function analysis of the putative anchor site of yeast telomerase
Neal F. Lue and Zhaohui Li
Nucleic Acids Res. 2007 August; 35(15): 5213–5222. Published online 2007 August 1. doi: 10.1093/nar/gkm531.
PMCID: PMC1976438
Chromosome-specific and noisy IFNB1 transcription in individual virus-infected human primary dendritic cells
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
Nucleic Acids Res. 2007 August; 35(15): 5232–5241. Published online 2007 August 2. doi: 10.1093/nar/gkm557.
PMCID: PMC1976463
RNA
Changes in the conformation of 5S rRNA cause alterations in principal functions of the ribosomal nanomachine
Ekaterini C. Kouvela, George V. Gerbanas, Maria A. Xaplanteri, Alexandros D. Petropoulos, George P. Dinos, and Dimitrios L. Kalpaxis
Nucleic Acids Res. 2007 August; 35(15): 5108–5119. Published online 2007 July 25. doi: 10.1093/nar/gkm546.
PMCID: PMC1976436
An intact ribose moiety at A2602 of 23S rRNA is key to trigger peptidyl-tRNA hydrolysis during translation termination
Melanie Amort, Brigitte Wotzel, Kamilla Bakowska-Zywicka, Matthias D. Erlacher, Ronald Micura, and Norbert Polacek
Nucleic Acids Res. 2007 August; 35(15): 5130–5140. Published online 2007 July 26. doi: 10.1093/nar/gkm539.
PMCID: PMC1976462
Vif is a RNA chaperone that could temporally regulate RNA dimerization and the early steps of HIV-1 reverse transcription
S. Henriet, L. Sinck, G. Bec, R. J. Gorelick, R. Marquet, and J.-C. Paillart
Nucleic Acids Res. 2007 August; 35(15): 5141–5153. Published online 2007 July 26. doi: 10.1093/nar/gkm542.
PMCID: PMC1976464
Combinatorial delivery of small interfering RNAs reduces RNAi efficacy by selective incorporation into RISC
Daniela Castanotto, Kumi Sakurai, Robert Lingeman, Haitang Li, Louise Shively, Lars Aagaard, Harris Soifer, Anne Gatignol, Arthur Riggs, and John J. Rossi
Nucleic Acids Res. 2007 August; 35(15): 5154–5164. Published online 2007 July 26. doi: 10.1093/nar/gkm543.
PMCID: PMC1976469
Circularization of the HIV-1 RNA genome
Marcel Ooms, Truus E. M. Abbink, Chi Pham, and Ben Berkhout
Nucleic Acids Res. 2007 August; 35(15): 5253–5261. Published online 2007 August 7. doi: 10.1093/nar/gkm564.
PMCID: PMC1976439
Metal-ion binding and metal-ion induced folding of the adenine-sensing riboswitch aptamer domain
Jonas Noeske, Harald Schwalbe, and Jens Wöhnert
Nucleic Acids Res. 2007 August; 35(15): 5262–5273. Published online 2007 August 7. doi: 10.1093/nar/gkm565.
PMCID: PMC1976443
Structural Biology
Structure of the Hybrid-2 type intramolecular human telomeric G-quadruplex in K+ solution: insights into structure polymorphism of the human telomeric sequence
Jixun Dai, Megan Carver, Chandanamali Punchihewa, Roger A. Jones, and Danzhou Yang
Nucleic Acids Res. 2007 August; 35(15): 4927–4940. Published online 2007 July 10. doi: 10.1093/nar/gkm522.
PMCID: PMC1976458
Structural basis for recognition of the matrix attachment region of DNA by transcription factor SATB1
Kazuhiko Yamasaki, Toshihiko Akiba, Tomoko Yamasaki, and Kazuaki Harata
Nucleic Acids Res. 2007 August; 35(15): 5073–5084. Published online 2007 July 25. doi: 10.1093/nar/gkm504.
PMCID: PMC1976457
Electron attachment to DNA single strands: gas phase and aqueous solution
Jiande Gu, Yaoming Xie, and Henry F. Schaefer, III
Nucleic Acids Res. 2007 August; 35(15): 5165–5172. Published online 2007 July 27. doi: 10.1093/nar/gkm135.
