Nucl. Acids Res. -- Nucleic Acids Research Advance Access

Nucleic Acids Research Advance Access

Nucleic Acids Research Advance Access articles are papers that have been copyedited and typeset but not yet paginated for inclusion in an issue of the journal. More information, including how to cite Advance Access papers, can be found on the Advance Access page.

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10 July 2009

Abstract Gene Regulation, Chromatin and Epigenetics: Alexey Protsenko, Marina Zakharova, Maxim Nagornykh, Alexander Solonin, and Konstantin Severinov
Transcription regulation of restriction-modification system Ecl18kI
Nucleic Acids Research Advance Access published on July 10, 2009.
doi:10.1093/nar/gkp579
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Methods Online: Peter Kötter, Julia E. Weigand, Britta Meyer, Karl-Dieter Entian, and Beatrix Suess
A fast and efficient translational control system for conditional expression of yeast genes
Nucleic Acids Research Advance Access published on July 10, 2009.
doi:10.1093/nar/gkp578
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

9 July 2009

Abstract Methods Online: Markus Schmitt and Michael Pawlita
High-throughput detection and multiplex identification of cell contaminations
Nucleic Acids Research Advance Access published on July 9, 2009.
doi:10.1093/nar/gkp581
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Abstract Nucleic Acid Enzymes: Jaroslav Malina, Oldrich Vrana, and Viktor Brabec
Mechanistic studies of the modulation of cleavage activity of topoisomerase I by DNA adducts of mono- and bi-functional Pt^II complexes
Nucleic Acids Research Advance Access published on July 9, 2009.
doi:10.1093/nar/gkp580
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Computational Biology: Aaron J. Arvey, Rajeev K. Azad, Alpan Raval, and Jeffrey G. Lawrence
Detection of genomic islands via segmental genome heterogeneity
Nucleic Acids Research Advance Access published on July 9, 2009.
doi:10.1093/nar/gkp576
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Nucleic Acid Enzymes: Miloje Savic, Josip Lovric, Tatjana Ilic Tomic, Branka Vasiljevic, and Graeme L. Conn
Determination of the target nucleosides for members of two families of 16S rRNA methyltransferases that confer resistance to partially overlapping groups of aminoglycoside antibiotics
Nucleic Acids Research Advance Access published on July 9, 2009.
doi:10.1093/nar/gkp575
[Abstract] [Full Text] [Print PDF] [Screen PDF]

8 July 2009

Abstract Nucleic Acid Enzymes: Niels Laurens, Stuart R. W. Bellamy, August F. Harms, Yana S. Kovacheva, Stephen E. Halford, and Gijs J. L. Wuite
Dissecting protein-induced DNA looping dynamics in real time
Nucleic Acids Research Advance Access published on July 8, 2009.
doi:10.1093/nar/gkp570
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data] [Supplementary Data]

Abstract Chemistry and Synthetic Biology: Nathalie Berthet, Caroline Crey-Desbiolles, Mitsuharu Kotera, and Pascal Dumy
Chemical synthesis, DNA incorporation and biological study of a new photocleavable 2'-deoxyadenosine mimic
Nucleic Acids Research Advance Access published on July 8, 2009.
doi:10.1093/nar/gkp562
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Structural Biology: Graham L. Randall, Lynn Zechiedrich, and B. Montgomery Pettitt
In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form
Nucleic Acids Research Advance Access published on July 8, 2009.
doi:10.1093/nar/gkp556
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7 July 2009

Abstract Methods Online: Lin Wan, Kelian Sun, Qi Ding, Yuehua Cui, Ming Li, Yalu Wen, Robert C. Elston, Minping Qian, and Wenjiang J Fu
Hybridization modeling of oligonucleotide SNP arrays for accurate DNA copy number estimation
Nucleic Acids Research Advance Access published on July 7, 2009.
doi:10.1093/nar/gkp559
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Nucleic Acid Enzymes: Sylvestre Grizot, Julianne Smith, Fayza Daboussi, Jesús Prieto, Pilar Redondo, Nekane Merino, Maider Villate, Séverine Thomas, Laetitia Lemaire, Guillermo Montoya, Francisco J. Blanco, Frédéric Pâques, and Philippe Duchateau
Efficient targeting of a SCID gene by an engineered single-chain homing endonuclease
Nucleic Acids Research Advance Access published on July 7, 2009.
doi:10.1093/nar/gkp548
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

6 July 2009

Abstract Structural Biology: Aurore Guédin, Patrizia Alberti, and Jean-Louis Mergny
Stability of intramolecular quadruplexes: sequence effects in the central loop
Nucleic Acids Research Advance Access published on July 6, 2009.
doi:10.1093/nar/gkp563
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Abstract Genomics: Wei Sun, Fred A. Wright, Zhengzheng Tang, Silje H. Nordgard, Peter Van Loo, Tianwei Yu, Vessela N. Kristensen, and Charles M. Perou
Integrated study of copy number states and genotype calls using high-density SNP arrays
Nucleic Acids Research Advance Access published on July 6, 2009.
doi:10.1093/nar/gkp493
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

3 July 2009

Abstract Nucleic Acid Enzymes: Anastasia Rogozina, Evgeny Zaychikov, Malcolm Buckle, Hermann Heumann, and Bianca Sclavi
DNA melting by RNA polymerase at the T7A1 promoter precedes the rate-limiting step at 37°C and results in the accumulation of an off-pathway intermediate
Nucleic Acids Research Advance Access published on July 3, 2009.
doi:10.1093/nar/gkp560
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Abstract Structural Biology: Denise S. Tevis, Arvind Kumar, Chad E. Stephens, David W. Boykin, and W. David Wilson
Large, sequence-dependent effects on DNA conformation by minor groove binding compounds
Nucleic Acids Research Advance Access published on July 3, 2009.
doi:10.1093/nar/gkp558
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Genome Integrity, Repair and Replication: Jacques Oberto, Norman Breuil, Arnaud Hecker, Francesca Farina, Céline Brochier-Armanet, Emmanuel Culetto, and Patrick Forterre
Qri7/OSGEPL, the mitochondrial version of the universal Kae1/YgjD protein, is essential for mitochondrial genome maintenance
Nucleic Acids Research Advance Access published on July 3, 2009.
doi:10.1093/nar/gkp557
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Computational Biology: Leonid Zamdborg and Ping Ma
Discovery of protein–DNA interactions by penalized multivariate regression
Nucleic Acids Research Advance Access published on July 3, 2009.
doi:10.1093/nar/gkp554
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Abstract RNA: Rosa Díaz-Toledano, Ascensión Ariza-Mateos, Alex Birk, Belén Martínez-García, and Jordi Gómez
In vitro characterization of a miR-122-sensitive double-helical switch element in the 5' region of hepatitis C virus RNA
Nucleic Acids Research Advance Access published on July 3, 2009.
doi:10.1093/nar/gkp553
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Nucleic Acid Enzymes: Michelle Mitchell, Song Xue, Rachel Erdman, Lennart Randau, Dieter Söll, and Hong Li
Crystal structure and assembly of the functional Nanoarchaeum equitans tRNA splicing endonuclease
Nucleic Acids Research Advance Access published on July 3, 2009.
doi:10.1093/nar/gkp537
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Nucleic Acid Enzymes: Richard D. Morgan, Elizabeth A. Dwinell, Tanya K. Bhatia, Elizabeth M. Lang, and Yvette A. Luyten
The MmeI family: type II restriction–modification enzymes that employ single-strand modification for host protection
Nucleic Acids Research Advance Access published on July 3, 2009.
doi:10.1093/nar/gkp534
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

