Nucleic Acids Research

Articles:

Jonathan R. Mathias, Sean E. Hanlon, Ruadhan A. O'Flanagan, Anirvan M. Sengupta, and Andrew K. Vershon

Repression of the yeast HO gene by the MAT2 and MATa1 homeodomain proteins
Nucl. Acids Res. 2004 32: 6469-6478; doi:10.1093/nar/gkh985 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Sheng Yun, Chadwick Lie-A-Cheong, and Andrew C. G. Porter

Discriminatory suppression of homologous recombination by p53
Nucl. Acids Res. 2004 32: 6479-6489; doi:10.1093/nar/gkh986 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Tatiana G. Ortolan, Li Chen, Prasad Tongaonkar, and Kiran Madura

Rad23 stabilizes Rad4 from degradation by the Ub/proteasome pathway
Nucl. Acids Res. 2004 32: 6490-6500; doi:10.1093/nar/gkh987 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

P. Christoph Champ, Sandor Maurice, Jeffrey M. Vargason, Tracy Camp, and P. Shing Ho

Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation
Nucl. Acids Res. 2004 32: 6501-6510; doi:10.1093/nar/gkh988 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Lianna Johnson, Sahana Mollah, Benjamin A. Garcia, Tara L. Muratore, Jeffrey Shabanowitz, Donald F. Hunt, and Steven E. Jacobsen

Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct combinations of post-translational modifications
Nucl. Acids Res. 2004 32: 6511-6518; doi:10.1093/nar/gkh992 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Bryan M. O'Neill, Denise Hanway, Elizabeth A. Winzeler, and Floyd E. Romesberg

Coordinated functions of WSS1, PSY2 and TOF1 in the DNA damage response
Nucl. Acids Res. 2004 32: 6519-6530; doi:10.1093/nar/gkh994 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Alessandro A. Sartori, Gondichatnahalli M. Lingaraju, Peter Hunziker, Fritz K. Winkler, and Josef Jiricny

Pa-AGOG, the founding member of a new family of archaeal 8-oxoguanine DNA-glycosylases
Nucl. Acids Res. 2004 32: 6531-6539; doi:10.1093/nar/gkh995 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

John van Noort, Thijn van der Heijden, Christina F. Dutta, Keith Firman, and Cees Dekker

Initiation of translocation by Type I restriction-modification enzymes is associated with a short DNA extrusion
Nucl. Acids Res. 2004 32: 6540-6547; doi:10.1093/nar/gkh999 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Wayne Huggins and Paul Wollenzien

A 16S rRNA–tRNA product containing a nucleotide phototrimer and specific for tRNA in the P/E hybrid state in the Escherichia coli ribosome
Nucl. Acids Res. 2004 32: 6548-6556; doi:10.1093/nar/gkh1001 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Adonis Skandalis and Elke Uribe

A survey of splice variants of the human hypoxanthine phosphoribosyl transferase and DNA polymerase beta genes: products of alternative or aberrant splicing?
Nucl. Acids Res. 2004 32: 6557-6564; doi:10.1093/nar/gkh967 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Lata I. Shukla, Amitava Adhikary, Robert Pazdro, David Becker, and Michael D. Sevilla

Formation of 8-oxo-7,8-dihydroguanine-radicals in -irradiated DNA by multiple one-electron oxidations
Nucl. Acids Res. 2004 32: 6565-6574; doi:10.1093/nar/gkh989 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Christian J. Janzen, Fabian Lander, Oliver Dreesen, and George A. M. Cross

Telomere length regulation and transcriptional silencing in KU80-deficient Trypanosoma brucei
Nucl. Acids Res. 2004 32: 6575-6584; doi:10.1093/nar/gkh991 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Denis Drygin, Stephen Barone, and C. Frank Bennett

Sequence-dependent cytotoxicity of second-generation oligonucleotides
Nucl. Acids Res. 2004 32: 6585-6594; doi:10.1093/nar/gkh997 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Faye A. Rogers, Muthiah Manoharan, Peter Rabinovitch, David C. Ward, and Peter M. Glazer

