Nucleic Acids Research

Survey and Summary

Get checked abstract Hinanit Koltai and Carmiya Weingarten-Baror

Specificity of DNA microarray hybridization: characterization, effectors and approaches for data correction
Nucleic Acids Research Advance Access published on February 24, 2008
Nucl. Acids Res. 2008 36: 2395-2405; doi:10.1093/nar/gkn087 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Computational Biology

Get checked abstract Lutz Krause, Naryttza N. Diaz, Alexander Goesmann, Scott Kelley, Tim W. Nattkemper, Forest Rohwer, Robert A. Edwards, and Jens Stoye

Phylogenetic classification of short environmental DNA fragments
Nucleic Acids Research Advance Access published on February 19, 2008
Nucl. Acids Res. 2008 36: 2230-2239; doi:10.1093/nar/gkn038 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Ruslan I. Sadreyev and Nick V. Grishin

Accurate statistical model of comparison between multiple sequence alignments
Nucleic Acids Research Advance Access published on February 19, 2008
Nucl. Acids Res. 2008 36: 2240-2248; doi:10.1093/nar/gkn065 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jeremy Curuksu, Krystyna Zakrzewska, and Martin Zacharias

Magnitude and direction of DNA bending induced by screw-axis orientation: influence of sequence, mismatches and abasic sites
Nucleic Acids Research Advance Access published on February 20, 2008
Nucl. Acids Res. 2008 36: 2268-2283; doi:10.1093/nar/gkm1135 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Surya Saha, Susan Bridges, Zenaida V. Magbanua, and Daniel G. Peterson

Empirical comparison of ab initio repeat finding programs
Nucleic Acids Research Advance Access published on February 20, 2008
Nucl. Acids Res. 2008 36: 2284-2294; doi:10.1093/nar/gkn064 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jimin Pei, Bong-Hyun Kim, and Nick V. Grishin

PROMALS3D: a tool for multiple protein sequence and structure alignments
Nucleic Acids Research Advance Access published on February 20, 2008
Nucl. Acids Res. 2008 36: 2295-2300; doi:10.1093/nar/gkn072 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Arif Ozgun Harmanci, Gaurav Sharma, and David H. Mathews

PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction
Nucleic Acids Research Advance Access published on February 26, 2008
Nucl. Acids Res. 2008 36: 2406-2417; doi:10.1093/nar/gkn043 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Francesca Demichelis, Heidi Greulich, Jill A. Macoska, Rameen Beroukhim, William R. Sellers, Levi Garraway, and Mark A. Rubin

SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines
Nucleic Acids Research Advance Access published on February 27, 2008
Nucl. Acids Res. 2008 36: 2446-2456; doi:10.1093/nar/gkn089 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genomics

Get checked abstract Stephan Greiner, Xi Wang, Uwe Rauwolf, Martina V. Silber, Klaus Mayer, Jörg Meurer, Georg Haberer, and Reinhold G. Herrmann

The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera, subsection Oenothera: I. Sequence evaluation and plastome evolution
Nucleic Acids Research Advance Access published on February 24, 2008
Nucl. Acids Res. 2008 36: 2366-2378; doi:10.1093/nar/gkn081 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology

Get checked abstract Prabhat Kumar Purbey, Sunita Singh, P. Pavan Kumar, Sameet Mehta, K. N. Ganesh, Debashis Mitra, and Sanjeev Galande

PDZ domain-mediated dimerization and homeodomain-directed specificity are required for high-affinity DNA binding by SATB1
Nucleic Acids Research Advance Access published on January 10, 2008
Nucl. Acids Res. 2008 36: 2107-2122; doi:10.1093/nar/gkm1151 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jeffrey M. Chen, Huiping Ren, James E. Shaw, Yu Jing Wang, Ming Li, Andrea S. Leung, Vanessa Tran, Nicolas M. Berbenetz, Dana Kocíncová, Christopher M. Yip, Jean-Marc Reyrat, and Jun Liu

Lsr2 of Mycobacterium tuberculosis is a DNA-bridging protein
Nucleic Acids Research Advance Access published on January 10, 2008
Nucl. Acids Res. 2008 36: 2123-2135; doi:10.1093/nar/gkm1162 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Brian S. Plosky, Ekaterina G. Frank, David A. Berry, Graham P. Vennall, John P. McDonald, and Roger Woodgate

Eukaryotic Y-family polymerases bypass a 3-methyl-2'-deoxyadenosine analog in vitro and methyl methanesulfonate-induced DNA damage in vivo
Nucleic Acids Research Advance Access published on February 14, 2008
Nucl. Acids Res. 2008 36: 2152-2162; doi:10.1093/nar/gkn058 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Zachary F. Pursell, J. Tyson McDonald, Christopher K. Mathews, and Thomas A. Kunkel

Trace amounts of 8-oxo-dGTP in mitochondrial dNTP pools reduce DNA polymerase replication fidelity
Nucleic Acids Research Advance Access published on February 14, 2008
Nucl. Acids Res. 2008 36: 2174-2181; doi:10.1093/nar/gkn062 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Koji Tsumagari, Lixin Qi, Kesmic Jackson, Chunbo Shao, Michelle Lacey, Janet Sowden, Rabi Tawil, Vettaikorumakankav Vedanarayanan, and Melanie Ehrlich