1 July 2009

Abstract Survey and Summary: Thomas LaFramboise
Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances
Nucleic Acids Research Advance Access published on July 1, 2009.
doi:10.1093/nar/gkp552
[Abstract] [Full Text] [Print PDF] [Screen PDF]

30 June 2009

Abstract Nucleic Acid Enzymes: Richard D. Morgan and Yvette A. Luyten
Rational engineering of type II restriction endonuclease DNA binding and cleavage specificity
Nucleic Acids Research Advance Access published on June 30, 2009.
doi:10.1093/nar/gkp535
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Gene Regulation, Chromatin and Epigenetics: Karim Bouazoune, Tina B. Miranda, Peter A. Jones, and Robert E. Kingston
Analysis of individual remodeled nucleosomes reveals decreased histone–DNA contacts created by hSWI/SNF
Nucleic Acids Research Advance Access published on June 30, 2009.
doi:10.1093/nar/gkp524
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Gene Regulation, Chromatin, and Epigenetics: Julie Ross, Stefania Bottardi, Vincent Bourgoin, Alex Wollenschlaeger, Elliot Drobetsky, Marie Trudel, and Eric Milot
Differential requirement of a distal regulatory region for pre-initiation complex formation at globin gene promoters
Nucleic Acids Research Advance Access published on June 30, 2009.
doi:10.1093/nar/gkp545
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

26 June 2009

Abstract Methods online: Ana M. Blanco, Laura Rausell, Begoña Aguado, Manuel Perez-Alonso, and Rubén Artero
A FRET-based assay for characterization of alternative splicing events using peptide nucleic acid fluorescence in situ hybridization
Nucleic Acids Research Advance Access published on June 26, 2009.
doi:10.1093/nar/gkp551
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data] [Supplementary Data]

Abstract Gene Regulation, Chromatin and Epigenetics: Caroline Conte, Nadera Ainaoui, Aurélie Delluc-Clavières, Marie P. Khoury, Rania Azar, Françoise Pujol, Yvan Martineau, Stéphane Pyronnet, and Anne-Catherine Prats
Fibroblast growth factor 1 induced during myogenesis by a transcription–translation coupling mechanism
Nucleic Acids Research Advance Access published on June 26, 2009.
doi:10.1093/nar/gkp550
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Abstract RNA: Sara Chirayil, Rachel Chirayil, and Kevin J. Luebke
Discovering ligands for a microRNA precursor with peptoid microarrays
Nucleic Acids Research Advance Access published on June 26, 2009.
doi:10.1093/nar/gkp549
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Molecular Biology: Markella Ponticos, Clare Harvey, Tetsuro Ikeda, David Abraham, and George Bou-Gharios
JunB mediates enhancer/promoter activity of COL1A2 following TGF-β induction
Nucleic Acids Research Advance Access published on June 26, 2009.
doi:10.1093/nar/gkp544
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract RNA: Regis Marty, Christophe N. N’soukpoé-Kossi, David M. Charbonneau, Laurent Kreplak, and Heidar-Ali Tajmir-Riahi
Structural characterization of cationic lipid–tRNA complexes
Nucleic Acids Research Advance Access published on June 26, 2009.
doi:10.1093/nar/gkp543
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Methods online: Caroline C. Friedel, Lars Dölken, Zsolt Ruzsics, Ulrich H. Koszinowski, and Ralf Zimmer
Conserved principles of mammalian transcriptional regulation revealed by RNA half-life
Nucleic Acids Research Advance Access published on June 26, 2009.
doi:10.1093/nar/gkp542
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Gene Regulation, Chromatin and Epigenetics: Rui Zhou, Limin Han, Guodong Li, and Tanjun Tong
Senescence delay and repression of p16^INK4a by Lsh via recruitment of histone deacetylases in human diploid fibroblasts
Nucleic Acids Research Advance Access published on June 26, 2009.
doi:10.1093/nar/gkp533
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Molecular Biology: Yingpu Yu, Assen Marintchev, Victoria G. Kolupaeva, Anett Unbehaun, Tatyana Veryasova, Shao-Chiang Lai, Peng Hong, Gerhard Wagner, Christopher U. T. Hellen, and Tatyana V. Pestova
Position of eukaryotic translation initiation factor eIF1A on the 40S ribosomal subunit mapped by directed hydroxyl radical probing
Nucleic Acids Research Advance Access published on June 26, 2009.
doi:10.1093/nar/gkp519
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

24 June 2009

Abstract Structural Biology: Kengo Tsuda, Kanako Kuwasako, Mari Takahashi, Tatsuhiko Someya, Makoto Inoue, Takaho Terada, Naohiro Kobayashi, Mikako Shirouzu, Takanori Kigawa, Akiko Tanaka, Sumio Sugano, Peter Güntert, Yutaka Muto, and Shigeyuki Yokoyama
Structural basis for the sequence-specific RNA-recognition mechanism of human CUG-BP1 RRM3
Nucleic Acids Research Advance Access published on June 24, 2009.
doi:10.1093/nar/gkp546
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Gene Regulation, Chromatin and Epigenetics: Patricia C. Burrows, Nicolas Joly, B. Tracy Nixon, and Martin Buck
Comparative analysis of activator-E ${sigma}$ ⁵⁴ complexes formed with nucleotide-metal fluoride analogues
Nucleic Acids Research Advance Access published on June 24, 2009.
doi:10.1093/nar/gkp541
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Methods online: Frank H. T. Nelissen, Frederic C. Girard, Marco Tessari, Hans A. Heus, and Sybren S. Wijmenga
Preparation of selective and segmentally labeled single-stranded DNA for NMR by self-primed PCR and asymmetrical endonuclease double digestion
Nucleic Acids Research Advance Access published on June 24, 2009.
doi:10.1093/nar/gkp540
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods online: Geetu Tuteja, Peter White, Jonathan Schug, and Klaus H. Kaestner
Extracting transcription factor targets from ChIP-Seq data
Nucleic Acids Research Advance Access published on June 24, 2009.
doi:10.1093/nar/gkp536
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Structural Biology: María Luisa Martínez-Robles, Guillaume Witz, Pablo Hernández, Jorge B. Schvartzman, Andrzej Stasiak, and Dora B. Krimer
Interplay of DNA supercoiling and catenation during the segregation of sister duplexes
Nucleic Acids Research Advance Access published on June 24, 2009.
doi:10.1093/nar/gkp530
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Nucleic Acid Enzymes: Ming Fang, Wencke-Maria Zeisberg, Ciaran Condon, Vasily Ogryzko, Antoine Danchin, and Undine Mechold
Degradation of nanoRNA is performed by multiple redundant RNases in Bacillus subtilis
Nucleic Acids Research Advance Access published on June 24, 2009.
doi:10.1093/nar/gkp527
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