Peptide conjugates for chromosomal gene targeting by triplex-forming oligonucleotides
Nucl. Acids Res. 2004 32: 6595-6604; doi:10.1093/nar/gkh998 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

I. Williams, J. Richardson, A. Starkey, and I. Stansfield

Genome-wide prediction of stop codon readthrough during translation in the yeast Saccharomyces cerevisiae
Nucl. Acids Res. 2004 32: 6605-6616; doi:10.1093/nar/gkh1004 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ivan Erill, Mónica Jara, Noelia Salvador, Marcos Escribano, Susana Campoy, and Jordi Barbé

Differences in LexA regulon structure among Proteobacteria through in vivo assisted comparative genomics
Nucl. Acids Res. 2004 32: 6617-6626; doi:10.1093/nar/gkh996 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Victor X. Jin, Yu-Wei Leu, Sandya Liyanarachchi, Hao Sun, Meiyun Fan, Kenneth P. Nephew, Tim H.-M. Huang, and Ramana V. Davuluri

Identifying estrogen receptor target genes using integrated computational genomics and chromatin immunoprecipitation microarray
Nucl. Acids Res. 2004 32: 6627-6635; doi:10.1093/nar/gkh1005 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Nathan O. Hodas and Daniel P. Aalberts

Efficient computation of optimal oligo–RNA binding
Nucl. Acids Res. 2004 32: 6636-6642; doi:10.1093/nar/gkh1008 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Hong-Wu Ma, Bharani Kumar, Uta Ditges, Florian Gunzer, Jan Buer, and An-Ping Zeng

An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs
Nucl. Acids Res. 2004 32: 6643-6649; doi:10.1093/nar/gkh1009 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Leven M. Wadley and Anna Marie Pyle

The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery
Nucl. Acids Res. 2004 32: 6650-6659; doi:10.1093/nar/gkh1002 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Richard Ting, Jason M. Thomas, Leonard Lermer, and David M. Perrin

Substrate specificity and kinetic framework of a DNAzyme with an expanded chemical repertoire: a putative RNaseA mimic that catalyzes RNA hydrolysis independent of a divalent metal cation
Nucl. Acids Res. 2004 32: 6660-6672; doi:10.1093/nar/gkh1007 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Guillaume Paillard, Cyril Deremble, and Richard Lavery

Looking into DNA recognition: zinc finger binding specificity
Nucl. Acids Res. 2004 32: 6673-6682; doi:10.1093/nar/gkh1003 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jin Yu, Taekjip Ha, and Klaus Schulten

Conformational model of the Holliday junction transition deduced from molecular dynamics simulations
Nucl. Acids Res. 2004 32: 6683-6695; doi:10.1093/nar/gkh1006 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Regula Muheim-Lenz, Tonko Buterin, Giancarlo Marra, and Hanspeter Naegeli

Short-patch correction of C/C mismatches in human cells
Nucl. Acids Res. 2004 32: 6696-6705; doi:10.1093/nar/gkh990 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Makoto Kimura and Akira Ishihama

Tfg3, a subunit of the general transcription factor TFIIF in Schizosaccharomyces pombe, functions under stress conditions
Nucl. Acids Res. 2004 32: 6706-6715; doi:10.1093/nar/gkh1000 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Corrigenda:

E. A. Worthey, Santiago Martinez-Calvillo, Achim Schnaufer, Gautam Aggarwal, Jason Cawthra, Gholam Fazelinia, Chris Fong, Guoliang Fu, Melissa Hassebrock, Greg Hixson, Alasdair C. Ivens, Patti Kiser, Felicia Marsolini, Erica Rickell, Reza Salavati, Ellen Sisk, Susan M. Sunkin, Kenneth D. Stuart, and Peter J. Myler

Leishmania major chromosome 3 contains two long convergent polycistronic gene clusters separated by a tRNA gene
Nucl. Acids Res. 2004 32: 6716; doi:10.1093/nar/gki172 [Extract] [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: 6717; doi:10.1093/nar/gki147 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

Errata:

Corrigenda
Nucl. Acids Res. 2005 32: 6718; doi:10.1093/nar/gkh993 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

Methods Online:

