Nucleic Acids Research

Computational Biology:

Jian-Hua Yang, Xiao-Chen Zhang, Zhan-Peng Huang, Hui Zhou, Mian-Bo Huang, Shu Zhang, Yue-Qin Chen, and Liang-Hu Qu

snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome
Nucleic Acids Research Advance Access published on September 20, 2006
Nucl. Acids Res. 2006 34: 5112-5123; doi:10.1093/nar/gkl672 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Samiul Hasan and Mark Schreiber

Recovering motifs from biased genomes: application of signal correction
Nucleic Acids Research Advance Access published on September 20, 2006
Nucl. Acids Res. 2006 34: 5124-5132; doi:10.1093/nar/gkl676 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Andrew F. Neuwald

Hypothesis: bacterial clamp loader ATPase activation through DNA-dependent repositioning of the catalytic base and of a trans-acting catalytic threonine
Nucleic Acids Research Advance Access published on September 29, 2006
Nucl. Acids Res. 2006 34: 5280-5290; doi:10.1093/nar/gkl519 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Anthony P. Malanoski, Baochuan Lin, Zheng Wang, Joel M. Schnur, and David A. Stenger

Automated identification of multiple micro-organisms from resequencing DNA microarrays
Nucleic Acids Research Advance Access published on September 29, 2006
Nucl. Acids Res. 2006 34: 5300-5311; doi:10.1093/nar/gkl565 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Genomics:

Nicole C. Hauser, Rafael Martinez, Anette Jacob, Steffen Rupp, Jörg D. Hoheisel, and Stefan Matysiak

Utilising the left-helical conformation of L-DNA for analysing different marker types on a single universal microarray platform
Nucleic Acids Research Advance Access published on September 20, 2006
Nucl. Acids Res. 2006 34: 5101-5111; doi:10.1093/nar/gkl671 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Magnus Alm Rosenblad, Marcela Dávila López, Paul Piccinelli, and Tore Samuelsson

Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes
Nucleic Acids Research Advance Access published on September 22, 2006
Nucl. Acids Res. 2006 34: 5145-5156; doi:10.1093/nar/gkl626 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Céline Loot, Néstor Santiago, Alicia Sanz, and Josep M. Casacuberta

The proteins encoded by the pogo-like Lemi1 element bind the TIRs and subterminal repeated motifs of the Arabidopsis Emigrant MITE: consequences for the transposition mechanism of MITEs
Nucleic Acids Research Advance Access published on September 26, 2006
Nucl. Acids Res. 2006 34: 5238-5246; doi:10.1093/nar/gkl688 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Molecular Biology:

Nikolaus Deigendesch, Friedrich Koch-Nolte, and Stefan Rothenburg

ZBP1 subcellular localization and association with stress granules is controlled by its Z-DNA binding domains
Nucleic Acids Research Advance Access published on September 20, 2006
Nucl. Acids Res. 2006 34: 5007-5020; doi:10.1093/nar/gkl575 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Young-Ho Lee and Michael R. Stallcup

Interplay of Fli-I and FLAP1 for regulation of ß-catenin dependent transcription
Nucleic Acids Research Advance Access published on September 20, 2006
Nucl. Acids Res. 2006 34: 5052-5059; doi:10.1093/nar/gkl652 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Silvia Smaldone and Francesco Ramirez

Multiple pathways regulate intracellular shuttling of MoKA, a co-activator of transcription factor KLF7
Nucleic Acids Research Advance Access published on September 20, 2006
Nucl. Acids Res. 2006 34: 5060-5068; doi:10.1093/nar/gkl659 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yung-Tsi Bolon and Anja-Katrin Bielinsky

The spatial arrangement of ORC binding modules determines the functionality of replication origins in budding yeast
Nucleic Acids Research Advance Access published on September 19, 2006
Nucl. Acids Res. 2006 34: 5069-5080; doi:10.1093/nar/gkl661 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Oleg V. Kovalenko, Claudia Wiese, and David Schild

RAD51AP2, a novel vertebrate- and meiotic-specific protein, shares a conserved RAD51-interacting C-terminal domain with RAD51AP1/PIR51
Nucleic Acids Research Advance Access published on September 20, 2006
Nucl. Acids Res. 2006 34: 5081-5092; doi:10.1093/nar/gkl665 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Christophe Marchand, Krzysztof Krajewski, Hsiu-Fang Lee, Smitha Antony, Allison A. Johnson, Ronak Amin, Peter Roller, Mamuka Kvaratskhelia, and Yves Pommier

Covalent binding of the natural antimicrobial peptide indolicidin to DNA abasic sites
Nucleic Acids Research Advance Access published on September 22, 2006
Nucl. Acids Res. 2006 34: 5157-5165; doi:10.1093/nar/gkl667 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Dominique A. Glauser and Werner Schlegel

Mechanisms of transcriptional regulation underlying temporal integration of signals
Nucleic Acids Research Advance Access published on September 22, 2006
Nucl. Acids Res. 2006 34: 5175-5183; doi:10.1093/nar/gkl654 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Heather A. Baird, Román Galetto, Yong Gao, Etienne Simon-Loriere, Measho Abreha, John Archer, Jun Fan, David L. Robertson, Eric J. Arts, and Matteo Negroni