23 June 2009

Abstract Methods online: Éva Hegedüs, Endre Kókai, Alexander Kotlyar, Viktor Dombrádi, and Gábor Szabó
Separation of 1–23-kb complementary DNA strands by urea–agarose gel electrophoresis
Nucleic Acids Research Advance Access published on June 23, 2009.
doi:10.1093/nar/gkp539
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Genome Integrity, Repair and Replication: Songmin Ying, Katie Myers, Sarah Bottomley, Thomas Helleday, and Helen E. Bryant
BRCA2-dependent homologous recombination is required for repair of Arsenite-induced replication lesions in mammalian cells
Nucleic Acids Research Advance Access published on June 23, 2009.
doi:10.1093/nar/gkp538
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract RNA: Felix Grewe, Prisca Viehoever, Bernd Weisshaar, and Volker Knoop
A trans-splicing group I intron and tRNA-hyperediting in the mitochondrial genome of the lycophyte Isoetes engelmannii
Nucleic Acids Research Advance Access published on June 23, 2009.
doi:10.1093/nar/gkp532
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Genome Integrity, Repair and Replication: Neta Agmon, Shiri Pur, Batia Liefshitz, and Martin Kupiec
Analysis of repair mechanism choice during homologous recombination
Nucleic Acids Research Advance Access published on June 23, 2009.
doi:10.1093/nar/gkp495
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

22 June 2009

Abstract Computational Biology: Eugene Melamud and John Moult
Stochastic noise in splicing machinery
Nucleic Acids Research Advance Access published on June 22, 2009.
doi:10.1093/nar/gkp471
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

19 June 2009

Abstract Gene Regulation, Chromatin and Epigenetics: Federica Ferri, Haniaa Bouzinba-Segard, Guillaume Velasco, Florent Hubé, and Claire Francastel
Non-coding murine centromeric transcripts associate with and potentiate Aurora B kinase
Nucleic Acids Research Advance Access published on June 19, 2009.
doi:10.1093/nar/gkp529
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods Online: Agnieszka Doroszuk, L. Basten Snoek, Emilie Fradin, Joost Riksen, and Jan Kammenga
A genome-wide library of CB4856/N2 introgression lines of Caenorhabditis elegans
Nucleic Acids Research Advance Access published on June 19, 2009.
doi:10.1093/nar/gkp528
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Genomics: Silvio Bicciato, Roberta Spinelli, Mattia Zampieri, Eleonora Mangano, Francesco Ferrari, Luca Beltrame, Ingrid Cifola, Clelia Peano, Aldo Solari, and Cristina Battaglia
A computational procedure to identify significant overlap of differentially expressed and genomic imbalanced regions in cancer datasets
Nucleic Acids Research Advance Access published on June 19, 2009.
doi:10.1093/nar/gkp520
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

18 June 2009

Abstract Methods Online: Jochen B. Geigl, Anna C. Obenauf, Julie Waldispuehl-Geigl, Eva M. Hoffmann, Martina Auer, Martina Hörmann, Maria Fischer, Zlatko Trajanoski, Michael A. Schenk, Lars O. Baumbusch, and Michael R. Speicher
Identification of small gains and losses in single cells after whole genome amplification on tiling oligo arrays
Nucleic Acids Research Advance Access published on June 18, 2009.
doi:10.1093/nar/gkp526
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract RNA: Christian D. Sadik, Malte Bachmann, Josef Pfeilschifter, and Heiko Mühl
Activation of interferon regulatory factor-3 via toll-like receptor 3 and immunomodulatory functions detected in A549 lung epithelial cells exposed to misplaced U1-snRNA
Nucleic Acids Research Advance Access published on June 18, 2009.
doi:10.1093/nar/gkp525
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Gene Regulation, Chromatin and Epigenetics: Annette N. D. Scharf, Teresa K. Barth, and Axel Imhof
Establishment of Histone Modifications after Chromatin Assembly
Nucleic Acids Research Advance Access published on June 18, 2009.
doi:10.1093/nar/gkp518
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

16 June 2009

Abstract Gene Regulation, Chromatin and Epigenetics: Asmaa M. Baker, Qiang Fu, William Hayward, Stuart M. Lindsay, and Terace M. Fletcher
The Myb/SANT domain of the telomere-binding protein TRF2 alters chromatin structure
Nucleic Acids Research Advance Access published on June 16, 2009.
doi:10.1093/nar/gkp515
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract RNA: Simon Haenni, Erwin Studer, Gabriela Schumann Burkard, and Isabel Roditi
Bidirectional silencing of RNA polymerase I transcription by a strand switch region in Trypanosoma brucei
Nucleic Acids Research Advance Access published on June 16, 2009.
doi:10.1093/nar/gkp513
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract RNA: Richard S. P. Horler and Carin K. Vanderpool
Homologs of the small RNA SgrS are broadly distributed in enteric bacteria but have diverged in size and sequence
Nucleic Acids Research Advance Access published on June 16, 2009.
doi:10.1093/nar/gkp501
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods online: Marco Severgnini, Paola Cremonesi, Clarissa Consolandi, Giada Caredda, Gianluca De Bellis, and Bianca Castiglioni
ORMA: a tool for identification of species-specific variations in 16S rRNA gene and oligonucleotides design
Nucleic Acids Research Advance Access published on June 16, 2009.
doi:10.1093/nar/gkp499
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods online: Nicolas Philippe, Anthony Boureux, Laurent Bréhélin, Jorma Tarhio, Thérèse Commes, and Éric Rivals
Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity
Nucleic Acids Research Advance Access published on June 16, 2009.
doi:10.1093/nar/gkp492
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Chemistry and Synthetic Biology: Shawn M. Douglas, Adam H. Marblestone, Surat Teerapittayanon, Alejandro Vazquez, George M. Church, and William M. Shih
Rapid prototyping of 3D DNA-origami shapes with caDNAno
Nucleic Acids Research Advance Access published on June 16, 2009.
doi:10.1093/nar/gkp436
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Molecular Biology: Kunio Kikuchi, Makiha Fukuda, Tomoya Ito, Mitsuko Inoue, Takahide Yokoi, Suenori Chiku, Toutai Mitsuyama, Kiyoshi Asai, Tetsuro Hirose, and Yasunori Aizawa
Transcripts of unknown function in multiple-signaling pathways involved in human stem cell differentiation
Nucleic Acids Research Advance Access published on June 16, 2009.
doi:10.1093/nar/gkp426
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

