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Previous Next 		Contents: Volume 35, Number 16, August 2007   [Index by Author] 

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To see an article, click its [Full Text] or [PDF] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.

Computational Biology Back

Andreas Wagner, Christopher Lewis, and Manuel Bichsel
A survey of bacterial insertion sequences using IScan
Nucleic Acids Research Advance Access published on August 7, 2007
Nucl. Acids Res. 2007 35: 5284-5293; doi:10.1093/nar/gkm597 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Paul Fisher, Cornelia Hedeler, Katherine Wolstencroft, Helen Hulme, Harry Noyes, Stephen Kemp, Robert Stevens, and Andrew Brass
A systematic strategy for large-scale analysis of genotype–phenotype correlations: identification of candidate genes involved in African trypanosomiasis
Nucleic Acids Research Advance Access published on August 20, 2007
Nucl. Acids Res. 2007 35: 5625-5633; doi:10.1093/nar/gkm623 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genomics Back

Martin Akerman and Yael Mandel-Gutfreund
Does distance matter? Variations in alternative 3' splicing regulation
Nucleic Acids Research Advance Access published on August 17, 2007
Nucl. Acids Res. 2007 35: 5487-5498; doi:10.1093/nar/gkm603 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology Back

Ryan K. Shultzaberger, Lindsey R. Roberts, Ilya G. Lyakhov, Igor A. Sidorov, Andrew G. Stephen, Robert J. Fisher, and Thomas D. Schneider
Correlation between binding rate constants and individual information of E. coli Fis binding sites
Nucleic Acids Research Advance Access published on July 7, 2007
Nucl. Acids Res. 2007 35: 5275-5283; doi:10.1093/nar/gkm471 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Ivan M. Munoz, Paul A. Jowsey, Rachel Toth, and John Rouse
Phospho-epitope binding by the BRCT domains of hPTIP controls multiple aspects of the cellular response to DNA damage
Nucleic Acids Research Advance Access published on August 8, 2007
Nucl. Acids Res. 2007 35: 5312-5322; doi:10.1093/nar/gkm493 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Naomi Fersht, Damien Hermand, Jacqueline Hayles, and Paul Nurse
Cdc18/CDC6 activates the Rad3-dependent checkpoint in the fission yeast
Nucleic Acids Research Advance Access published on August 8, 2007
Nucl. Acids Res. 2007 35: 5323-5337; doi:10.1093/nar/gkm527 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Qi-En Wang, Mette Prætorius-Ibba, Qianzheng Zhu, Mohamed A. El-Mahdy, Gulzar Wani, Qun Zhao, Song Qin, Srinivas Patnaik, and Altaf A. Wani
Ubiquitylation-independent degradation of Xeroderma pigmentosum group C protein is required for efficient nucleotide excision repair
Nucleic Acids Research Advance Access published on August 9, 2007
Nucl. Acids Res. 2007 35: 5338-5350; doi:10.1093/nar/gkm550 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Ed Grabczyk, Miriam Mancuso, and Mimi C. Sammarco
A persistent RNA·DNA hybrid formed by transcription of the Friedreich ataxia triplet repeat in live bacteria, and by T7 RNAP in vitro
Nucleic Acids Research Advance Access published on August 9, 2007
Nucl. Acids Res. 2007 35: 5351-5359; doi:10.1093/nar/gkm589 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Gemma Serrano-Heras, José A. Ruiz-Masó, Gloria del Solar, Manuel Espinosa, Alicia Bravo, and Margarita Salas
Protein p56 from the Bacillus subtilis phage {phi}29 inhibits DNA-binding ability of uracil-DNA glycosylase
Nucleic Acids Research Advance Access published on August 13, 2007
Nucl. Acids Res. 2007 35: 5393-5401; doi:10.1093/nar/gkm584 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Noopur Agarwal, Tanja Hardt, Alessandro Brero, Danny Nowak, Ulrich Rothbauer, Annette Becker, Heinrich Leonhardt, and M. Cristina Cardoso
