| | Articles Repression of the yeast HO gene by the MATα2 and MATa1 homeodomain proteins Jonathan R. Mathias, Sean E. Hanlon, Ruadhan A. O'Flanagan, Anirvan M. Sengupta, and Andrew K. Vershon PMCID: PMC545453 Discriminatory suppression of homologous recombination by p53 Sheng Yun, Chadwick Lie-A-Cheong, and Andrew C. G. Porter PMCID: PMC545454 Rad23 stabilizes Rad4 from degradation by the Ub/proteasome pathway Tatiana G. Ortolan, Li Chen, Prasad Tongaonkar, and Kiran Madura PMCID: PMC545455 Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation P. Christoph Champ, Sandor Maurice, Jeffrey M. Vargason, Tracy Camp, and P. Shing Ho PMCID: PMC545456 Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct combinations of post-translational modifications Lianna Johnson, Sahana Mollah, Benjamin A. Garcia, Tara L. Muratore, Jeffrey Shabanowitz, Donald F. Hunt, and Steven E. Jacobsen PMCID: PMC545460 Coordinated functions of WSS1, PSY2 and TOF1 in the DNA damage response Bryan M. O'Neill, Denise Hanway, Elizabeth A. Winzeler, and Floyd E. Romesberg PMCID: PMC545462 Pa-AGOG, the founding member of a new family of archaeal 8-oxoguanine DNA-glycosylases Alessandro A. Sartori, Gondichatnahalli M. Lingaraju, Peter Hunziker, Fritz K. Winkler, and Josef Jiricny PMCID: PMC545463 Initiation of translocation by Type I restriction-modification enzymes is associated with a short DNA extrusion John van Noort, Thijn van der Heijden, Christina F. Dutta, Keith Firman, and Cees Dekker PMCID: PMC545467 A 16S rRNA–tRNA product containing a nucleotide phototrimer and specific for tRNA in the P/E hybrid state in the Escherichia coli ribosome Wayne Huggins and Paul Wollenzien PMCID: PMC545443 A survey of splice variants of the human hypoxanthine phosphoribosyl transferase and DNA polymerase beta genes: products of alternative or aberrant splicing? Adonis Skandalis and Elke Uribe PMCID: PMC545452 Formation of 8-oxo-7,8-dihydroguanine-radicals in γ-irradiated DNA by multiple one-electron oxidations Lata I. Shukla, Amitava Adhikary, Robert Pazdro, David Becker, and Michael D. Sevilla PMCID: PMC545457 Telomere length regulation and transcriptional silencing in KU80-deficient Trypanosoma brucei Christian J. Janzen, Fabian Lander, Oliver Dreesen, and George A. M. Cross PMCID: PMC545459 Sequence-dependent cytotoxicity of second-generation oligonucleotides Denis Drygin, Stephen Barone, and C. Frank Bennett PMCID: PMC545465 Peptide conjugates for chromosomal gene targeting by triplex-forming oligonucleotides Faye A. Rogers, Muthiah Manoharan, Peter Rabinovitch, David C. Ward, and Peter M. Glazer PMCID: PMC545466 Genome-wide prediction of stop codon readthrough during translation in the yeast Saccharomyces cerevisiae I. Williams, J. Richardson, A. Starkey, and I. Stansfield PMCID: PMC545446 Differences in LexA regulon structure among Proteobacteria through in vivo assisted comparative genomics Ivan Erill, Mónica Jara, Noelia Salvador, Marcos Escribano, Susana Campoy, and Jordi Barbé PMCID: PMC545464 Identifying estrogen receptor α target genes using integrated computational genomics and chromatin immunoprecipitation microarray Victor X. Jin, Yu-Wei Leu, Sandya Liyanarachchi, Hao Sun, Meiyun Fan, Kenneth P. Nephew, Tim H.-M. Huang, and Ramana V. Davuluri PMCID: PMC545447 Efficient computation of optimal oligo–RNA binding Nathan O. Hodas and Daniel P. Aalberts PMCID: PMC545450 An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs Hong-Wu Ma, Bharani Kumar, Uta Ditges, Florian Gunzer, Jan Buer, and An-Ping Zeng PMCID: PMC545451 The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery Leven M. Wadley and Anna Marie Pyle PMCID: PMC545444 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 Richard Ting, Jason M. Thomas, Leonard Lermer, and David M. Perrin PMCID: PMC545449 Looking into DNA recognition: zinc finger binding specificity Guillaume Paillard, Cyril Deremble, and Richard Lavery PMCID: PMC545445 Conformational model of the Holliday