| | Articles Facile FMR1 mRNA structure regulation by interruptions in CGG repeats Marek Napierala, Daniel Michalowski, Mateusz de Mezer, and Wlodzimierz J. Krzyzosiak PMCID: PMC548340 Conserved and specific functions of mammalian ssu72 Benoit St-Pierre, Xudong Liu, Lan-Chau T. Kha, Xudong Zhu, Owen Ryan, Zhe Jiang, and Eldad Zacksenhaus PMCID: PMC548335 Ribosomal protein L1 recognizes the same specific structural motif in its target sites on the autoregulatory mRNA and 23S rRNA Natalia Nevskaya, Svetlana Tishchenko, Azat Gabdoulkhakov, Ekaterina Nikonova, Oleg Nikonov, Alexei Nikulin, Olga Platonova, Maria Garber, Stanislav Nikonov, and Wolfgang Piendl PMCID: PMC548342 hnRNP A2, a potential ssDNA/RNA molecular adapter at the telomere Kim Moran-Jones, Lyndal Wayman, Derek D. Kennedy, Roger R. Reddel, Sergio Sara, Mark J. Snee, and Ross Smith PMCID: PMC548348 Preferential binding and structural distortion by Fe2+ at RGGG-containing DNA sequences correlates with enhanced oxidative cleavage at such sequences Priyamvada Rai, David E. Wemmer, and Stuart Linn PMCID: PMC548341 MAFFT version 5: improvement in accuracy of multiple sequence alignment Kazutaka Katoh, Kei-ichi Kuma, Hiroyuki Toh, and Takashi Miyata PMCID: PMC548345 A statistical analysis of RNA folding algorithms through thermodynamic parameter perturbation D. M. Layton and R. Bundschuh PMCID: PMC548333 In vitro synthesis of uniform poly(dG)–poly(dC) by Klenow exo− fragment of polymerase I Alexander B. Kotlyar, Natalia Borovok, Tatiana Molotsky, Ludmila Fadeev, and Michael Gozin PMCID: PMC548336 The herpes simplex virus type 1 DNA polymerase processivity factor, UL42, does not alter the catalytic activity of the UL9 origin-binding protein but facilitates its loading onto DNA Kelly S. Trego, Yali Zhu, and Deborah S. Parris PMCID: PMC548344 Quantitative evaluation of protein–DNA interactions using an optimized knowledge-based potential Zhijie Liu, Fenglou Mao, Jun-tao Guo, Bo Yan, Peng Wang, Youxing Qu, and Ying Xu PMCID: PMC548349 Noncoding DNA, isochores and gene expression: nucleosome formation potential Alexander E. Vinogradov PMCID: PMC548339 Functional interaction of reverse gyrase with single-strand binding protein of the archaeon Sulfolobus Alessandra Napoli, Anna Valenti, Vincenzo Salerno, Marc Nadal, Florence Garnier, Mosè Rossi, and Maria Ciaramella PMCID: PMC548347 The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice Byoung-Moo Lee, Young-Jin Park, Dong-Suk Park, Hee-Wan Kang, Jeong-Gu Kim, Eun-Sung Song, In-Cheol Park, Ung-Han Yoon, Jang-Ho Hahn, Bon-Sung Koo, Gil-Bok Lee, Hyungtae Kim, Hyun-Seok Park, Kyong-Oh Yoon, Jeong-Hyun Kim, Chol-hee Jung, Nae-Hyung Koh, Jeong-Sun Seo, and Seung-Joo Go PMCID: PMC548351 Rapid creation of BAC-based human artificial chromosome vectors by transposition with synthetic alpha-satellite arrays Joydeep Basu, Gregory Stromberg, George Compitello, Huntington F. Willard, and Gil Van Bokkelen PMCID: PMC548352 Functional characterization of two human MutY homolog (hMYH) missense mutations (R227W and V232F) that lie within the putative hMSH6 binding domain and are associated with hMYH polyposis Haibo Bai, Siân Jones, Xin Guan, Teresa M. Wilson, Julian R. Sampson, Jeremy P. Cheadle, and A-Lien Lu PMCID: PMC548354 Extraction of transcription regulatory signals from genome-wide DNA–protein interaction data Yael Garten, Shai Kaplan, and Yitzhak Pilpel PMCID: PMC548334 Measuring genome conservation across taxa: divided strains and united kingdoms Victor Kunin, Dag Ahren, Leon Goldovsky, Paul Janssen, and Christos A. Ouzounis PMCID: PMC548337 Engineered allosteric ribozymes that respond to specific divalent metal ions Maris Zivarts, Yong Liu, and Ronald R. Breaker PMCID: PMC548338 A graphical simulation model of the entire DNA process associated with the analysis of short tandem repeat loci Peter Gill, James Curran, and Keith Elliot PMCID: PMC548350 Choosing between DNA and RNA: the polymer specificity of RNA helicase NPH-II Jane Kawaoka and Anna Marie Pyle PMCID: PMC548353 A highly specific phosphatase that acts on ADP-ribose 1″-phosphate, a metabolite of tRNA splicing in Saccharomyces cerevisiae Neil P. Shull, Sherry L. Spinelli, and Eric M. Phizicky PMCID: PMC548356 Inference of relationships in the ‘twilight zone’ of homology using a combination of bioinformatics and site-directed mutagenesis: a case study of restriction endonucleases Bsp6I and PvuII Sebastian D. Pawlak, Monika Radlinska, Agnieszka A. Chmiel, Janusz M. Bujnicki, and Krzysztof J. Skowronek PMCID: PMC548357 A functional analysis of the DNA glycosylase activity of mouse MUTYH protein excising 