MeCP2 interacts with HP1 and modulates its heterochromatin association during myogenic differentiation
Nucleic Acids Research Advance Access published on August 13, 2007
Nucl. Acids Res. 2007 35: 5402-5408; doi:10.1093/nar/gkm599 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Shuren Liao, Yoshihiro Matsumoto, and Hong Yan
Biochemical reconstitution of abasic DNA lesion replication in Xenopus extracts
Nucleic Acids Research Advance Access published on August 15, 2007
Nucl. Acids Res. 2007 35: 5422-5429; doi:10.1093/nar/gkm552 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Mikhail S. Klenov, Sergey A. Lavrov, Anastasia D. Stolyarenko, Sergey S. Ryazansky, Alexei A. Aravin, Thomas Tuschl, and Vladimir A. Gvozdev
Repeat-associated siRNAs cause chromatin silencing of retrotransposons in the Drosophila melanogaster germline
Nucleic Acids Research Advance Access published on August 15, 2007
Nucl. Acids Res. 2007 35: 5430-5438; doi:10.1093/nar/gkm576 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Saravanakumar Dhakshinamoorthy, Shiva Ranjani Sridharan, Lei Li, Poh Yong Ng, Linda M. Boxer, and Alan G. Porter
Protein/DNA arrays identify nitric oxide-regulated cis-element and trans-factor activities some of which govern neuroblastoma cell viability
Nucleic Acids Research Advance Access published on August 15, 2007
Nucl. Acids Res. 2007 35: 5439-5451; doi:10.1093/nar/gkm594 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Elzbieta Sarnowska, Ewa A. Grzybowska, Krzysztof Sobczak, Ryszard Konopinski, Anna Wilczynska, Maria Szwarc, Tomasz J. Sarnowski, Wlodzimierz J. Krzyzosiak, and Janusz A. Siedlecki
Hairpin structure within the 3'UTR of DNA polymerase ß mRNA acts as a post-transcriptional regulatory element and interacts with Hax-1
Nucleic Acids Research Advance Access published on August 17, 2007
Nucl. Acids Res. 2007 35: 5499-5510; doi:10.1093/nar/gkm502 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yong Seok Choi, Jung Hur, and Sunjoo Jeong
ß-Catenin binds to the downstream region and regulates the expression C-reactive protein gene
Nucleic Acids Research Advance Access published on August 17, 2007
Nucl. Acids Res. 2007 35: 5511-5519; doi:10.1093/nar/gkm547 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Alastair B. Fleming and Sari Pennings
Tup1-Ssn6 and Swi-Snf remodelling activities influence long-range chromatin organization upstream of the yeast SUC2 gene
Nucleic Acids Research Advance Access published on August 17, 2007
Nucl. Acids Res. 2007 35: 5520-5531; doi:10.1093/nar/gkm573 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Xingguo Zhu, Jianhua Ling, Ling Zhang, Wenhu Pi, Min Wu, and Dorothy Tuan
A facilitated tracking and transcription mechanism of long-range enhancer function
Nucleic Acids Research Advance Access published on August 17, 2007
Nucl. Acids Res. 2007 35: 5532-5544; doi:10.1093/nar/gkm595 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Lior Weissman, Dong-Gyu Jo, Martin M. Sørensen, Nadja C. de Souza-Pinto, William R. Markesbery, Mark P. Mattson, and Vilhelm A. Bohr
Defective DNA base excision repair in brain from individuals with Alzheimer's disease and amnestic mild cognitive impairment
Nucleic Acids Research Advance Access published on August 17, 2007
Nucl. Acids Res. 2007 35: 5545-5555; doi:10.1093/nar/gkm605 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jonathan A. Stead, Joe L. Costello, Michaela J. Livingstone, and Phil Mitchell
The PMC2NT domain of the catalytic exosome subunit Rrp6p provides the interface for binding with its cofactor Rrp47p, a nucleic acid-binding protein
Nucleic Acids Research Advance Access published on August 17, 2007
Nucl. Acids Res. 2007 35: 5556-5567; doi:10.1093/nar/gkm614 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Nucleic Acid Enzymes Back