junction transition deduced from molecular dynamics simulations Jin Yu, Taekjip Ha, and Klaus Schulten PMCID: PMC545448 Short-patch correction of C/C mismatches in human cells Regula Muheim-Lenz, Tonko Buterin, Giancarlo Marra, and Hanspeter Naegeli PMCID: PMC545458 Tfg3, a subunit of the general transcription factor TFIIF in Schizosaccharomyces pombe, functions under stress conditions Makoto Kimura and Akira Ishihama PMCID: PMC545442 NAR Methods Online Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes Anna Válóczi, Csaba Hornyik, Nóra Varga, József Burgyán, Sakari Kauppinen, and Zoltán Havelda PMCID: PMC545470 Low-fidelity Pyrococcus furiosus DNA polymerase mutants useful in error-prone PCR Benjamin D. Biles and Bernard A. Connolly PMCID: PMC545472 Surface plasmon field-enhanced fluorescence spectroscopy in PCR product analysis by peptide nucleic acid probes Danfeng Yao, Fang Yu, Junyoung Kim, Judith Scholz, Peter E. Nielsen, Eva-Kathrin Sinner, and Wolfgang Knoll PMCID: PMC545473 Sigmoidal curve-fitting redefines quantitative real-time PCR with the prospective of developing automated high-throughput applications R. G. Rutledge PMCID: PMC545475 Dissecting RNA silencing in protoplasts uncovers novel effects of viral suppressors on the silencing pathway at the cellular level Yijun Qi, Xuehua Zhong, Asuka Itaya, and Biao Ding PMCID: PMC545478 Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data Keith Le, Katherine Mitsouras, Meenakshi Roy, Qi Wang, Qiang Xu, Stanley F. Nelson, and Christopher Lee PMCID: PMC545471 MARA: a novel approach for highly multiplexed locus-specific SNP genotyping using high-density DNA oligonucleotide arrays Michael H. Shapero, Jane Zhang, Ann Loraine, Weiwei Liu, Xiaojun Di, Guoying Liu, and Keith W. Jones PMCID: PMC545476 Selection of genomic sequences that bind tightly to Ff gene 5 protein: primer-free genomic SELEX Jin-Der Wen and Donald M. Gray PMCID: PMC545477 Evaluation of vector-primed cDNA library production from microgram quantities of total RNA Jonathan Kuo, Jason Inman, Michael Brownstein, and Ted B. Usdin PMCID: PMC545479 Tris-borate is a poor counterion for RNA: a cautionary tale for RNA folding studies Karen L. Buchmueller and Kevin M. Weeks PMCID: PMC545480 Using DSP, a reversible cross-linker, to fix tissue sections for immunostaining, microdissection and expression profiling Charlie C. Xiang, Eva Mezey, Mei Chen, Sharon Key, Li Ma, and Michael J. Brownstein PMCID: PMC545482 A simple, bead-based approach for multi-SNP molecular haplotyping James D. Hurley, Linda J. Engle, Jesse T. Davis, Adam M. Welsh, and John E. Landers PMCID: PMC545484 Spatially and temporally controlled gene transfer by electroporation into adherent cells on plasmid DNA-loaded electrodes Fumio Yamauchi, Koichi Kato, and Hiroo Iwata PMCID: PMC545474 Development of a micro-array to detect human and mouse microRNAs and characterization of expression in human organs Yingqing Sun, Seongjoon Koo, Neill White, Eigen Peralta, Christine Esau, Nicholas M. Dean, and Ranjan J. Perera PMCID: PMC545483 Expression of the sorghum 10-member kafirin gene cluster in maize endosperm Rentao Song, Gregorio Segal, and Joachim Messing PMCID: PMC545481 Corrigenda Nucleic Acids Res. 2004; 32(22): 6716. Published online 2004 December 29. doi: 10.1093/nar/gki172.PMCID: PMC545469 Corrects: E. A. Worthey, et al. Leishmania major chromosome 3 contains two long convergent polycistronic gene clusters separated by a tRNA gene. Nucleic Acids Res. 2003 July 15; 31(14): 4201–4210. Nucleic Acids Res. 2004; 32(22): 6717. Published online 2004 December 29. doi: 10.1093/nar/gki147.PMCID: PMC545468 Corrects: Vera I. Hashem, et al. Chemotherapeutic deletion of CTG repeats in lymphoblast cells from DM1 patients. Nucleic Acids Res. 2004; 32(21): 6334–6346. Erratum Nucleic Acids Res. 2004; 32(22): 6718. Published online 2005 January 6. doi: 10.1093/nar/gkh993.PMCID: PMC545461 Corrects: CORRIGENDA. Nucleic Acids Res. 2004; 32(19): 5972. |