15 June 2009

Abstract RNA: Nitin Nitin, Won Jong Rhee, and Gang Bao
Translation inhibition reveals interaction of 2'-deoxy and 2'-O-methyl molecular beacons with mRNA targets in living cells
Nucleic Acids Research Advance Access published on June 15, 2009.
doi:10.1093/nar/gkp517
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Molecular Biology: A. Scoumanne, J. Zhang, and X. Chen
PRMT5 is required for cell-cycle progression and p53 tumor suppressor function
Nucleic Acids Research Advance Access published on June 15, 2009.
doi:10.1093/nar/gkp516
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods online: Junichi Yamaguchi, Mohammed Naimuddin, Manish Biyani, Toru Sasaki, Masayuki Machida, Tai Kubo, Takashi Funatsu, Yuzuru Husimi, and Naoto Nemoto
cDNA display: a novel screening method for functional disulfide-rich peptides by solid-phase synthesis and stabilization of mRNA–protein fusions
Nucleic Acids Research Advance Access published on June 15, 2009.
doi:10.1093/nar/gkp514
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Methods online: Shuwen Wang, Yuanjun Zhao, Melanie A. Leiby, and Jiyue Zhu
Studying human telomerase gene transcription by a chromatinized reporter generated by recombinase-mediated targeting of a bacterial artificial chromosome
Nucleic Acids Research Advance Access published on June 15, 2009.
doi:10.1093/nar/gkp511
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods online: Dimos Gaidatzis, Kirsten Jacobeit, Edward J. Oakeley, and Michael B. Stadler
Overestimation of alternative splicing caused by variable probe characteristics in exon arrays
Nucleic Acids Research Advance Access published on June 15, 2009.
doi:10.1093/nar/gkp508
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods online: Iouri Chepelev, Gang Wei, Qingsong Tang, and Keji Zhao
Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq
Nucleic Acids Research Advance Access published on June 15, 2009.
doi:10.1093/nar/gkp507
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Molecular Biology: Virginia Castilla-Llorente, Wilfried J. J. Meijer, and Margarita Salas
Differential Spo0A-mediated effects on transcription and replication of the related Bacillus subtilis phages Nf and ${varphi}$ 29 explain their different behaviours in vivo
Nucleic Acids Research Advance Access published on June 15, 2009.
doi:10.1093/nar/gkp504
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data] [Supplementary Data]

Abstract Gene Regulation, Chromatin and Epigenetics: Debashree Basu, Garima Khare, Shashi Singh, Anil Tyagi, Sanjeev Khosla, and Shekhar C. Mande
A novel nucleoid-associated protein of Mycobacterium tuberculosis is a sequence homolog of GroEL
Nucleic Acids Research Advance Access published on June 15, 2009.
doi:10.1093/nar/gkp502
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract RNA: Emiliano P. Ricci, Fabrice Mure, Henri Gruffat, Didier Decimo, Cahora Medina-Palazon, Théophile Ohlmann, and Evelyne Manet
Translation of intronless RNAs is strongly stimulated by the Epstein–Barr virus mRNA export factor EB2
Nucleic Acids Research Advance Access published on June 15, 2009.
doi:10.1093/nar/gkp497
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Computational Biology: K. S. Shavkunov, I. S. Masulis, M. N. Tutukina, A. A. Deev, and O. N. Ozoline
Gains and unexpected lessons from genome-scale promoter mapping
Nucleic Acids Research Advance Access published on June 15, 2009.
doi:10.1093/nar/gkp490
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Computational Biology: Eugene Melamud and John Moult
Structural implication of splicing stochastics
Nucleic Acids Research Advance Access published on June 15, 2009.
doi:10.1093/nar/gkp444
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Methods online: Tobias Mann, Richard Humbert, Michael Dorschner, John Stamatoyannopoulos, and William Stafford Noble
A thermodynamic approach to PCR primer design
Nucleic Acids Research Advance Access originally published on June 15, 2009. This version published June 23, 2009.
doi:10.1093/nar/gkp443
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data] [Supplementary Data]

14 June 2009

Abstract Gene Regulation, Chromatin and Epigenetics: Poornima Bhat-Nakshatri, Guohua Wang, Nikail R. Collins, Michael J. Thomson, Tim R. Geistlinger, Jason S. Carroll, Myles Brown, Scott Hammond, Edward F. Srour, Yunlong Liu, and Harikrishna Nakshatri
Estradiol-regulated microRNAs control estradiol response in breast cancer cells
Nucleic Acids Research Advance Access published on June 14, 2009.
doi:10.1093/nar/gkp500
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract RNA: Craig L. Zirbel, Judit E. Sponer, Jiri Sponer, Jesse Stombaugh, and Neocles B. Leontis
Classification and energetics of the base-phosphate interactions in RNA
Nucleic Acids Research Advance Access published on June 14, 2009.
doi:10.1093/nar/gkp468
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

11 June 2009

Abstract Gene Regulation, Chromatin and Epigenetics: Yuval Mazor and Martin Kupiec
Developmentally regulated MAPK pathways modulate heterochromatin in Saccharomyces cerevisiae
Nucleic Acids Research Advance Access published on June 11, 2009.
doi:10.1093/nar/gkp512
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Gene Regulation, Chromatin and Epigenetics: Feng Jin and Joseph D. Fondell
A novel androgen receptor-binding element modulates Cdc6 transcription in prostate cancer cells during cell-cycle progression
Nucleic Acids Research Advance Access published on June 11, 2009.
doi:10.1093/nar/gkp510
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Gene Regulation, Chromatin and Epigenetics: José F. da Silva Neto, Vânia S. Braz, Valéria C. S. Italiani, and Marilis V. Marques
Fur controls iron homeostasis and oxidative stress defense in the oligotrophic alpha-proteobacterium Caulobacter crescentus
Nucleic Acids Research Advance Access published on June 11, 2009.
doi:10.1093/nar/gkp509
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Gene Regulation, Chromatin and Epigenetics: Ana M. Hernández-Arriaga, Tania S. Rubio-Lepe, Manuel Espinosa, and Gloria del Solar
Repressor CopG prevents access of RNA polymerase to promoter and actively dissociates open complexes
Nucleic Acids Research Advance Access published on June 11, 2009.
doi:10.1093/nar/gkp503
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