Chongli Yuan, Xiong Wen Lou, Elizabeth Rhoades, Huimin Chen, and Lynden A. Archer
T4 DNA ligase is more than an effective trap of cyclized dsDNA
Nucleic Acids Research Advance Access published on August 7, 2007
Nucl. Acids Res. 2007 35: 5294-5302; doi:10.1093/nar/gkm582 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Elizabeth Fidalgo da Silva and Linda J. Reha-Krantz
DNA polymerase proofreading: active site switching catalyzed by the bacteriophage T4 DNA polymerase
Nucleic Acids Research Advance Access published on August 15, 2007
Nucl. Acids Res. 2007 35: 5452-5463; doi:10.1093/nar/gkm591 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jamie Sheren, Stephen J. Langer, and Leslie A. Leinwand
A randomized library approach to identifying functional lox site domains for the Cre recombinase
Nucleic Acids Research Advance Access published on August 15, 2007
Nucl. Acids Res. 2007 35: 5464-5473; doi:10.1093/nar/gkm604 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

RNA Back

Kazuhiro Fukumura, Ayako Kato, Yui Jin, Takashi Ideue, Tetsuro Hirose, Naoyuki Kataoka, Toshinobu Fujiwara, Hiroshi Sakamoto, and Kunio Inoue
Tissue-specific splicing regulator Fox-1 induces exon skipping by interfering E complex formation on the downstream intron of human F1{gamma} gene
Nucleic Acids Research Advance Access published on August 7, 2007
Nucl. Acids Res. 2007 35: 5303-5311; doi:10.1093/nar/gkm569 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Michiko Kimoto, Tsuneo Mitsui, Yoko Harada, Akira Sato, Shigeyuki Yokoyama, and Ichiro Hirao
Fluorescent probing for RNA molecules by an unnatural base-pair system
Nucleic Acids Research Advance Access published on August 9, 2007
Nucl. Acids Res. 2007 35: 5360-5369; doi:10.1093/nar/gkm508 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Kathrin Lang, Renate Rieder, and Ronald Micura
Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach
Nucleic Acids Research Advance Access published on August 9, 2007
Nucl. Acids Res. 2007 35: 5370-5378; doi:10.1093/nar/gkm580 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Lakshmi Menon and Mihaela-Rita Mihailescu
Interactions of the G quartet forming semaphorin 3F RNA with the RGG box domain of the fragile X protein family
Nucleic Acids Research Advance Access published on August 9, 2007
Nucl. Acids Res. 2007 35: 5379-5392; doi:10.1093/nar/gkm581 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Debojyoti Dhar, Swagata Roy, and Saumitra Das
Translational control of the interferon regulatory factor 2 mRNA by IRES element
Nucleic Acids Research Advance Access published on August 13, 2007
Nucl. Acids Res. 2007 35: 5409-5421; doi:10.1093/nar/gkm524 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yuan Yuan, Sarah A. Compton, Krzysztof Sobczak, Myrna G. Stenberg, Charles A. Thornton, Jack D. Griffith, and Maurice S. Swanson
Muscleblind-like 1 interacts with RNA hairpins in splicing target and pathogenic RNAs
Nucleic Acids Research Advance Access published on August 15, 2007
Nucl. Acids Res. 2007 35: 5474-5486; doi:10.1093/nar/gkm601 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jérôme Mulhbacher and Daniel A. Lafontaine
Ligand recognition determinants of guanine riboswitches
Nucleic Acids Research Advance Access published on August 17, 2007
Nucl. Acids Res. 2007 35: 5568-5580; doi:10.1093/nar/gkm572 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Mélissa Léger, Dominic Dulude, Sergey V. Steinberg, and Léa Brakier-Gingras
The three transfer RNAs occupying the A, P and E sites on the ribosome are involved in viral programmed -1 ribosomal frameshift
Nucleic Acids Research Advance Access published on August 17, 2007
Nucl. Acids Res. 2007 35: 5581-5592; doi:10.1093/nar/gkm578 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Éena Jakó, Péter Ittzés, Áron Szenes, Ádám Kun, Eörs Szathmáry, and Gábor Pál
In silico detection of tRNA sequence features characteristic to aminoacyl-tRNA synthetase class membership
Nucleic Acids Research Advance Access published on August 17, 2007
Nucl. Acids Res. 2007 35: 5593-5609; doi:10.1093/nar/gkm598 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Sébastien Muller, Jean-Baptiste Fourmann, Christine Loegler, Bruno Charpentier, and Christiane Branlant
Identification of determinants in the protein partners aCBF5 and aNOP10 necessary for the tRNA:{Psi}55-synthase and RNA-guided RNA:{Psi}-synthase activities
Nucleic Acids Research Advance Access published on August 17, 2007
Nucl. Acids Res. 2007 35: 5610-5624; doi:10.1093/nar/gkm606 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online Back

