Nucleic Acids Research

Chemistry:

Anna Pasternak, Elzbieta Kierzek, Karol Pasternak, Douglas H. Turner, and Ryszard Kierzek

A chemical synthesis of LNA-2,6-diaminopurine riboside, and the influence of 2'-O-methyl-2,6-diaminopurine and LNA-2,6-diaminopurine ribosides on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes
Nucleic Acids Research Advance Access published on June 12, 2007
Nucl. Acids Res. 2007 35: 4055-4063; doi:10.1093/nar/gkm421 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Computational Biology:

G.X. Yu, E.E. Snyder, S.M. Boyle, O.R. Crasta, M. Czar, S.P. Mane, A. Purkayastha, B. Sobral, and J.C. Setubal

A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case
Nucleic Acids Research Advance Access published on June 6, 2007
Nucl. Acids Res. 2007 35: 3953-3962; doi:10.1093/nar/gkm377 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Marc Sturm, Sascha Quinten, Christian G. Huber, and Oliver Kohlbacher

A statistical learning approach to the modeling of chromatographic retention of oligonucleotides incorporating sequence and secondary structure data
Nucleic Acids Research Advance Access published on June 13, 2007
Nucl. Acids Res. 2007 35: 4195-4202; doi:10.1093/nar/gkm338 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Molecular Biology:

Henrik Sahlin Pettersen, Ottar Sundheim, Karin Margaretha Gilljam, Geir Slupphaug, Hans Einar Krokan, and Bodil Kavli

Uracil–DNA glycosylases SMUG1 and UNG2 coordinate the initial steps of base excision repair by distinct mechanisms
Nucleic Acids Research Advance Access published on May 30, 2007
Nucl. Acids Res. 2007 35: 3879-3892; doi:10.1093/nar/gkm372 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Hélène Gaillard, Ralf Erik Wellinger, and Andrés Aguilera

A new connection of mRNP biogenesis and export with transcription-coupled repair
Nucleic Acids Research Advance Access published on May 30, 2007
Nucl. Acids Res. 2007 35: 3893-3906; doi:10.1093/nar/gkm373 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Fatima Boutimah-Hamoudi, Erwan Leforestier, Catherine Sénamaud-Beaufort, Peter E. Nielsen, Carine Giovannangeli, and Tula Ester Saison-Behmoaras

Cellular antisense activity of peptide nucleic acid (PNAs) targeted to HIV-1 polypurine tract (PPT) containing RNA
Nucleic Acids Research Advance Access published on May 30, 2007
Nucl. Acids Res. 2007 35: 3907-3917; doi:10.1093/nar/gkm374 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nobuo Maita, Hideyuki Aoyagi, Mizuko Osanai, Masahiro Shirakawa, and Haruhiko Fujiwara

Characterization of the sequence specificity of the R1Bm endonuclease domain by structural and biochemical studies
Nucleic Acids Research Advance Access published on May 30, 2007
Nucl. Acids Res. 2007 35: 3918-3927; doi:10.1093/nar/gkm397 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Marcus Klotzsche, Dagmar Goeke, Christian Berens, and Wolfgang Hillen

Efficient and exclusive induction of Tet repressor by the oligopeptide Tip results from co-variation of their interaction site
Nucleic Acids Research Advance Access published on June 1, 2007
Nucl. Acids Res. 2007 35: 3945-3952; doi:10.1093/nar/gkm357 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Peter R. Hoffmann, Simone C. Höge, Ping-An Li, Fukun W. Hoffmann, Ann C. Hashimoto, and Marla J. Berry

The selenoproteome exhibits widely varying, tissue-specific dependence on selenoprotein P for selenium supply
Nucleic Acids Research Advance Access published on June 6, 2007
Nucl. Acids Res. 2007 35: 3963-3973; doi:10.1093/nar/gkm355 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tiyun Wu, Susan L. Heilman-Miller, and Judith G. Levin

Effects of nucleic acid local structure and magnesium ions on minus-strand transfer mediated by the nucleic acid chaperone activity of HIV-1 nucleocapsid protein
Nucleic Acids Research Advance Access published on June 6, 2007
Nucl. Acids Res. 2007 35: 3974-3987; doi:10.1093/nar/gkm375 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nicole A. Becker, Jason D. Kahn, and L. James Maher, III

Effects of nucleoid proteins on DNA repression loop formation in Escherichia coli
Nucleic Acids Research Advance Access published on June 6, 2007
Nucl. Acids Res. 2007 35: 3988-4000; doi:10.1093/nar/gkm419 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Chaoyong James Yang, Lin Wang, Yanrong Wu, Youngmi Kim, Colin D. Medley, Hui Lin, and Weihong Tan

Synthesis and investigation of deoxyribonucleic acid/locked nucleic acid chimeric molecular beacons
Nucleic Acids Research Advance Access published on June 8, 2007
Nucl. Acids Res. 2007 35: 4030-4041; doi:10.1093/nar/gkm358 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Justin Cotney, Zhibo Wang, and Gerald S. Shadel