PMCID: PMC1976433
Local selection rules that can determine specific pathways of DNA unknotting by type II DNA topoisomerases
Yannis Burnier, Cedric Weber, Alessandro Flammini, and Andrzej Stasiak
Nucleic Acids Res. 2007 August; 35(15): 5223–5231. Published online 2007 August 1. doi: 10.1093/nar/gkm532.
PMCID: PMC1976442
Genomics
High content of proteins containing 21st and 22nd amino acids, selenocysteine and pyrrolysine, in a symbiotic deltaproteobacterium of gutless worm Olavius algarvensis
Yan Zhang and Vadim N. Gladyshev
Nucleic Acids Res. 2007 August; 35(15): 4952–4963. Published online 2007 July 11. doi: 10.1093/nar/gkm514.
PMCID: PMC1976440
A predicted operon map for Mycobacterium tuberculosis
P. Roback, J. Beard, D. Baumann, C. Gille, K. Henry, S. Krohn, H. Wiste, M.I. Voskuil, C. Rainville, and R. Rutherford
Nucleic Acids Res. 2007 August; 35(15): 5085–5095. Published online 2007 July 25. doi: 10.1093/nar/gkm518.
PMCID: PMC1976454
Chemistry
G-quadruplex induced stabilization by 2′-deoxy-2′-fluoro-d-arabinonucleic acids (2′F-ANA)
Chang Geng Peng and Masad J. Damha
Nucleic Acids Res. 2007 August; 35(15): 4977–4988. Published online 2007 July 17. doi: 10.1093/nar/gkm520.
PMCID: PMC1976452
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
Margaret Gaskell, Balvinder Kaur, Peter B. Farmer, and Rajinder Singh
Nucleic Acids Res. 2007 August; 35(15): 5014–5027. Published online 2007 July 18. doi: 10.1093/nar/gkm526.
PMCID: PMC1976470
Methods Online
Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)
Olivier Loudig, Ekaterina Milova, Margaret Brandwein-Gensler, Aldo Massimi, Thomas J. Belbin, Geoffrey Childs, Robert H. Singer, Thomas Rohan, and Michael B. Prystowsky
Nucleic Acids Res. 2007 August; 35(15): e94. Published online 2007 July 17. doi: 10.1093/nar/gkm510.
PMCID: PMC1976468
Improved identification of enriched peptide–RNA cross-links from ribonucleoprotein particles (RNPs) by mass spectrometry
Eva Kühn-Hölsken, Olexandr Dybkov, Björn Sander, Reinhard Lührmann, and Henning Urlaub
Nucleic Acids Res. 2007 August; 35(15): e95. Published online 2007 July 25. doi: 10.1093/nar/gkm540.
PMCID: PMC1976460
Meta-prediction of protein subcellular localization with reduced voting
Jie Liu, Shuli Kang, Chuanning Tang, Lynda B.M. Ellis, and Tongbin Li
Nucleic Acids Res. 2007 August; 35(15): e96. Published online 2007 August 1. doi: 10.1093/nar/gkm562.
PMCID: PMC1976432
Targeted high-throughput sequencing of tagged nucleic acid samples
Matthias Meyer, Udo Stenzel, Sean Myles, Kay Prüfer, and Michael Hofreiter
Nucleic Acids Res. 2007 August; 35(15): e97. Published online 2007 August 1. doi: 10.1093/nar/gkm566.
PMCID: PMC1976447
An S/MAR-based infectious episomal genomic DNA expression vector provides long-term regulated functional complementation of LDLR deficiency
Michele M.P. Lufino, Roberto Manservigi, and Richard Wade-Martins
Nucleic Acids Res. 2007 August; 35(15): e98. Published online 2007 August 2. doi: 10.1093/nar/gkm570.
PMCID: PMC1976449
Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification
Thomas E. Royce, Joel S. Rozowsky, and Mark B. Gerstein
Nucleic Acids Res. 2007 August; 35(15): e99. Published online 2007 August 7. doi: 10.1093/nar/gkm549.