Sequence determinants of breakpoint location during HIV-1 intersubtype recombination
Nucleic Acids Research Advance Access published on September 26, 2006
Nucl. Acids Res. 2006 34: 5203-5216; doi:10.1093/nar/gkl669 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Marthe-Sandrine Eiymo Mwa Mpollo, Mélissa Beaudoin, Patricia E. Berg, Hugues Beauchemin, Vivette D'Agati, and Marie Trudel

BP1 is a negative modulator of definitive erythropoiesis
Nucleic Acids Research Advance Access published on September 26, 2006
Nucl. Acids Res. 2006 34: 5232-5237; doi:10.1093/nar/gkl680 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Charikleia Ioannou, Patrick M. Schaeffer, Nicholas E. Dixon, and Panos Soultanas

Helicase binding to DnaI exposes a cryptic DNA-binding site during helicase loading in Bacillus subtilis
Nucleic Acids Research Advance Access published on September 26, 2006
Nucl. Acids Res. 2006 34: 5247-5258; doi:10.1093/nar/gkl690 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Swetha Bolusani, Chien-Hui Ma, Andrew Paek, Jay H. Konieczka, Makkuni Jayaram, and Yuri Voziyanov

Evolution of variants of yeast site-specific recombinase Flp that utilize native genomic sequences as recombination target sites
Nucleic Acids Research Advance Access published on September 26, 2006
Nucl. Acids Res. 2006 34: 5259-5269; doi:10.1093/nar/gkl548 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Laura Manelyte, Claus Urbanke, Luis Giron-Monzon, and Peter Friedhoff

Structural and functional analysis of the MutS C-terminal tetramerization domain
Nucleic Acids Research Advance Access published on September 29, 2006
Nucl. Acids Res. 2006 34: 5270-5279; doi:10.1093/nar/gkl489 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Matthew Mayho, Katelyn Fenn, Paul Craddy, Susan Crosthwaite, and Keith Matthews

Post-transcriptional control of nuclear-encoded cytochrome oxidase subunits in Trypanosoma brucei: evidence for genome-wide conservation of life-cycle stage-specific regulatory elements
Nucleic Acids Research Advance Access published on September 29, 2006
Nucl. Acids Res. 2006 34: 5312-5324; doi:10.1093/nar/gkl598 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Stephanie Glanz, Astrid Bunse, Andrea Wimbert, Carsten Balczun, and Ulrich Kück

A nucleosome assembly protein-like polypeptide binds to chloroplast group II intron RNA in Chlamydomonas reinhardtii
Nucleic Acids Research Advance Access published on September 29, 2006
Nucl. Acids Res. 2006 34: 5337-5351; doi:10.1093/nar/gkl611 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acid Enzymes:

Dror Sagi, Tsvi Tlusty, and Joel Stavans

High fidelity of RecA-catalyzed recombination: a watchdog of genetic diversity
Nucleic Acids Research Advance Access published on September 20, 2006
Nucl. Acids Res. 2006 34: 5021-5031; doi:10.1093/nar/gkl586 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Paola Fiorani, Giovanni Chillemi, Carmen Losasso, Silvia Castelli, and Alessandro Desideri

The different cleavage DNA sequence specificity explains the camptothecin resistance of the human topoisomerase I Glu418Lys mutant
Nucleic Acids Research Advance Access published on September 20, 2006
Nucl. Acids Res. 2006 34: 5093-5100; doi:10.1093/nar/gkl670 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Bryony T. I. Payne, Ingeborg C. van Knippenberg, Hazel Bell, Sergio R. Filipe, David J. Sherratt, and Peter McGlynn

Replication fork blockage by transcription factor-DNA complexes in Escherichia coli
Nucleic Acids Research Advance Access published on September 25, 2006
Nucl. Acids Res. 2006 34: 5194-5202; doi:10.1093/nar/gkl682 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Radhakrishnan Kanagaraj, Nurten Saydam, Patrick L. Garcia, Lu Zheng, and Pavel Janscak

Human RECQ5ß helicase promotes strand exchange on synthetic DNA structures resembling a stalled replication fork
Nucleic Acids Research Advance Access published on September 26, 2006
Nucl. Acids Res. 2006 34: 5217-5231; doi:10.1093/nar/gkl677 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material][Supplementary Material] [Request Permissions]  

Jens Georg, Lars Schomacher, James P. J. Chong, Alan I. Majerník, Monika Raabe, Henning Urlaub, Sabine Müller, Elena Ciirdaeva, Wilfried Kramer, and Hans-Joachim Fritz

The Methanothermobacter thermautotrophicus ExoIII homologue Mth212 is a DNA uridine endonuclease
Nucleic Acids Research Advance Access published on September 29, 2006
Nucl. Acids Res. 2006 34: 5325-5336; doi:10.1093/nar/gkl604 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

RNA:

Sergey Amontov and Andres Jäschke

Controlling the rate of organic reactions: rational design of allosteric Diels-Alderase ribozymes
Nucleic Acids Research Advance Access published on September 20, 2006
Nucl. Acids Res. 2006 34: 5032-5038; doi:10.1093/nar/gkl613 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

