| | 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. |