Nucleic Acids Research

Articles:

François Bergeron, Daniel Houde, Darel J. Hunting, and J. Richard Wagner

Electron transfer in DNA duplexes containing 2-methyl-1,4-naphthoquinone
Nucl. Acids Res. 2004 32: 6154-6163; doi:10.1093/nar/gkh950 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Rami N. Hannoush, Kyung-Lyum Min, and Masad J. Damha

Diversity-oriented solid-phase synthesis and biological evaluation of oligonucleotide hairpins as HIV-1 RT RNase H inhibitors
Nucl. Acids Res. 2004 32: 6164-6175; doi:10.1093/nar/gkh948 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Colin P. Guy, Alan I. Majerník, James P. J. Chong, and Edward L. Bolt

A novel nuclease-ATPase (Nar71) from archaea is part of a proposed thermophilic DNA repair system
Nucl. Acids Res. 2004 32: 6176-6186; doi:10.1093/nar/gkh960 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Siu-hong Chan, Zhenyu Zhu, James L. Van Etten, and Shuang-yong Xu

Cloning of CviPII nicking and modification system from chlorella virus NYs-1 and application of Nt.CviPII in random DNA amplification
Nucl. Acids Res. 2004 32: 6187-6199; doi:10.1093/nar/gkh958 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Caroline Köhrer, Eric L. Sullivan, and Uttam L. RajBhandary

Complete set of orthogonal 21st aminoacyl-tRNA synthetase-amber, ochre and opal suppressor tRNA pairs: concomitant suppression of three different termination codons in an mRNA in mammalian cells
Nucl. Acids Res. 2004 32: 6200-6211; doi:10.1093/nar/gkh959 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Suisheng Tang, Sin Lam Tan, Suresh Kumar Ramadoss, Arun Prashanth Kumar, Man-Hung Eric Tang, and Vladimir B. Bajic

Computational method for discovery of estrogen responsive genes
Nucl. Acids Res. 2004 32: 6212-6217; doi:10.1093/nar/gkh943 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Monika E. Mysiak, Claire Wyman, P. Elly Holthuizen, and Peter C. van der Vliet

NFI and Oct-1 bend the Ad5 origin in the same direction leading to optimal DNA replication
Nucl. Acids Res. 2004 32: 6218-6225; doi:10.1093/nar/gkh944 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Weidong Tian, Adrian K. Arakaki, and Jeffrey Skolnick

EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference
Nucl. Acids Res. 2004 32: 6226-6239; doi:10.1093/nar/gkh956 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Yana S. Kovacheva, Svetomir B. Tzokov, Iain A. Murray, and Jane A. Grasby

The role of phosphate groups in the VS ribozyme–substrate interaction
Nucl. Acids Res. 2004 32: 6240-6250; doi:10.1093/nar/gkh957 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Gen Ishikawa, Yoshihiro Kanai, Kei-ichi Takata, Ryo Takeuchi, Kaori Shimanouchi, Tatsushi Ruike, Tomoyuki Furukawa, Seisuke Kimura, and Kengo Sakaguchi

DmGEN, a novel RAD2 family endo-exonuclease from Drosophila melanogaster
Nucl. Acids Res. 2004 32: 6251-6259; doi:10.1093/nar/gkh962 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Pål Ø. Falnes

Repair of 3-methylthymine and 1-methylguanine lesions by bacterial and human AlkB proteins
Nucl. Acids Res. 2004 32: 6260-6267; doi:10.1093/nar/gkh964 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Stephanie E. Corrette-Bennett, Claudia Borgeson, Debbie Sommer, Peter M. J. Burgers, and Robert S. Lahue

DNA polymerase , RFC and PCNA are required for repair synthesis of large looped heteroduplexes in Saccharomyces cerevisiae
Nucl. Acids Res. 2004 32: 6268-6275; doi:10.1093/nar/gkh965 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kirsten Krause and Carol L. Dieckmann

Analysis of transcription asymmetries along the tRNA^E-COB operon: evidence for transcription attenuation and rapid RNA degradation between coding sequences
Nucl. Acids Res. 2004 32: 6276-6283; doi:10.1093/nar/gkh966 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Wigard P. Kloosterman, Erno Wienholds, René F. Ketting, and Ronald H.A. Plasterk