John W. Hardin and Robert T. Batey

The bipartite architecture of the sRNA in an archaeal box C/D complex is a primary determinant of specificity
Nucleic Acids Research Advance Access published on September 19, 2006
Nucl. Acids Res. 2006 34: 5039-5051; doi:10.1093/nar/gkl644 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Weizhong Wang, Jung W. Park, John L. Wang, and Ronald J. Patterson

Immunoprecipitation of spliceosomal RNAs by antisera to galectin-1 and galectin-3
Nucleic Acids Research Advance Access published on September 22, 2006
Nucl. Acids Res. 2006 34: 5166-5174; doi:10.1093/nar/gkl673 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Masashi Arita, Takuma Suematsu, Arihiro Osanai, Takashi Inaba, Haruo Kamiya, Kiyoshi Kita, Masahiko Sisido, Yoh-ichi Watanabe, and Takashi Ohtsuki

An evolutionary ‘intermediate state’ of mitochondrial translation systems found in Trichinella species of parasitic nematodes: co-evolution of tRNA and EF-Tu
Nucleic Acids Research Advance Access published on September 29, 2006
Nucl. Acids Res. 2006 34: 5291-5299; doi:10.1093/nar/gkl526 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Structural Biology:

Jixun Dai, Ding Chen, Roger A. Jones, Laurence H. Hurley, and Danzhou Yang

NMR solution structure of the major G-quadruplex structure formed in the human BCL2 promoter region
Nucleic Acids Research Advance Access published on September 22, 2006
Nucl. Acids Res. 2006 34: 5133-5144; doi:10.1093/nar/gkl610 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Yusuke Nomura, Masaki Kajikawa, Seiki Baba, Shinta Nakazato, Takayuki Imai, Taiichi Sakamoto, Norihiro Okada, and Gota Kawai

Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2
Nucleic Acids Research Advance Access published on September 25, 2006
Nucl. Acids Res. 2006 34: 5184-5193; doi:10.1093/nar/gkl664 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Corrigendum:

Corrigendum
Nucl. Acids Res. 2006 34: 5352; doi:10.1093/nar/gkl759 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Siu-Wai Yeung, Thomas Ming-Hung Lee, Hong Cai, and I-Ming Hsing

A DNA biochip for on-the-spot multiplexed pathogen identification
Nucleic Acids Research Advance Access published on September 25, 2006
Nucl. Acids Res. 2006 34: e118; doi:10.1093/nar/gkl702 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alexey Epanchintsev, Peter Jung, Antje Menssen, and Heiko Hermeking

Inducible microRNA expression by an all-in-one episomal vector system
Nucleic Acids Research Advance Access published on September 22, 2006
Nucl. Acids Res. 2006 34: e119; doi:10.1093/nar/gkl624 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Philipp Koch, Henrike Siemen, Andrea Biegler, Joseph Itskovitz-Eldor, and Oliver Brüstle

Transduction of human embryonic stem cells by ecotropic retroviral vectors
Nucleic Acids Research Advance Access published on September 22, 2006
Nucl. Acids Res. 2006 34: e120; doi:10.1093/nar/gkl674 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

C. H. Cannon, C. S. Kua, E. K. Lobenhofer, and P. Hurban

Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform
Nucleic Acids Research Advance Access published on September 25, 2006
Nucl. Acids Res. 2006 34: e121; doi:10.1093/nar/gkl478 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Hussam H. Nour-Eldin, Bjarne G. Hansen, Morten H. H. Nørholm, Jacob K. Jensen, and Barbara A. Halkier

Advancing uracil-excision based cloning towards an ideal technique for cloning PCR fragments
Nucleic Acids Research Advance Access published on September 25, 2006
Nucl. Acids Res. 2006 34: e122; doi:10.1093/nar/gkl635 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tom Morrison, James Hurley, Javier Garcia, Karl Yoder, Arrin Katz, Douglas Roberts, Jamie Cho, Tanya Kanigan, Sergey E. Ilyin, Daniel Horowitz, James M. Dixon, and Colin J.H. Brenan

Nanoliter high throughput quantitative PCR
Nucleic Acids Research Advance Access published on September 25, 2006
Nucl. Acids Res. 2006 34: e123; doi:10.1093/nar/gkl639 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Matti Kankainen, Günter Brader, Petri Törönen, E. Tapio Palva, and Liisa Holm

Identifying functional gene sets from hierarchically clustered expression data: map of abiotic stress regulated genes in Arabidopsis thaliana
Nucleic Acids Research Advance Access published on September 26, 2006
Nucl. Acids Res. 2006 34: e124; doi:10.1093/nar/gkl694 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Arnaud Amzallag, Cédric Vaillant, Mathews Jacob, Michael Unser, Jan Bednar, Jason D. Kahn, Jacques Dubochet, Andrzej Stasiak, and John H. Maddocks

3D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy
Nucleic Acids Research Advance Access published on September 29, 2006
Nucl. Acids Res. 2006 34: e125; doi:10.1093/nar/gkl675 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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