PMCID: PMC1976448
Analysis of a nuclease activity of catalytic domain of Thermus thermophilus MutS2 by high-accuracy mass spectrometry
Kenji Fukui, Yoshio Takahata, Noriko Nakagawa, Seiki Kuramitsu, and Ryoji Masui
Nucleic Acids Res. 2007 August; 35(15): e100. Published online 2007 August 7. doi: 10.1093/nar/gkm575.
PMCID: PMC1976465
Computational Biology
Automated recognition of retroviral sequences in genomic data—RetroTector©
Göran O. Sperber, Tove Airola, Patric Jern, and Jonas Blomberg
Nucleic Acids Res. 2007 August; 35(15): 4964–4976. Published online 2007 July 17. doi: 10.1093/nar/gkm515.
PMCID: PMC1976444
Dissecting the action of an evolutionary conserved non-coding region on renin promoter activity
Ralf Mrowka, Andreas Steege, Charlotte Kaps, Hanspeter Herzel, Bernd J. Thiele, Pontus B. Persson, and Nils Blüthgen
Nucleic Acids Res. 2007 August; 35(15): 5120–5129. Published online 2007 July 26. doi: 10.1093/nar/gkm535.
PMCID: PMC1976450
Nucleic Acid Enzymes
Cockayne syndrome protein B interacts with and is phosphorylated by c-Abl tyrosine kinase
Syed Z. Imam, Fred E. Indig, Wen-Hsing Cheng, Satya P. Saxena, Tinna Stevnsner, Donald Kufe, and Vilhelm A. Bohr
Nucleic Acids Res. 2007 August; 35(15): 4941–4951. Published online 2007 July 11. doi: 10.1093/nar/gkm386.
PMCID: PMC1976445
HMGB1 interacts with human topoisomerase IIα and stimulates its catalytic activity
Michal Štros, Alena Bačíková, Eva Polanská, Jitka Štokrová, and François Strauss
Nucleic Acids Res. 2007 August; 35(15): 5001–5013. Published online 2007 July 18. doi: 10.1093/nar/gkm525.
PMCID: PMC1976466
Polymerase-catalyzed synthesis of DNA from phosphoramidate conjugates of deoxynucleotides and amino acids
O. Adelfinskaya, M. Terrazas, M. Froeyen, P. Marlière, K. Nauwelaerts, and P. Herdewijn
Nucleic Acids Res. 2007 August; 35(15): 5060–5072. Published online 2007 July 25. doi: 10.1093/nar/gkm498.
PMCID: PMC1976459
A highly conserved Tyrosine residue of family B DNA polymerases contributes to dictate translesion synthesis past 8-oxo-7,8-dihydro-2′-deoxyguanosine
Miguel de Vega and Margarita Salas
Nucleic Acids Res. 2007 August; 35(15): 5096–5107. Published online 2007 July 25. doi: 10.1093/nar/gkm545.
PMCID: PMC1976434
Error-free bypass of 2-hydroxyadenine by human DNA polymerase λ with Proliferating Cell Nuclear Antigen and Replication Protein A in different sequence contexts
Emmanuele Crespan, Ulrich Hübscher, and Giovanni Maga
Nucleic Acids Res. 2007 August; 35(15): 5173–5181. Published online 2007 July 30. doi: 10.1093/nar/gkm568.
PMCID: PMC1976453
Haemophilus influenzae phasevarions have evolved from type III DNA restriction systems into epigenetic regulators of gene expression
Kate L. Fox, Stefanie J. Dowideit, Alice L. Erwin, Yogitha N. Srikhanta, Arnold L. Smith, and Michael P. Jennings
Nucleic Acids Res. 2007 August; 35(15): 5242–5252. Published online 2007 August 2. doi: 10.1093/nar/gkm571.
PMCID: PMC1976455
Corrigendum
Design and synthesis of boronic-acid-labeled thymidine triphosphate for incorporation into DNA
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
Nucleic Acids Res. 2007 August; 35(15): 5274. Published online 2007 August. doi: 10.1093/nar/gkm399.
PMCID: PMC1976437
Corrects: Na Lin, et al. Design and synthesis of boronic-acid-labeled thymidine triphosphate for incorporation into DNA. Nucleic Acids Res. 2007 February; 35(4): 1222–1229.
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