Nucleic Acids Research

Editorial:

CHANGES TO THE INSTRUCTIONS TO AUTHORS
Nucl. Acids Res. 2006 34: 4311-4312; doi:10.1093/nar/gkl647 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Chemistry:

Kohji Seio, Takeshi Sasami, Ryuya Tawarada, and Mitsuo Sekine

Synthesis of 2'-O-methyl-RNAs incorporating a 3-deazaguanine, and UV melting and computational studies on its hybridization properties
Nucleic Acids Research Advance Access published on August 26, 2006
Nucl. Acids Res. 2006 34: 4324-4334; doi:10.1093/nar/gkl088 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Junpei Yamamoto, Kenichi Hitomi, Takeshi Todo, and Shigenori Iwai

Chemical synthesis of oligodeoxyribonucleotides containing the Dewar valence isomer of the (6–4) photoproduct and their use in (6–4) photolyase studies
Nucleic Acids Research Advance Access published on August 26, 2006
Nucl. Acids Res. 2006 34: 4406-4415; doi:10.1093/nar/gkl572 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jawad Alzeer and Orlando D. Schärer

A modified thymine for the synthesis of site-specific thymine-guanine DNA interstrand crosslinks
Nucleic Acids Research Advance Access published on August 31, 2006
Nucl. Acids Res. 2006 34: 4458-4466; doi:10.1093/nar/gkl587 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Computational Biology:

Marshall Bern, David Goldberg, and Eugenia Lyashenko

Data mining for proteins characteristic of clades
Nucleic Acids Research Advance Access published on August 26, 2006
Nucl. Acids Res. 2006 34: 4342-4353; doi:10.1093/nar/gkl440 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jimin Pei and Nick V. Grishin

MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information
Nucleic Acids Research Advance Access published on August 26, 2006
Nucl. Acids Res. 2006 34: 4364-4374; doi:10.1093/nar/gkl514 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Yehonathan Hazony, Jun Lu, Cynthia St. Hilaire, and Katya Ravid

Hematopoietic gene promoters subjected to a group-combinatorial study of DNA samples: identification of a megakaryocytic selective DNA signature
Nucleic Acids Research Advance Access published on August 26, 2006
Nucl. Acids Res. 2006 34: 4416-4428; doi:10.1093/nar/gkl578 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Alison Yao, Rosane Charlab, and Peter Li

Systematic identification of pseudogenes through whole genome expression evidence profiling
Nucleic Acids Research Advance Access published on August 31, 2006
Nucl. Acids Res. 2006 34: 4477-4485; doi:10.1093/nar/gkl591 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Genomics:

Igor Vorechovsky

Aberrant 3' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization
Nucleic Acids Research Advance Access published on September 8, 2006
Nucl. Acids Res. 2006 34: 4630-4641; doi:10.1093/nar/gkl535 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Molecular Biology:

Ola Larsson, David M. Perlman, Danhua Fan, Cavan S. Reilly, Mark Peterson, Cecilia Dahlgren, Zicai Liang, Shunan Li, Vitaly A. Polunovsky, Claes Wahlestedt, and Peter B. Bitterman

Apoptosis resistance downstream of eIF4E: posttranscriptional activation of an anti-apoptotic transcript carrying a consensus hairpin structure
Nucleic Acids Research Advance Access published on August 26, 2006
Nucl. Acids Res. 2006 34: 4375-4386; doi:10.1093/nar/gkl558 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Maria Kalyna, Sergiy Lopato, Viktor Voronin, and Andrea Barta

Evolutionary conservation and regulation of particular alternative splicing events in plant SR proteins
Nucleic Acids Research Advance Access published on August 26, 2006
Nucl. Acids Res. 2006 34: 4395-4405; doi:10.1093/nar/gkl570 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Naoyuki Sarai, Wataru Kagawa, Takashi Kinebuchi, Ako Kagawa, Kozo Tanaka, Kiyoshi Miyagawa, Shukuko Ikawa, Takehiko Shibata, Hitoshi Kurumizaka, and Shigeyuki Yokoyama

Stimulation of Dmc1-mediated DNA strand exchange by the human Rad54B protein
Nucleic Acids Research Advance Access published on August 31, 2006
Nucl. Acids Res. 2006 34: 4429-4437; doi:10.1093/nar/gkl562 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

F. Hartung, S. Suer, T. Bergmann, and H. Puchta

The role of AtMUS81 in DNA repair and its genetic interaction with the helicase AtRecQ4A
Nucleic Acids Research Advance Access published on August 31, 2006
Nucl. Acids Res. 2006 34: 4438-4448; doi:10.1093/nar/gkl576 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Brian T. Farrell and Robert S. Lahue

CAG·CTG repeat instability in cultured human astrocytes
Nucleic Acids Research Advance Access published on August 31, 2006
Nucl. Acids Res. 2006 34: 4495-4505; doi:10.1093/nar/gkl614 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sven Kappel, Yves Matthess, Brigitte Zimmer, Manfred Kaufmann, and Klaus Strebhardt