Shihai Huang, John Salituro, Ning Tang, Ka-Cheung Luk, John Hackett, Jr, Priscilla Swanson, Gavin Cloherty, Wai-Bing Mak, John Robinson, and Klara Abravaya
Thermodynamically modulated partially double-stranded linear DNA probe design for homogeneous real-time PCR
Nucleic Acids Research Advance Access published on August 9, 2007
Nucl. Acids Res. 2007 35: e101; doi:10.1093/nar/gkm551 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Stefano Calza, Wolfgang Raffelsberger, Alexander Ploner, Jose Sahel, Thierry Leveillard, and Yudi Pawitan
Filtering genes to improve sensitivity in oligonucleotide microarray data analysis
Nucleic Acids Research Advance Access published on August 15, 2007
Nucl. Acids Res. 2007 35: e102; doi:10.1093/nar/gkm537 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Maria Pajunen, Hilkka Turakainen, Eini Poussu, Johan Peränen, Mauno Vihinen, and Harri Savilahti
High-precision mapping of protein–protein interfaces: an integrated genetic strategy combining en masse mutagenesis and DNA-level parallel analysis on a yeast two-hybrid platform
Nucleic Acids Research Advance Access published on August 15, 2007
Nucl. Acids Res. 2007 35: e103; doi:10.1093/nar/gkm563 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Al-Muataz Khalil, Jeffrey A. Julius, and Jeff Bachant
One step construction of PCR mutagenized libraries for genetic analysis by recombination cloning
Nucleic Acids Research Advance Access published on August 15, 2007
Nucl. Acids Res. 2007 35: e104; doi:10.1093/nar/gkm583 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Antony K. Chen, Mark A. Behlke, and Andrew Tsourkas
Avoiding false-positive signals with nuclease-vulnerable molecular beacons in single living cells
Nucleic Acids Research Advance Access published on August 15, 2007
Nucl. Acids Res. 2007 35: e105; doi:10.1093/nar/gkm593 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Mogens Engelhardt
Choreography for nucleosomes: the conformational freedom of the nucleosomal filament and its limitations
Nucleic Acids Research Advance Access published on August 17, 2007
Nucl. Acids Res. 2007 35: e106; doi:10.1093/nar/gkm560 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Beatrice I. Lindhout, Paul Fransz, Federico Tessadori, Tobias Meckel, Paul J.J. Hooykaas, and Bert J. van der Zaal
Live cell imaging of repetitive DNA sequences via GFP-tagged polydactyl zinc finger proteins
Nucleic Acids Research Advance Access published on August 17, 2007
Nucl. Acids Res. 2007 35: e107; doi:10.1093/nar/gkm618 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

To see an article, click its [Full Text] or [PDF] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.