Relative abundance of the human mitochondrial transcription system and distinct roles for h-mtTFB1 and h-mtTFB2 in mitochondrial biogenesis and gene expression
Nucleic Acids Research Advance Access published on June 8, 2007
Nucl. Acids Res. 2007 35: 4042-4054; doi:10.1093/nar/gkm424 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Wenyan Zhu, Tadashi Wada, Sachiko Okabe, Takuya Taneda, Yuki Yamaguchi, and Hiroshi Handa

DSIF contributes to transcriptional activation by DNA-binding activators by preventing pausing during transcription elongation
Nucleic Acids Research Advance Access published on June 12, 2007
Nucl. Acids Res. 2007 35: 4064-4075; doi:10.1093/nar/gkm430 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jessica P. Wyles, Zhongqin Wu, Shelagh E.L. Mirski, and Susan P.C. Cole

Nuclear interactions of topoisomerase II and ß with phospholipid scramblase 1
Nucleic Acids Research Advance Access published on June 12, 2007
Nucl. Acids Res. 2007 35: 4076-4085; doi:10.1093/nar/gkm434 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yoshiharu Sasaki, Daisuke Miyoshi, and Naoki Sugimoto

Regulation of DNA nucleases by molecular crowding
Nucleic Acids Research Advance Access published on June 12, 2007
Nucl. Acids Res. 2007 35: 4086-4093; doi:10.1093/nar/gkm445 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Nucleic Acid Enzymes:

Lawrence F. Povirk, Rui-Zhe Zhou, Dale A. Ramsden, Susan P. Lees-Miller, and Kristoffer Valerie

Phosphorylation in the serine/threonine 2609–2647 cluster promotes but is not essential for DNA-dependent protein kinase-mediated nonhomologous end joining in human whole-cell extracts
Nucleic Acids Research Advance Access published on May 25, 2007
Nucl. Acids Res. 2007 35: 3869-3878; doi:10.1093/nar/gkm339 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Donghong Min, Song Xue, Hong Li, and Wei Yang

‘In-line attack’ conformational effect plays a modest role in an enzyme-catalyzed RNA cleavage: a free energy simulation study
Nucleic Acids Research Advance Access published on June 6, 2007
Nucl. Acids Res. 2007 35: 4001-4006; doi:10.1093/nar/gkm394 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Michael R. G. Hodskinson, Lee M. Allen, Duncan P. Thomson, and Jon R. Sayers

Molecular interactions of Escherichia coli ExoIX and identification of its associated 3'–5' exonuclease activity
Nucleic Acids Research Advance Access published on June 12, 2007
Nucl. Acids Res. 2007 35: 4094-4102; doi:10.1093/nar/gkm396 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Heng-Kuan Wong, Meltem Muftuoglu, Gad Beck, Syed Z. Imam, Vilhelm A. Bohr, and David M. Wilson, III

Cockayne syndrome B protein stimulates apurinic endonuclease 1 activity and protects against agents that introduce base excision repair intermediates
Nucleic Acids Research Advance Access published on June 12, 2007
Nucl. Acids Res. 2007 35: 4103-4113; doi:10.1093/nar/gkm404 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Alan B. Clark, Leesa Deterding, Kenneth B. Tomer, and Thomas A. Kunkel

Multiple functions for the N-terminal region of Msh6
Nucleic Acids Research Advance Access published on June 12, 2007
Nucl. Acids Res. 2007 35: 4114-4123; doi:10.1093/nar/gkm409 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Xuan Li, Xiao-Ping Zhang, Jachen A. Solinger, Konstantin Kiianitsa, Xiong Yu, Edward H. Egelman, and Wolf-Dietrich Heyer

Rad51 and Rad54 ATPase activities are both required to modulate Rad51-dsDNA filament dynamics
Nucleic Acids Research Advance Access published on June 12, 2007
Nucl. Acids Res. 2007 35: 4124-4140; doi:10.1093/nar/gkm412 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Lisa A. Schroeder, Ae-Jin Choi, and Pieter L. deHaseth

The –11A of promoter DNA and two conserved amino acids in the melting region of ⁷⁰ both directly affect the rate limiting step in formation of the stable RNA polymerase-promoter complex, but they do not necessarily interact
Nucleic Acids Research Advance Access published on June 12, 2007
Nucl. Acids Res. 2007 35: 4141-4153; doi:10.1093/nar/gkm431 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

RNA:

Yen-I G. Chen, Roger E. Moore, Helen Y. Ge, Mary K. Young, Terry D. Lee, and Scott W. Stevens

Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors
Nucleic Acids Research Advance Access published on May 30, 2007
Nucl. Acids Res. 2007 35: 3928-3944; doi:10.1093/nar/gkm347 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Filip Rázga, Jaroslav Koca, Ali Mokdad, and Jirí Sponer

Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA
Nucleic Acids Research Advance Access published on June 6, 2007
Nucl. Acids Res. 2007 35: 4007-4017; doi:10.1093/nar/gkm245 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Kei Kitahara, Akimasa Kajiura, Neuza Satomi Sato, and Tsutomu Suzuki

Functional genetic selection of Helix 66 in Escherichia coli 23S rRNA identified the eukaryotic-binding sequence for ribosomal protein L2
Nucleic Acids Research Advance Access published on June 6, 2007
Nucl. Acids Res. 2007 35: 4018-4029; doi:10.1093/nar/gkm356 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Dmitriy Skvortsov, Diana Abdueva, Christina Curtis, Betty Schaub, and Simon Tavaré

Explaining differences in saturation levels for Affymetrix GeneChip® arrays
Nucleic Acids Research Advance Access published on June 12, 2007
Nucl. Acids Res. 2007 35: 4154-4163; doi:10.1093/nar/gkm348 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Erming Wang, Neviana Dimova, and Franca Cambi

PLP/DM20 ratio is regulated by hnRNPH and F and a novel G-rich enhancer in oligodendrocytes
Nucleic Acids Research Advance Access published on June 12, 2007
Nucl. Acids Res. 2007 35: 4164-4178; doi:10.1093/nar/gkm387 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Julia E. Weigand and Beatrix Suess

Tetracycline aptamer-controlled regulation of pre-mRNA splicing in yeast
Nucleic Acids Research Advance Access published on June 12, 2007
Nucl. Acids Res. 2007 35: 4179-4185; doi:10.1093/nar/gkm425 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Taek Jin Kang and Hiroaki Suga

In vitro selection of a 5'-purine ribonucleotide transferase ribozyme
Nucleic Acids Research Advance Access published on June 12, 2007
Nucl. Acids Res. 2007 35: 4186-4194; doi:10.1093/nar/gkm438 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Iván V. Rosado, Dieter Kressler, and Jesús de la Cruz

Functional analysis of Saccharomyces cerevisiae ribosomal protein Rpl3p in ribosome synthesis
Nucleic Acids Research Advance Access published on June 13, 2007
Nucl. Acids Res. 2007 35: 4203-4213; doi:10.1093/nar/gkm388 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Structural Biology:

Phillip A. Rachwal, I. Stuart Findlow, Joern M. Werner, Tom Brown, and Keith R. Fox

Intramolecular DNA quadruplexes with different arrangements of short and long loops
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4214-4222; doi:10.1093/nar/gkm316 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Methods Online:

Jin Li, Ross Berbeco, Robert J. Distel, Pasi A. Jänne, Lilin Wang, and G. Mike Makrigiorgos

s-RT-MELT for rapid mutation scanning using enzymatic selection and real time DNA-melting: new potential for multiplex genetic analysis
Nucleic Acids Research Advance Access published on June 1, 2007
Nucl. Acids Res. 2007 35: e84; doi:10.1093/nar/gkm403 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Dimitrios Lykidis, Susan Van Noorden, Alan Armstrong, Bradley Spencer-Dene, Jie Li, Zhengping Zhuang, and Gordon W. H. Stamp

Novel zinc-based fixative for high quality DNA, RNA and protein analysis
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: e85; doi:10.1093/nar/gkm433 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Roosmarijn E. Vandenbroucke, Bart Lucas, Joseph Demeester, Stefaan C. De Smedt, and Niek N. Sanders

Nuclear accumulation of plasmid DNA can be enhanced by non-selective gating of the nuclear pore
Nucleic Acids Research Advance Access published on June 21, 2007
Nucl. Acids Res. 2007 35: e86; doi:10.1093/nar/gkm440 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Juan Cadiñanos and Allan Bradley

Generation of an inducible and optimized piggyBac transposon system
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: e87; doi:10.1093/nar/gkm446 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Silvia Berkner, Dennis Grogan, Sonja-Verena Albers, and Georg Lipps

Small multicopy, non-integrative shuttle vectors based on the plasmid pRN1 for Sulfolobus acidocaldarius and Sulfolobus solfataricus, model organisms of the (cren-)archaea
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: e88; doi:10.1093/nar/gkm449 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tom Ellis, David A. Evans, Christopher R. H. Martin, and John A. Hartley

A 96-well DNase I footprinting screen for drug–DNA interactions
Nucleic Acids Research Advance Access published on June 22, 2007
Nucl. Acids Res. 2007 35: e89; doi:10.1093/nar/gkm467 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Christiane Hitz, Wolfgang Wurst, and Ralf Kühn

Conditional brain-specific knockdown of MAPK using Cre/loxP regulated RNA interference
Nucleic Acids Research Advance Access published on June 22, 2007
Nucl. Acids Res. 2007 35: e90; doi:10.1093/nar/gkm475 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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