Tumor inhibition by genomically integrated inducible RNAi-cassettes
Nucleic Acids Research Advance Access published on August 31, 2006
Nucl. Acids Res. 2006 34: 4527-4536; doi:10.1093/nar/gkl628 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Marcelo Rogalski, Stephanie Ruf, and Ralph Bock

Tobacco plastid ribosomal protein S18 is essential for cell survival
Nucleic Acids Research Advance Access published on August 31, 2006
Nucl. Acids Res. 2006 34: 4537-4545; doi:10.1093/nar/gkl634 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Erika Brunet, Maddalena Corgnali, Fabio Cannata, Loïc Perrouault, and Carine Giovannangeli

Targeting chromosomal sites with locked nucleic acid-modified triplex-forming oligonucleotides: study of efficiency dependence on DNA nuclear environment
Nucleic Acids Research Advance Access published on September 1, 2006
Nucl. Acids Res. 2006 34: 4546-4553; doi:10.1093/nar/gkl630 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Hubert Charles, Federica Calevro, José Vinuelas, Jean-Michel Fayard, and Yvan Rahbe

Codon usage bias and tRNA over-expression in Buchnera aphidicola after aromatic amino acid nutritional stress on its host Acyrthosiphon pisum
Nucleic Acids Research Advance Access published on September 8, 2006
Nucl. Acids Res. 2006 34: 4583-4592; doi:10.1093/nar/gkl597 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Takeshi Sekiguchi, Toshiya Hayano, Mitsuaki Yanagida, Nobuhiro Takahashi, and Takeharu Nishimoto

NOP132 is required for proper nucleolus localization of DEAD-box RNA helicase DDX47
Nucleic Acids Research Advance Access published on September 8, 2006
Nucl. Acids Res. 2006 34: 4593-4608; doi:10.1093/nar/gkl603 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Marianne Stabell, Ragnhild Eskeland, Mona Bjørkmo, Jan Larsson, Reidunn B. Aalen, Axel Imhof, and Andrew Lambertsson

The Drosophila G9a gene encodes a multi-catalytic histone methyltransferase required for normal development
Nucleic Acids Research Advance Access published on September 8, 2006
Nucl. Acids Res. 2006 34: 4609-4621; doi:10.1093/nar/gkl640 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

David C. Grainger, Douglas Hurd, Martin D. Goldberg, and Stephen J. W. Busby

Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome
Nucleic Acids Research Advance Access published on September 8, 2006
Nucl. Acids Res. 2006 34: 4642-4652; doi:10.1093/nar/gkl542 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Nucleic Acid Enzymes:

John M. Fortune, Carrie M. Stith, Grace E. Kissling, Peter M. J. Burgers, and Thomas A. Kunkel

RPA and PCNA suppress formation of large deletion errors by yeast DNA polymerase
Nucleic Acids Research Advance Access published on August 26, 2006
Nucl. Acids Res. 2006 34: 4335-4341; doi:10.1093/nar/gkl403 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Louise K. Stanley and Mark D. Szczelkun

Direct and random routing of a molecular motor protein at a DNA junction
Nucleic Acids Research Advance Access published on August 26, 2006
Nucl. Acids Res. 2006 34: 4387-4394; doi:10.1093/nar/gkl569 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Raquel Juárez, José F. Ruiz, Stephanie A. Nick McElhinny, Dale Ramsden, and Luis Blanco

A specific loop in human DNA polymerase mu allows switching between creative and DNA-instructed synthesis
Nucleic Acids Research Advance Access published on September 8, 2006
Nucl. Acids Res. 2006 34: 4572-4582; doi:10.1093/nar/gkl457 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

RNA:

Erich Koller, Stephanie Propp, Heather Murray, Walter Lima, Balkrishen Bhat, Thaza P. Prakash, Charles R. Allerson, Eric E. Swayze, Eric G. Marcusson, and Nicholas M. Dean

Competition for RISC binding predicts in vitro potency of siRNA
Nucleic Acids Research Advance Access published on August 31, 2006
Nucl. Acids Res. 2006 34: 4467-4476; doi:10.1093/nar/gkl589 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Angus T. De Souza, Xudong Dai, Andrew G. Spencer, Tom Reppen, Ann Menzie, Paula L. Roesch, Yudong He, Michelle J. Caguyong, Sherri Bloomer, Hans Herweijer, Jon A. Wolff, James E. Hagstrom, David L. Lewis, Peter S. Linsley, and Roger G. Ulrich

Transcriptional and phenotypic comparisons of Ppara knockout and siRNA knockdown mice
Nucleic Acids Research Advance Access published on August 31, 2006
Nucl. Acids Res. 2006 34: 4486-4494; doi:10.1093/nar/gkl609 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kyu-Hyeon Yeom, Yoontae Lee, Jinju Han, Mi Ra Suh, and V. Narry Kim