Epigenetics of a tandem DNA repeat: chromatin DNaseI sensitivity and opposite methylation changes in cancers
Nucleic Acids Research Advance Access published on February 16, 2008
Nucl. Acids Res. 2008 36: 2196-2207; doi:10.1093/nar/gkn055 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Hiroaki Tachiwana, Akihisa Osakabe, Hiroshi Kimura, and Hitoshi Kurumizaka

Nucleosome formation with the testis-specific histone H3 variant, H3t, by human nucleosome assembly proteins in vitro
Nucleic Acids Research Advance Access published on February 16, 2008
Nucl. Acids Res. 2008 36: 2208-2218; doi:10.1093/nar/gkn060 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Brian J. Krueger, Célia Jeronimo, Bibhuti Bhusan Roy, Annie Bouchard, Charlotte Barrandon, Sarah A. Byers, Courtney E. Searcey, Jeffrey J. Cooper, Olivier Bensaude, Éric A. Cohen, Benoit Coulombe, and David H. Price

LARP7 is a stable component of the 7SK snRNP while P-TEFb, HEXIM1 and hnRNP A1 are reversibly associated
Nucleic Acids Research Advance Access published on February 16, 2008
Nucl. Acids Res. 2008 36: 2219-2229; doi:10.1093/nar/gkn061 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Fátima Gasset-Rosa, María Jesús Maté, Cristina Dávila-Fajardo, Jerónimo Bravo, and Rafael Giraldo

Binding of sulphonated indigo derivatives to RepA-WH1 inhibits DNA-induced protein amyloidogenesis
Nucleic Acids Research Advance Access published on February 19, 2008
Nucl. Acids Res. 2008 36: 2249-2256; doi:10.1093/nar/gkn067 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Laurent Houzet, Zakia Morichaud, Ludovic Didierlaurent, Delphine Muriaux, Jean-Luc Darlix, and Marylène Mougel

Nucleocapsid mutations turn HIV-1 into a DNA-containing virus
Nucleic Acids Research Advance Access published on February 22, 2008
Nucl. Acids Res. 2008 36: 2311-2319; doi:10.1093/nar/gkn069 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Adam Williams, Nicola Harker, Eleni Ktistaki, Henrique Veiga-Fernandes, Kathleen Roderick, Mauro Tolaini, Trisha Norton, Keith Williams, and Dimitris Kioussis

Position effect variegation and imprinting of transgenes in lymphocytes
Nucleic Acids Research Advance Access published on February 22, 2008
Nucl. Acids Res. 2008 36: 2320-2329; doi:10.1093/nar/gkn085 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Nicolas Viphakone, Florence Voisinet-Hakil, and Lionel Minvielle-Sebastia

Molecular dissection of mRNA poly(A) tail length control in yeast
Nucleic Acids Research Advance Access published on February 26, 2008
Nucl. Acids Res. 2008 36: 2418-2433; doi:10.1093/nar/gkn080 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Amandine Bastide, Zeineb Karaa, Stéphanie Bornes, Corinne Hieblot, Eric Lacazette, Hervé Prats, and Christian Touriol

An upstream open reading frame within an IRES controls expression of a specific VEGF-A isoform
Nucleic Acids Research Advance Access published on February 26, 2008
Nucl. Acids Res. 2008 36: 2434-2445; doi:10.1093/nar/gkn093 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes

Get checked abstract Emmanuel Fajardo-Sanchez, François Stricher, Frédéric Pâques, Mark Isalan, and Luis Serrano

Computer design of obligate heterodimer meganucleases allows efficient cutting of custom DNA sequences
Nucleic Acids Research Advance Access published on February 14, 2008
Nucl. Acids Res. 2008 36: 2163-2173; doi:10.1093/nar/gkn059 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Kirk Tevebaugh Ehmsen and Wolf-Dietrich Heyer

Saccharomyces cerevisiae Mus81-Mms4 is a catalytic, DNA structure-selective endonuclease
Nucleic Acids Research Advance Access published on February 16, 2008
Nucl. Acids Res. 2008 36: 2182-2195; doi:10.1093/nar/gkm1152 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Daniel A. Koster, Fabian Czerwinski, Ludovic Halby, Aurélien Crut, Pierre Vekhoff, Komaraiah Palle, Paola B. Arimondo, and Nynke H. Dekker

Single-molecule observations of topotecan-mediated TopIB activity at a unique DNA sequence
Nucleic Acids Research Advance Access published on February 21, 2008
Nucl. Acids Res. 2008 36: 2301-2310; doi:10.1093/nar/gkn035 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

RNA

Get checked abstract Kumiko Ui-Tei, Yuki Naito, Shuhei Zenno, Kenji Nishi, Kenji Yamato, Fumitaka Takahashi, Aya Juni, and Kaoru Saigo

Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect
Nucleic Acids Research Advance Access published on February 11, 2008
Nucl. Acids Res. 2008 36: 2136-2151; doi:10.1093/nar/gkn042 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Kaiping Gao, Akio Masuda, Tohru Matsuura, and Kinji Ohno

Human branch point consensus sequence is yUnAy
Nucleic Acids Research Advance Access published on February 19, 2008
Nucl. Acids Res. 2008 36: 2257-2267; doi:10.1093/nar/gkn073 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Mirko Cevec, Christophe Thibaudeau, and Janez Plavec

Solution structure of a let-7 miRNA:lin-41 mRNA complex from C. elegans
Nucleic Acids Research Advance Access published on February 22, 2008
Nucl. Acids Res. 2008 36: 2330-2337; doi:10.1093/nar/gkn088 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Xabi Abad, Maria Vera, Stephen P. Jung, Evelyn Oswald, Inés Romero, Vaibhav Amin, Puri Fortes, and Samuel I. Gunderson

Requirements for gene silencing mediated by U1 snRNA binding to a target sequence
Nucleic Acids Research Advance Access published on February 24, 2008
Nucl. Acids Res. 2008 36: 2338-2352; doi:10.1093/nar/gkn068 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Dominique L. Ouellet, Isabelle Plante, Patricia Landry, Corinne Barat, Marie-Ève Janelle, Louis Flamand, Michel J. Tremblay, and Patrick Provost

Identification of functional microRNAs released through asymmetrical processing of HIV-1 TAR element
Nucleic Acids Research Advance Access published on February 24, 2008
Nucl. Acids Res. 2008 36: 2353-2365; doi:10.1093/nar/gkn076 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Structural Biology

Get checked abstract Alberto Pérez, Filip Lankas, F. Javier Luque, and Modesto Orozco

Towards a molecular dynamics consensus view of B-DNA flexibility
Nucleic Acids Research Advance Access published on February 24, 2008
Nucl. Acids Res. 2008 36: 2379-2394; doi:10.1093/nar/gkn082 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Corrigendum

Brian Saunders, Stephen Lyon, Matthew Day, Brenda Riley, Emily Chenette, and Shankar Subramaniam

The Molecule Pages Database
Nucl. Acids Res. 2008 36: 2457; doi:10.1093/nar/gkn139 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online

Get checked abstract Jan Gründemann, Falk Schlaudraff, Olga Haeckel, and Birgit Liss

Elevated -synuclein mRNA levels in individual UV-laser-microdissected dopaminergic substantia nigra neurons in idiopathic Parkinson's disease
Nucleic Acids Research Advance Access published on March 10, 2008
Nucl. Acids Res. 2008 36: e38; doi:10.1093/nar/gkn084 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Christine Fuhrmann, Oleg Schmidt-Kittler, Nikolas H. Stoecklein, Karina Petat-Dutter, Christian Vay, Kerstin Bockler, Richard Reinhardt, Thomas Ragg, and Christoph A. Klein

High-resolution array comparative genomic hybridization of single micrometastatic tumor cells
Nucleic Acids Research Advance Access published on March 15, 2008
Nucl. Acids Res. 2008 36: e39; doi:10.1093/nar/gkn101 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Heiko Kuhn and Maxim D. Frank-Kamenetskii

Labeling of unique sequences in double-stranded DNA at sites of vicinal nicks generated by nicking endonucleases
Nucleic Acids Research Advance Access published on March 15, 2008
Nucl. Acids Res. 2008 36: e40; doi:10.1093/nar/gkn107 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Patrick Cahan, Laura E. Godfrey, Peggy S. Eis, Todd A. Richmond, Rebecca R. Selzer, Michael Brent, Howard L. McLeod, Timothy J. Ley, and Timothy A. Graubert

wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data
Nucleic Acids Research Advance Access published on March 11, 2008
Nucl. Acids Res. 2008 36: e41; doi:10.1093/nar/gkn110 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Lasse S. Kristensen, Thomas Mikeska, Michael Krypuy, and Alexander Dobrovic

Sensitive Melting Analysis after Real Time- Methylation Specific PCR (SMART-MSP): high-throughput and probe-free quantitative DNA methylation detection
Nucleic Acids Research Advance Access published on March 15, 2008
Nucl. Acids Res. 2008 36: e42; doi:10.1093/nar/gkn113 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Katleen De Preter, Roland Barriot, Frank Speleman, Jo Vandesompele, and Yves Moreau

Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions
Nucleic Acids Research Advance Access published on March 16, 2008
Nucl. Acids Res. 2008 36: e43; doi:10.1093/nar/gkn114 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Alexandra Kukat, Christian Kukat, Jan Brocher, Ingo Schäfer, Georg Krohne, Ian A. Trounce, Gaetano Villani, and Peter Seibel

Generation of ⁰ cells utilizing a mitochondrially targeted restriction endonuclease and comparative analyses
Nucleic Acids Research Advance Access published on March 19, 2008
Nucl. Acids Res. 2008 36: e44; doi:10.1093/nar/gkn124 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

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