10 June 2009

Abstract Nucleic Acid Enzymes: Shigeo Yoshinari, Tomoo Shiba, Daniel-Ken Inaoka, Takashi Itoh, Genji Kurisu, Shigeharu Harada, Kiyoshi Kita, and Yoh-ichi Watanabe
Functional importance of Crenarchaea-specific extra-loop revealed by an X-ray structure of a heterotetrameric crenarchaeal splicing endonuclease
Nucleic Acids Research Advance Access published on June 10, 2009.
doi:10.1093/nar/gkp506
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Methods Online: Nobutaka Nakashima and Tomohiro Tamura
Conditional gene silencing of multiple genes with antisense RNAs and generation of a mutator strain of Escherichia coli
Nucleic Acids Research Advance Access published on June 10, 2009.
doi:10.1093/nar/gkp498
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods Online: Stanislaw K. Jozwiakowski and Bernard A. Connolly
Plasmid-based lacZ ${alpha}$ assay for DNA polymerase fidelity: application to archaeal family-B DNA polymerase
Nucleic Acids Research Advance Access published on June 10, 2009.
doi:10.1093/nar/gkp494
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract RNA: Alessandra Villa, Jens Wöhnert, and Gerhard Stock
Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch
Nucleic Acids Research Advance Access published on June 10, 2009.
doi:10.1093/nar/gkp486
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Nucleic Acid Enzymes: Andrew R. McEwan, Paul A. Rowley, and Margaret C. M. Smith
DNA binding and synapsis by the large C-terminal domain of ${phi}$ C31 integrase
Nucleic Acids Research Advance Access published on June 10, 2009.
doi:10.1093/nar/gkp485
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Methods Online: Jing Lu and Andrew Tsourkas
Imaging individual microRNAs in single mammalian cells in situ
Nucleic Acids Research Advance Access published on June 10, 2009.
doi:10.1093/nar/gkp482
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Chemistry and Synthetic Biology: Gil Tae Hwang, Yoshiyuki Hari, and Floyd E. Romesberg
The effects of unnatural base pairs and mispairs on DNA duplex stability and solvation
Nucleic Acids Research Advance Access published on June 10, 2009.
doi:10.1093/nar/gkp467
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Nucleic Acid Enzymes: Gautam Dhar, Meghan M. McLean, John K. Heiss, and Reid C. Johnson
The Hin recombinase assembles a tetrameric protein swivel that exchanges DNA strands
Nucleic Acids Research Advance Access published on June 10, 2009.
doi:10.1093/nar/gkp466
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract RNA: Stefan Prasch, Marcel Jurk, Robert S. Washburn, Max E. Gottesman, Birgitta M. Wöhrl, and Paul Rösch
RNA-binding specificity of E. coli NusA
Nucleic Acids Research Advance Access published on June 10, 2009.
doi:10.1093/nar/gkp452
[Abstract] [Full Text] [Print PDF] [Screen PDF]

9 June 2009

Abstract Structural Biology: Thirumananseri Kumarevel, Tomoyuki Tanaka, Takashi Umehara, and Shigeyuki Yokoyama
ST1710–DNA complex crystal structure reveals the DNA binding mechanism of the MarR family of regulators
Nucleic Acids Research Advance Access published on June 9, 2009.
doi:10.1093/nar/gkp496
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods Online: Guojun Li, Qin Ma, Haibao Tang, Andrew H. Paterson, and Ying Xu
QUBIC: a qualitative biclustering algorithm for analyses of gene expression data
Nucleic Acids Research Advance Access published on June 9, 2009.
doi:10.1093/nar/gkp491
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods Online: Anders Gunnarsson, Peter Jönsson, Vladimir P. Zhdanov, and Fredrik Höök
Kinetic and thermodynamic characterization of single-mismatch discrimination using single-molecule imaging
Nucleic Acids Research Advance Access published on June 9, 2009.
doi:10.1093/nar/gkp487
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Computational Biology: Alexandre V. Morozov, Karissa Fortney, Daria A. Gaykalova, Vasily M. Studitsky, Jonathan Widom, and Eric D. Siggia
Using DNA mechanics to predict in vitro nucleosome positions and formation energies
Nucleic Acids Research Advance Access published on June 9, 2009.
doi:10.1093/nar/gkp475
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract RNA: Martha E. Christiansen and Brent M. Znosko
Thermodynamic characterization of tandem mismatches found in naturally occurring RNA
Nucleic Acids Research Advance Access published on June 9, 2009.
doi:10.1093/nar/gkp465
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

8 June 2009

Abstract Structural Biology: Stephen A. McMahon, Gareth A. Roberts, Kenneth A. Johnson, Laurie P. Cooper, Huanting Liu, John H. White, Lester G. Carter, Bansi Sanghvi, Muse Oke, Malcolm D. Walkinshaw, Garry W. Blakely, James H. Naismith, and David T. F. Dryden
Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance
Nucleic Acids Research Advance Access published on June 8, 2009.
doi:10.1093/nar/gkp478
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Gene Regulation, Chromatin and Epigenetics: Sajad Hussain Syed, Mathieu Boulard, Manu Shubhdarshan Shukla, Thierry Gautier, Andrew Travers, Jan Bednar, Cendrine Faivre-Moskalenko, Stefan Dimitrov, and Dimitar Angelov
The incorporation of the novel histone variant H2AL2 confers unusual structural and functional properties of the nucleosome
Nucleic Acids Research Advance Access published on June 8, 2009.
doi:10.1093/nar/gkp473
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract RNA: Stefania Millevoi, Adrien Decorsière, Clarisse Loulergue, Jason Iacovoni, Sandra Bernat, Michael Antoniou, and Stéphan Vagner
A physical and functional link between splicing factors promotes pre-mRNA 3' end processing
Nucleic Acids Research Advance Access published on June 8, 2009.
doi:10.1093/nar/gkp470
[Abstract] [Full Text] [Print PDF] [Screen PDF]