Substrate requirements for let-7 function in the developing zebrafish embryo
Nucl. Acids Res. 2004 32: 6284-6291; doi:10.1093/nar/gkh968 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hideto Takami, Yoshihiro Takaki, Gab-Joo Chee, Shinro Nishi, Shigeru Shimamura, Hiroko Suzuki, Satomi Matsui, and Ikuo Uchiyama

Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus
Nucl. Acids Res. 2004 32: 6292-6303; doi:10.1093/nar/gkh970 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Martin Zacharias and Joachim W. Engels

Influence of a fluorobenzene nucleobase analogue on the conformational flexibility of RNA studied by molecular dynamics simulations
Nucl. Acids Res. 2004 32: 6304-6311; doi:10.1093/nar/gkh971 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Dong-Soo Han, Hong-Soog Kim, Woo-Hyuk Jang, Sung-Doke Lee, and Jung-Keun Suh

PreSPI: a domain combination based prediction system for protein–protein interaction
Nucl. Acids Res. 2004 32: 6312-6320; doi:10.1093/nar/gkh972 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Tobias Doerks, Christian von Mering, and Peer Bork

Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes
Nucl. Acids Res. 2004 32: 6321-6326; doi:10.1093/nar/gkh973 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Kathleen F. Benson, Richard E. Person, Feng-Qian Li, Kayleen Williams, and Marshall Horwitz

Paradoxical homozygous expression from heterozygotes and heterozygous expression from homozygotes as a consequence of transcriptional infidelity through a polyadenine tract in the AP3B1 gene responsible for canine cyclic neutropenia
Nucl. Acids Res. 2004 32: 6327-6333; doi:10.1093/nar/gkh974 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Vera I. Hashem, Malgorzata J. Pytlos, Elzbieta A. Klysik, Kuniko Tsuji, Merhdad Khajav, Tetsuo Ashizawa, and Richard R. Sinden

Chemotherapeutic deletion of CTG repeats in lymphoblast cells from DM1 patients
Nucl. Acids Res. 2004 32: 6334-6346; doi:10.1093/nar/gkh976 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yu Zheng, Richard J. Roberts, and Simon Kasif

Identification of genes with fast-evolving regions in microbial genomes
Nucl. Acids Res. 2004 32: 6347-6357; doi:10.1093/nar/gkh935 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Michael Schmitz

Change of RNase P RNA function by single base mutation correlates with perturbation of metal ion binding in P4 as determined by NMR spectroscopy
Nucl. Acids Res. 2004 32: 6358-6366; doi:10.1093/nar/gkh961 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hiroyuki Tanaka, Gi-Hyuck Ryu, Yeon-Soo Seo, and Stuart A. MacNeill

Genetics of lagging strand DNA synthesis and maturation in fission yeast: suppression analysis links the Dna2–Cdc24 complex to DNA polymerase
Nucl. Acids Res. 2004 32: 6367-6377; doi:10.1093/nar/gkh963 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Chris J. Cadman and Peter McGlynn

PriA helicase and SSB interact physically and functionally
Nucl. Acids Res. 2004 32: 6378-6387; doi:10.1093/nar/gkh980 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Arturo Gutierrez and Ralf J. Sommer

Evolution of dnmt-2 and mbd-2-like genes in the free-living nematodes Pristionchus pacificus, Caenorhabditis elegans and Caenorhabditis briggsae
Nucl. Acids Res. 2004 32: 6388-6396; doi:10.1093/nar/gkh982 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

David Choury, Jean-Claude Farré, Xavier Jordana, and Alejandro Araya

Different patterns in the recognition of editing sites in plant mitochondria
Nucl. Acids Res. 2004 32: 6397-6406; doi:10.1093/nar/gkh969 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Christopher D. Wassman, Phillip Y. Tam, Richard H. Lathrop, and Gregory A. Weiss

Predicting oligonucleotide-directed mutagenesis failures in protein engineering
Nucl. Acids Res. 2004 32: 6407-6413; doi:10.1093/nar/gkh977 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yu Chen and Dong Xu

Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiae
Nucl. Acids Res. 2004 32: 6414-6424; doi:10.1093/nar/gkh978 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Michel Siep, Esther Sleddens-Linkels, Sabine Mulders, Hans van Eenennaam, Evelyne Wassenaar, Wiggert A. Van Cappellen, Jos Hoogerbrugge, J. Anton Grootegoed, and Willy M. Baarends