Anna Válóczi, Csaba Hornyik, Nóra Varga, József Burgyán, Sakari Kauppinen, and Zoltán Havelda

Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes
Nucl. Acids Res. 2004 32: e175; doi:10.1093/nar/gnh171 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Benjamin D. Biles and Bernard A. Connolly

Low-fidelity Pyrococcus furiosus DNA polymerase mutants useful in error-prone PCR
Nucl. Acids Res. 2004 32: e176; doi:10.1093/nar/gnh174 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Danfeng Yao, Fang Yu, Junyoung Kim, Judith Scholz, Peter E. Nielsen, Eva-Kathrin Sinner, and Wolfgang Knoll

Surface plasmon field-enhanced fluorescence spectroscopy in PCR product analysis by peptide nucleic acid probes
Nucl. Acids Res. 2004 32: e177; doi:10.1093/nar/gnh175 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

R. G. Rutledge

Sigmoidal curve-fitting redefines quantitative real-time PCR with the prospective of developing automated high-throughput applications
Nucl. Acids Res. 2004 32: e178; doi:10.1093/nar/gnh177 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Yijun Qi, Xuehua Zhong, Asuka Itaya, and Biao Ding

Dissecting RNA silencing in protoplasts uncovers novel effects of viral suppressors on the silencing pathway at the cellular level
Nucl. Acids Res. 2004 32: e179; doi:10.1093/nar/gnh180 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Keith Le, Katherine Mitsouras, Meenakshi Roy, Qi Wang, Qiang Xu, Stanley F. Nelson, and Christopher Lee

Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data
Nucl. Acids Res. 2004 32: e180; doi:10.1093/nar/gnh173 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Michael H. Shapero, Jane Zhang, Ann Loraine, Weiwei Liu, Xiaojun Di, Guoying Liu, and Keith W. Jones

MARA: a novel approach for highly multiplexed locus-specific SNP genotyping using high-density DNA oligonucleotide arrays
Nucl. Acids Res. 2004 32: e181; doi:10.1093/nar/gnh178 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jin-Der Wen and Donald M. Gray

Selection of genomic sequences that bind tightly to Ff gene 5 protein: primer-free genomic SELEX
Nucl. Acids Res. 2004 32: e182; doi:10.1093/nar/gnh179 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jonathan Kuo, Jason Inman, Michael Brownstein, and Ted B. Usdin

Evaluation of vector-primed cDNA library production from microgram quantities of total RNA
Nucl. Acids Res. 2004 32: e183; doi:10.1093/nar/gnh181 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Karen L. Buchmueller and Kevin M. Weeks

Tris-borate is a poor counterion for RNA: a cautionary tale for RNA folding studies
Nucl. Acids Res. 2004 32: e184; doi:10.1093/nar/gnh182 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Charlie C. Xiang, Eva Mezey, Mei Chen, Sharon Key, Li Ma, and Michael J. Brownstein

Using DSP, a reversible cross-linker, to fix tissue sections for immunostaining, microdissection and expression profiling
Nucl. Acids Res. 2004 32: e185; doi:10.1093/nar/gnh185 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

James D. Hurley, Linda J. Engle, Jesse T. Davis, Adam M. Welsh, and John E. Landers

A simple, bead-based approach for multi-SNP molecular haplotyping
Nucl. Acids Res. 2005 32: e186; doi:10.1093/nar/gnh187 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Fumio Yamauchi, Koichi Kato, and Hiroo Iwata

Spatially and temporally controlled gene transfer by electroporation into adherent cells on plasmid DNA-loaded electrodes
Nucl. Acids Res. 2004 32: e187; doi:10.1093/nar/gnh176 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yingqing Sun, Seongjoon Koo, Neill White, Eigen Peralta, Christine Esau, Nicholas M. Dean, and Ranjan J. Perera

Development of a micro-array to detect human and mouse microRNAs and characterization of expression in human organs
Nucl. Acids Res. 2004 32: e188; doi:10.1093/nar/gnh186 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Rentao Song, Gregorio Segal, and Joachim Messing

Expression of the sorghum 10-member kafirin gene cluster in maize endosperm
Nucl. Acids Res. 2004 32: e189; doi:10.1093/nar/gnh183 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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