5 June 2009

Abstract Gene Regulation, Chromatin and Epigenetics: Mads Heilskov Rasmussen, Bruce Wang, Matthias Wabl, Anders Lade Nielsen, and Finn Skou Pedersen
Activation of alternative Jdp2 promoters and functional protein isoforms in T-cell lymphomas by retroviral insertion mutagenesis
Nucleic Acids Research Advance Access originally published on June 5, 2009. This version published June 15, 2009.
doi:10.1093/nar/gkp469
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Nucleic Acid Enzymes: Félix Romain, Isabelle Barbosa, Jérôme Gouge, François Rougeon, and Marc Delarue
Conferring a template-dependent polymerase activity to terminal deoxynucleotidyltransferase by mutations in the Loop1 region
Nucleic Acids Research Advance Access published on June 5, 2009.
doi:10.1093/nar/gkp460
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Computational Biology: Zeba Wunderlich and Leonid A. Mirny
Using genome-wide measurements for computational prediction of SH2–peptide interactions
Nucleic Acids Research Advance Access published on June 5, 2009.
doi:10.1093/nar/gkp394
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

4 June 2009

Abstract Molecular Biology: Xiaoxiao Cao, Shaohua Li, Liucun Chen, Hongmei Ding, Hua Xu, Yanping Huang, Jie Li, Nongle Liu, Weihong Cao, Yanjun Zhu, Beifen Shen, and Ningsheng Shao
Combining use of a panel of ssDNA aptamers in the detection of Staphylococcus aureus
Nucleic Acids Research Advance Access published on June 4, 2009.
doi:10.1093/nar/gkp489
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

3 June 2009

Abstract Computational Biology: Shrihari Sonavane and Pinak Chakrabarti
Cavities in protein–DNA and protein–RNA interfaces
Nucleic Acids Research Advance Access published on June 3, 2009.
doi:10.1093/nar/gkp488
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods Online: Mark Johnson, Hui Hui Phua, Sophia C. Bennett, Jennifer M. Spence, and Christine J. Farr
Studying vertebrate topoisomerase 2 function using a conditional knockdown system in DT40 cells
Nucleic Acids Research Advance Access published on June 3, 2009.
doi:10.1093/nar/gkp480
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Gene Regulation, Chromatin and Epigenetics: Katherine E. Varley, David G. Mutch, Tina B. Edmonston, Paul J. Goodfellow, and Robi D. Mitra
Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencing
Nucleic Acids Research Advance Access published on June 3, 2009.
doi:10.1093/nar/gkp457
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods Online: Justina Krawczyk, Thomas A. Kohl, Alexander Goesmann, Jörn Kalinowski, and Jan Baumbach
From Corynebacterium glutamicum to Mycobacterium tuberculosis—towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet
Nucleic Acids Research Advance Access published on June 3, 2009.
doi:10.1093/nar/gkp453
[Abstract] [Full Text] [Print PDF] [Screen PDF]

2 June 2009

Abstract Gene Regulation, Chromatin and Epigenetics: Yair Benita, Hirotoshi Kikuchi, Andrew D. Smith, Michael Q. Zhang, Daniel C. Chung, and Ramnik J. Xavier
An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia
Nucleic Acids Research Advance Access published on June 2, 2009.
doi:10.1093/nar/gkp425
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data] [Supplementary Data]

31 May 2009

Abstract Methods Online: Valentina De Riso, Raffaella Raniello, Florian Maumus, Alessandra Rogato, Chris Bowler, and Angela Falciatore
Gene silencing in the marine diatom Phaeodactylum tricornutum
Nucleic Acids Research Advance Access published on May 31, 2009.
doi:10.1093/nar/gkp448
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Structural Biology: Robert A. Forties, Ralf Bundschuh, and Michael G. Poirier
The flexibility of locally melted DNA
Nucleic Acids Research Advance Access published on May 31, 2009.
doi:10.1093/nar/gkp442
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods Online: Andrew J. Bonham, Thorsten Neumann, Matthew Tirrell, and Norbert O. Reich
Tracking transcription factor complexes on DNA using total internal reflectance fluorescence protein binding microarrays
Nucleic Acids Research Advance Access published on May 31, 2009.
doi:10.1093/nar/gkp424
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Genomics: Mark J. Lawson and Liqing Zhang
Sexy gene conversions: locating gene conversions on the X-chromosome
Nucleic Acids Research Advance Access published on May 31, 2009.
doi:10.1093/nar/gkp421
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

29 May 2009

Abstract RNA: Laurence Crombez, May Catherine Morris, Sandrine Dufort, Gudrun Aldrian-Herrada, Quan Nguyen, Gary Mc Master, Jean-Luc Coll, Frederic Heitz, and Gilles Divita
Targeting cyclin B1 through peptide-based delivery of siRNA prevents tumour growth
Nucleic Acids Research Advance Access published on May 29, 2009.
doi:10.1093/nar/gkp451
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Methods Online: Joachim G. Schulz, Guido David, and Bassem A. Hassan
A novel method for tissue-specific RNAi rescue in Drosophila
Nucleic Acids Research Advance Access published on May 29, 2009.
doi:10.1093/nar/gkp450
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Molecular Biology: Charlton Cooper, Jimin Guo, Yi Yan, Shilpa Chooniedass-Kothari, Florent Hube, Mohammad K. Hamedani, Leigh C. Murphy, Yvonne Myal, and Etienne Leygue
Increasing the relative expression of endogenous non-coding Steroid Receptor RNA Activator (SRA) in human breast cancer cells using modified oligonucleotides
Nucleic Acids Research Advance Access published on May 29, 2009.
doi:10.1093/nar/gkp441
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods Online: Ken Daigoro Yokoyama, Uwe Ohler, and Gregory A. Wray
Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships
Nucleic Acids Research Advance Access originally published on May 29, 2009. This version published June 2, 2009.
doi:10.1093/nar/gkp423
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data] [Supplementary Data]

28 May 2009

Abstract Chemistry and Synthetic Biology: Samit Shah, Piyush K. Jain, Ashish Kala, Dipu Karunakaran, and Simon H. Friedman
Light-activated RNA interference using double-stranded siRNA precursors modified using a remarkable regiospecificity of diazo-based photolabile groups
Nucleic Acids Research Advance Access published on May 28, 2009.
doi:10.1093/nar/gkp415
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