Basic helix–loop–helix transcription factor Tcfl5 interacts with the Calmegin gene promoter in mouse spermatogenesis
Nucl. Acids Res. 2004 32: 6425-6436; doi:10.1093/nar/gkh979 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

L. Y. Han, C. Z. Cai, Z. L. Ji, Z. W. Cao, J. Cui, and Y. Z. Chen

Predicting functional family of novel enzymes irrespective of sequence similarity: a statistical learning approach
Nucl. Acids Res. 2004 32: 6437-6444; doi:10.1093/nar/gkh984 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

S. D. Streeter, I. Papapanagiotou, J. E. McGeehan, and G. G. Kneale

DNA footprinting and biophysical characterization of the controller protein C.AhdI suggests the basis of a genetic switch
Nucl. Acids Res. 2004 32: 6445-6453; doi:10.1093/nar/gkh975 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Nuria Vilaboa, Rodrigo Bermejo, Pilar Martinez, Rafael Bornstein, and Carmela Calés

A novel E2 box-GATA element modulates Cdc6 transcription during human cells polyploidization
Nucl. Acids Res. 2004 32: 6454-6467; doi:10.1093/nar/gkh981 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Methods Online:

Ali Agah, Mariam Aghajan, Foad Mashayekhi, Sasan Amini, Ronald W. Davis, James D. Plummer, Mostafa Ronaghi, and Peter B. Griffin

A multi-enzyme model for pyrosequencing
Nucl. Acids Res. 2004 32: e166; doi:10.1093/nar/gnh159 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Philipp Schatz, Dimo Dietrich, and Matthias Schuster

Rapid analysis of CpG methylation patterns using RNase T1 cleavage and MALDI-TOF
Nucl. Acids Res. 2004 32: e167; doi:10.1093/nar/gnh165 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hélène Thomassin, Clémence Kress, and Thierry Grange

MethylQuant: a sensitive method for quantifying methylation of specific cytosines within the genome
Nucl. Acids Res. 2004 32: e168; doi:10.1093/nar/gnh166 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kenichi Horisawa, Seiji Tateyama, Masamichi Ishizaka, Nobutaka Matsumura, Hideaki Takashima, Etsuko Miyamoto-Sato, Nobuhide Doi, and Hiroshi Yanagawa

In vitro selection of Jun-associated proteins using mRNA display
Nucl. Acids Res. 2004 32: e169; doi:10.1093/nar/gnh167 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Marita Overhoff, Winfried Wünsche, and Georg Sczakiel

Quantitative detection of siRNA and single-stranded oligonucleotides: relationship between uptake and biological activity of siRNA
Nucl. Acids Res. 2004 32: e170; doi:10.1093/nar/gnh168 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Shanfa Lu, Rui Shi, Cheng-Chung Tsao, Xiaoping Yi, Laigeng Li, and Vincent L. Chiang

RNA silencing in plants by the expression of siRNA duplexes
Nucl. Acids Res. 2004 32: e171; doi:10.1093/nar/gnh170 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Michael Lindenbaum, Ed Perkins, Erika Csonka, Elena Fleming, Lisa Garcia, Amy Greene, Lindsay Gung, Gyula Hadlaczky, Edmond Lee, Josephine Leung, Neil MacDonald, Alexisann Maxwell, Kathleen Mills, Diane Monteith, Carl F. Perez, Joan Shellard, Sandy Stewart, Tom Stodola, Dana Vandenborre, Sandy Vanderbyl, and Harry C. Ledebur, Jr

A mammalian artificial chromosome engineering system (ACE System) applicable to biopharmaceutical protein production, transgenesis and gene-based cell therapy
Nucl. Acids Res. 2004 32: e172; doi:10.1093/nar/gnh169 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Tianyan Zhou, Guoshu Chen, Yifan Wang, Qiang Zhang, Ming Yang, and Tianhu Li

Synthesis of unimolecularly circular G-quadruplexes as prospective molecular probes
Nucl. Acids Res. 2004 32: e173; doi:10.1093/nar/gnh162 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Joyce Chiu, Paul E. March, Ryan Lee, and Daniel Tillett

Site-directed, Ligase-Independent Mutagenesis (SLIM): a single-tube methodology approaching 100% efficiency in 4 h
Nucl. Acids Res. 2004 32: e174; doi:10.1093/nar/gnh172 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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