Characterization of DGCR8/Pasha, the essential cofactor for Drosha in primary miRNA processing
Nucleic Acids Research Advance Access published on September 8, 2006
Nucl. Acids Res. 2006 34: 4622-4629; doi:10.1093/nar/gkl458 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Structural Biology:

N. Pouget, C. Turlan, N. Destainville, L. Salomé, and M. Chandler

IS911 transpososome assembly as analysed by tethered particle motion
Nucleic Acids Research Advance Access published on August 21, 2006
Nucl. Acids Res. 2006 34: 4313-4323; doi:10.1093/nar/gkl420 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Souvik Modi, Ajazul Hamid Wani, and Yamuna Krishnan

The PNA–DNA hybrid I-motif: implications for sugar–sugar contacts in i-motif tetramerization
Nucleic Acids Research Advance Access published on August 26, 2006
Nucl. Acids Res. 2006 34: 4354-4363; doi:10.1093/nar/gkl443 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Sara Flodell, Michael Petersen, Frederic Girard, Janusz Zdunek, Karin Kidd-Ljunggren, Jürgen Schleucher, and Sybren Wijmenga

Solution structure of the apical stem–loop of the human hepatitis B virus encapsidation signal
Nucleic Acids Research Advance Access published on August 31, 2006
Nucl. Acids Res. 2006 34: 4449-4457; doi:10.1093/nar/gkl582 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Michelle L. Gill, Scott A. Strobel, and J. Patrick Loria

Crystallization and characterization of the thallium form of the Oxytricha nova G-quadruplex
Nucleic Acids Research Advance Access published on August 31, 2006
Nucl. Acids Res. 2006 34: 4506-4514; doi:10.1093/nar/gkl616 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Andrew S. Doré, Mairi L. Kilkenny, Sarah A. Jones, Antony W. Oliver, S. Mark Roe, Stephen D. Bell, and Laurence H. Pearl

Structure of an archaeal PCNA1–PCNA2–FEN1 complex: elucidating PCNA subunit and client enzyme specificity
Nucleic Acids Research Advance Access published on August 31, 2006
Nucl. Acids Res. 2006 34: 4515-4526; doi:10.1093/nar/gkl623 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Chongli Yuan, Elizabeth Rhoades, Xiong Wen Lou, and Lynden A. Archer

Spontaneous sharp bending of DNA: role of melting bubbles
Nucleic Acids Research Advance Access published on September 5, 2006
Nucl. Acids Res. 2006 34: 4554-4560; doi:10.1093/nar/gkl394 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Markus Zeeb, Klaas E.A. Max, Ulrich Weininger, Christian Löw, Heinrich Sticht, and Jochen Balbach

Recognition of T-rich single-stranded DNA by the cold shock protein Bs-CspB in solution
Nucleic Acids Research Advance Access published on September 6, 2006
Nucl. Acids Res. 2006 34: 4561-4571; doi:10.1093/nar/gkl376 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Corrigenda:

Corrigendum
Nucl. Acids Res. 2006 34: 4653; doi:10.1093/nar/gkl579 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Corrigendum
Nucl. Acids Res. 2006 34: 4654; doi:10.1093/nar/gkl599 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Jeppe Vinther, Mads M. Hedegaard, Paul P. Gardner, Jens S. Andersen, and Peter Arctander

Identification of miRNA targets with stable isotope labeling by amino acids in cell culture
Nucleic Acids Research Advance Access published on August 31, 2006
Nucl. Acids Res. 2006 34: e107; doi:10.1093/nar/gkl590 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Daniel Christ, Kristoffer Famm, and Greg Winter

Tapping diversity lost in transformations—in vitro amplification of ligation reactions
Nucleic Acids Research Advance Access published on August 31, 2006
Nucl. Acids Res. 2006 34: e108; doi:10.1093/nar/gkl605 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Kristi Kincaid and Robert D. Kuchta

A mass spectrometry-based approach for identifying novel DNA polymerase substrates from a pool of dNTP analogues
Nucleic Acids Research Advance Access published on August 31, 2006
Nucl. Acids Res. 2006 34: e109; doi:10.1093/nar/gkl632 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Sarah Blair, Kathryn Richmond, Matthew Rodesch, Michael Bassetti, and Franco Cerrina

A scalable method for multiplex LED-controlled synthesis of DNA in capillaries
Nucleic Acids Research Advance Access published on September 8, 2006
Nucl. Acids Res. 2006 34: e110; doi:10.1093/nar/gkl641 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alexander Y. Lushnikov, Vladimir N. Potaman, and Yuri L. Lyubchenko

Site-specific labeling of supercoiled DNA
Nucleic Acids Research Advance Access published on September 8, 2006
Nucl. Acids Res. 2006 34: e111; doi:10.1093/nar/gkl642 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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