27 May 2009

Abstract Methods online: Rubin Cheng, Cuicui Miao, Qianhong Gong, Yuchao Gu, Xinzhi Lu, Feng Han, and Wengong Yu
Specific gene silencing by artificial trans-encoded small noncoding RNAs in bacteria
Nucleic Acids Research Advance Access published on May 27, 2009.
doi:10.1093/nar/gkp447
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods online: Abdullah Ely, Tanusha Naidoo, and Patrick Arbuthnot
Efficient silencing of gene expression with modular trimeric Pol II expression cassettes comprising microRNA shuttles
Nucleic Acids Research Advance Access published on May 27, 2009.
doi:10.1093/nar/gkp446
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Structural Biology: Sarah Sainsbury, Laura A. Lane, Jingshan Ren, Robert J. Gilbert, Nigel J. Saunders, Carol V. Robinson, David I. Stuart, and Raymond J. Owens
The structure of CrgA from Neisseria meningitidis reveals a new octameric assembly state for LysR transcriptional regulators
Nucleic Acids Research Advance Access published on May 27, 2009.
doi:10.1093/nar/gkp445
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Chemistry and Synthetic Biology: Mads E. Hansen, Thomas Bentin, and Peter E. Nielsen
High-affinity triplex targeting of double stranded DNA using chemically modified peptide nucleic acid oligomers
Nucleic Acids Research Advance Access published on May 27, 2009.
doi:10.1093/nar/gkp437
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods online: Lan Lin, Song Liu, Heather Brockway, Junhee Seok, Peng Jiang, Wing Hung Wong, and Yi Xing
Using high-density exon arrays to profile gene expression in closely related species
Nucleic Acids Research Advance Access published on May 27, 2009.
doi:10.1093/nar/gkp420
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Gene Regulation, Chromatin and Epigenetics: Yan Xiao, Siva R. Wigneshweraraj, Robert Weinzierl, Yi-Ping Wang, and Martin Buck
Construction and functional analyses of a comprehensive ${sigma}$ ⁵⁴ site-directed mutant library using alanine–cysteine mutagenesis
Nucleic Acids Research Advance Access published on May 27, 2009.
doi:10.1093/nar/gkp419
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods Online: Sitharthan Kamalakaran, Jude Kendall, Xiaoyue Zhao, Chunlao Tang, Sohail Khan, Kandasamy Ravi, Theresa Auletta, Michael Riggs, Yun Wang, Åslaug Helland, Bjørn Naume, Nevenka Dimitrova, Anne-Lise Børresen-Dale, Jim Hicks, and Robert Lucito
Methylation detection oligonucleotide microarray analysis: a high-resolution method for detection of CpG island methylation
Nucleic Acids Research Advance Access published on May 27, 2009.
doi:10.1093/nar/gkp413
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Nucleic Acid Enzymes: Lingfeng Liu, Yongfeng Li, Dennis Liotta, and Stefan Lutz
Directed evolution of an orthogonal nucleoside analog kinase via fluorescence-activated cell sorting
Nucleic Acids Research Advance Access published on May 27, 2009.
doi:10.1093/nar/gkp400
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Nucleic Acid Enzymes: Anne R. Karow and Dagmar Klostermeier
A conformational change in the helicase core is necessary but not sufficient for RNA unwinding by the DEAD box helicase YxiN
Nucleic Acids Research Advance Access published on May 27, 2009.
doi:10.1093/nar/gkp397
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Nucleic Acid Enzymes: Roger J. Heinze, Luis Giron-Monzon, Alexandra Solovyova, Sarah L. Elliot, Sven Geisler, Claire G. Cupples, Bernard A. Connolly, and Peter Friedhoff
Physical and functional interactions between Escherichia coli MutL and the Vsr repair endonuclease
Nucleic Acids Research Advance Access published on May 27, 2009.
doi:10.1093/nar/gkp380
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Nucleic Acid Enzymes: Martin Samuels, Gaurav Gulati, Jae-Ho Shin, Rejoice Opara, Elizabeth McSweeney, Matt Sekedat, Stephen Long, Zvi Kelman, and David Jeruzalmi
A biochemically active MCM-like helicase in Bacillus cereus
Nucleic Acids Research Advance Access published on May 27, 2009.
doi:10.1093/nar/gkp376
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

25 May 2009

Abstract Genome Integrity, Repair and Replication: Sophie Bellon, Naoya Shikazono, Siobhan Cunniffe, Martine Lomax, and Peter O’Neill
Processing of thymine glycol in a clustered DNA damage site: mutagenic or cytotoxic
Nucleic Acids Research Advance Access published on May 25, 2009.
doi:10.1093/nar/gkp422
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Genome Integrity, Repair and Replication: Junhua Zhao, Aklank Jain, Ravi R. Iyer, Paul L. Modrich, and Karen M. Vasquez
Mismatch repair and nucleotide excision repair proteins cooperate in the recognition of DNA interstrand crosslinks
Nucleic Acids Research Advance Access published on May 25, 2009.
doi:10.1093/nar/gkp399
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Gene Regulation, Chromatin and Epigenetics: Katsushi Yokoyama, Hideki Nogami, Mamiko Kabasawa, Sonomi Ebihara, Ai Shimowasa, Keiko Hashimoto, Tsuyoshi Kawashima, Sanae A. Ishijima, and Masashi Suzuki
The DNA-recognition mode shared by archaeal feast/famine-regulatory proteins revealed by the DNA-binding specificities of TvFL3, FL10, FL11 and Ss-LrpB
Nucleic Acids Research Advance Access published on May 25, 2009.
doi:10.1093/nar/gkp378
[Abstract] [Full Text] [Print PDF] [Screen PDF]

22 May 2009

Abstract Methods Online: Nir Yosef, Martin Kupiec, Eytan Ruppin, and Roded Sharan
A complex-centric view of protein network evolution
Nucleic Acids Research Advance Access published on May 22, 2009.
doi:10.1093/nar/gkp414
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract RNA: Veronica A. Raker, Andrei A. Mironov, Mikhail S. Gelfand, and Dmitri D. Pervouchine
Modulation of alternative splicing by long-range RNA structures in Drosophila
Nucleic Acids Research Advance Access published on May 22, 2009.
doi:10.1093/nar/gkp407
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Gene Regulation, Chromatin and Epigenetics: Mingming Fang, Xiaocen Kong, Ping Li, Fei Fang, Xiaoyan Wu, Hui Bai, Xiaohong Qi, Qi Chen, and Yong Xu
RFXB and its splice variant RFXBSV mediate the antagonism between IFN ${gamma}$ and TGFβ on COL1A2 transcription in vascular smooth muscle cells
Nucleic Acids Research Advance Access published on May 22, 2009.
doi:10.1093/nar/gkp398
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

21 May 2009

Abstract Methods Online: Yaroslav Chushak and Morley O. Stone
In silico selection of RNA aptamers
Nucleic Acids Research Advance Access published on May 21, 2009.
doi:10.1093/nar/gkp408
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Genome Integrity, Repair and Replication: Daman Kumari, Valentina Somma, Asako J. Nakamura, William M. Bonner, Ettoré D’Ambrosio, and Karen Usdin
The role of DNA damage response pathways in chromosome fragility in Fragile X syndrome
Nucleic Acids Research Advance Access published on May 21, 2009.
doi:10.1093/nar/gkp391
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Genome Integrity, Repair and Replication: Heike Summer, Ou Li, Qiuye Bao, Lihong Zhan, Sabrina Peter, Padmapriya Sathiyanathan, Dana Henderson, Thomas Klonisch, Steven D. Goodman, and Peter Dröge
HMGA2 exhibits dRP/AP site cleavage activity and protects cancer cells from DNA-damage-induced cytotoxicity during chemotherapy
Nucleic Acids Research Advance Access published on May 21, 2009.
doi:10.1093/nar/gkp375
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data] [Supplementary Data]

Abstract Genome Integrity, Repair and Replication: Ivan V. Rosado, Wojciech Niedzwiedz, Arno F. Alpi, and Ketan J. Patel
The Walker B motif in avian FANCM is required to limit sister chromatid exchanges but is dispensable for DNA crosslink repair
Nucleic Acids Research Advance Access published on May 21, 2009.
doi:10.1093/nar/gkp365
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Structural Biology: Doyoun Kim, Sanjith Reddy, Dong Young Kim, Alexander Rich, Sangho Lee, Kyeong Kyu Kim, and Yang-Gyun Kim
Base extrusion is found at helical junctions between right- and left-handed forms of DNA and RNA
Nucleic Acids Research Advance Access published on May 21, 2009.
doi:10.1093/nar/gkp364
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Gene Regulation, Chromatin and Epigenetics: Gabriel Leprivier, David Baillat, Agnès Begue, Brigitte Hartmann, and Marc Aumercier
Ets-1 p51 and p42 isoforms differentially modulate Stromelysin-1 promoter according to induced DNA bend orientation
Nucleic Acids Research Advance Access published on May 21, 2009.
doi:10.1093/nar/gkp307
[Abstract] [Full Text] [Print PDF] [Screen PDF]

20 May 2009

Abstract Gene Regulation, Chromatin and Epigenetics: Hehuang Xie, Min Wang, Maria de F. Bonaldo, Christina Smith, Veena Rajaram, Stewart Goldman, Tadanori Tomita, and Marcelo B. Soares
High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum
Nucleic Acids Research Advance Access published on May 20, 2009.
doi:10.1093/nar/gkp393
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

19 May 2009

Abstract Methods Online: Francesca Malentacchi, Giulia Forni, Serena Vinci, and Claudio Orlando
Quantitative evaluation of DNA methylation by optimization of a differential-high resolution melt analysis protocol
Nucleic Acids Research Advance Access published on May 19, 2009.
doi:10.1093/nar/gkp383
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Molecular Biology: Anne E. McBride, Ana K. Conboy, Shanique P. Brown, Chaiyaboot Ariyachet, and Kate L. Rutledge
Specific sequences within arginine–glycine-rich domains affect mRNA-binding protein function
Nucleic Acids Research Advance Access published on May 19, 2009.
doi:10.1093/nar/gkp349
[Abstract] [Full Text] [Print PDF] [Screen PDF]

18 May 2009

Abstract Gene Regulation, Chromatin and Epigenetics: Belén Gómez-González and Andrés Aguilera
R-loops do not accumulate in transcription-defective hpr1-101 mutants: implications for the functional role of THO/TREX
Nucleic Acids Research Advance Access published on May 18, 2009.
doi:10.1093/nar/gkp385
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods Online: Adam Ameur, Alvaro Rada-Iglesias, Jan Komorowski, and Claes Wadelius
Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP
Nucleic Acids Research Advance Access published on May 18, 2009.
doi:10.1093/nar/gkp381
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data] [Supplementary Data]

Abstract Genomics: Zheng Li, Min Liu, Li Zhang, Wenxia Zhang, Ge Gao, Zuoyan Zhu, Liping Wei, Qichang Fan, and Manyuan Long
Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster
Nucleic Acids Research Advance Access published on May 18, 2009.
doi:10.1093/nar/gkp334
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

15 May 2009

Abstract Molecular Biology: Yuichi Morozumi, Yoshimasa Takizawa, Motoki Takaku, and Hitoshi Kurumizaka
Human PSF binds to RAD51 and modulates its homologous-pairing and strand-exchange activities
Nucleic Acids Research Advance Access published on May 15, 2009.
doi:10.1093/nar/gkp298
[Abstract] [Full Text] [Print PDF] [Screen PDF]

14 May 2009

Abstract Genome Integrity, Repair and Replication: Anna Valenti, Giuseppe Perugino, Takehiko Nohmi, Mosè Rossi, and Maria Ciaramella
Inhibition of translesion DNA polymerase by archaeal reverse gyrase
Nucleic Acids Research Advance Access published on May 14, 2009.
doi:10.1093/nar/gkp386
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods Online: Engin Gürlevik, Norman Woller, Peter Schache, Nisar P. Malek, Thomas C. Wirth, Lars Zender, Michael P. Manns, Stefan Kubicka, and Florian Kühnel
p53-dependent antiviral RNA-interference facilitates tumor-selective viral replication
Nucleic Acids Research Advance Access published on May 14, 2009.
doi:10.1093/nar/gkp374
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract RNA: Young-Hwa Goo and Thomas A. Cooper
CUGBP2 directly interacts with U2 17S snRNP components and promotes U2 snRNA binding to cardiac troponin T pre-mRNA
Nucleic Acids Research Advance Access published on May 14, 2009.
doi:10.1093/nar/gkp346
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

13 May 2009

Abstract Nucleic Acid Enzymes: María Isabel Ponferrada-Marín, Teresa Roldán-Arjona, and Rafael R. Ariza
ROS1 5-methylcytosine DNA glycosylase is a slow-turnover catalyst that initiates DNA demethylation in a distributive fashion
Nucleic Acids Research Advance Access published on May 13, 2009.
doi:10.1093/nar/gkp390
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Abstract Molecular Biology: Bingsen Xu and Yingqun Huang
Histone H2a mRNA interacts with Lin28 and contains a Lin28-dependent posttranscriptional regulatory element
Nucleic Acids Research Advance Access published on May 13, 2009.
doi:10.1093/nar/gkp372
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Abstract Genome Integrity, Repair and Replication: Peter Burkovics, Ildikó Hajdú, Valéria Szukacsov, Ildiko Unk, and Lajos Haracska
Role of PCNA-dependent stimulation of 3'-phosphodiesterase and 3'–5' exonuclease activities of human Ape2 in repair of oxidative DNA damage
Nucleic Acids Research Advance Access published on May 13, 2009.
doi:10.1093/nar/gkp357
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Abstract Gene Regulation, Chromatin and Epigenetics: Ganit Yarden, Rofa Elfakess, Kfir Gazit, and Rivka Dikstein
Characterization of sINR, a strict version of the Initiator core promoter element
Nucleic Acids Research Advance Access published on May 13, 2009.
doi:10.1093/nar/gkp315
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12 May 2009