2-hydroxyadenine opposite guanine in DNA Yasuhiro Ushijima, Yohei Tominaga, Tomofumi Miura, Daisuke Tsuchimoto, Kunihiko Sakumi, and Yusaku Nakabeppu PMCID: PMC548358 A hepatitis C virus (HCV) internal ribosome entry site (IRES) domain III–IV-targeted aptamer inhibits translation by binding to an apical loop of domain IIId Kunio Kikuchi, Takuya Umehara, Kotaro Fukuda, Atsushi Kuno, Tsunemi Hasegawa, and Satoshi Nishikawa PMCID: PMC548359 Structural characterization of the highly conserved 98-base sequence at the 3′ end of HCV RNA genome and the complementary sequence located at the 5′ end of the replicative viral strand Mariola Dutkiewicz and Jerzy Ciesiołka PMCID: PMC548360 Limited TTP supply affects telomere length regulation in a telomerase-independent fashion Martin Toussaint, Isabelle Dionne, and Raymund J. Wellinger PMCID: PMC548361 The splicing regulatory element, UGCAUG, is phylogenetically and spatially conserved in introns that flank tissue-specific alternative exons Simon Minovitsky, Sherry L. Gee, Shiruyeh Schokrpur, Inna Dubchak, and John G. Conboy PMCID: PMC548355 Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site Jožica Dolenc, Chris Oostenbrink, Jože Koller, and Wilfred F. van Gunsteren PMCID: PMC548343 Comparative mitochondrial genomics in zygomycetes: bacteria-like RNase P RNAs, mobile elements and a close source of the group I intron invasion in angiosperms Elias Seif, Jessica Leigh, Yu Liu, Ingeborg Roewer, Lise Forget, and B. Franz Lang PMCID: PMC548346 NMR structures of double loops of an RNA aptamer against mammalian initiation factor 4A Taiichi Sakamoto, Akihiro Oguro, Gota Kawai, Takashi Ohtsu, and Yoshikazu Nakamura PMCID: PMC548364 RNA polymerase mutants defective in the initiation of transcription-coupled DNA repair A. J. Smith and N. J. Savery PMCID: PMC548365 Licensing for DNA replication requires a strict sequential assembly of Cdc6 and Cdt1 onto chromatin in Xenopus egg extracts Takashi Tsuyama, Shusuke Tada, Saori Watanabe, Masayuki Seki, and Takemi Enomoto PMCID: PMC548366 In vivo RNA localization of I factor, a non-LTR retrotransposon, requires a cis-acting signal in ORF2 and ORF1 protein Maria del Carmen Seleme, Olivier Disson, Stéphanie Robin, Christine Brun, Danielle Teninges, and Alain Bucheton PMCID: PMC548363 Fibroin-modulator-binding protein-1 (FMBP-1) contains a novel DNA-binding domain, repeats of the score and three amino acid peptide (STP), conserved from Caenorhabditis elegans to humans Shigeharu Takiya, Tetsurou Ishikawa, Katsuya Ohtsuka, Yoshinori Nishita, and Yoshiaki Suzuki PMCID: PMC548367 HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome Ellen M. Westerhout, Marcel Ooms, Monique Vink, Atze T. Das, and Ben Berkhout PMCID: PMC548362 Methods Online DNA analysis with multiplex microarray-enhanced PCR A. Pemov, H. Modi, D. P. Chandler, and S. Bavykin PMCID: PMC548369 A simple method for predicting the functional differentiation of duplicate genes and its application to MIKC-type MADS-box genes Jongmin Nam, Kerstin Kaufmann, Günter Theißen, and Masatoshi Nei PMCID: PMC548370 A molecular beacon, bead-based assay for the detection of nucleic acids by flow cytometry Douglas Horejsh, Federico Martini, Fabrizio Poccia, Giuseppe Ippolito, Antonino Di Caro, and Maria R. Capobianchi PMCID: PMC548373 Gene trap and gene inversion methods for conditional gene inactivation in the mouse Hong-Bo Xin, Ke-Yu Deng, Bo Shui, Shimian Qu, Qi Sun, Jane Lee, Kai Su Greene, Jason Wilson, Ying Yu, Morris Feldman, and Michael I. Kotlikoff PMCID: PMC548374 SNP identification in unamplified human genomic DNA with gold nanoparticle probes Y. Paul Bao, Martin Huber, Tai-Fen Wei, Sudhakar S. Marla, James J. Storhoff, and Uwe R. Müller PMCID: PMC548375 Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach Ilgar Z. Mamedov, Elena S. Arzumanyan, Anna L. Amosova, Yuri B. Lebedev, and Eugene D. Sverdlov PMCID: PMC548376 An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe Ru-Qiang Liang, Wei Li, Yang Li, Cui-yan Tan, Jian-Xun Li, You-Xin Jin, and Kang-Cheng Ruan PMCID: PMC548377 Novel mobilizable prokaryotic two-hybrid system vectors for high-throughput protein interaction mapping in Escherichia coli by bacterial conjugation Paul Clarke, Páraic Ó Cuív, and Michael O'Connell PMCID: PMC548371 Diagnosis of HNF-1α mutations on a PNA zip-code microarray by single base extension Jae Yang Song, Hyun Gyu Park, Sung-Ouk Jung, and JaeChan Park PMCID: PMC548378 Suppression of nonsense-mediated mRNA decay permits unbiased gene trapping in mouse embryonic stem cells Toshiaki Shigeoka, Masashi Kawaichi, and Yasumasa Ishida PMCID: PMC548380 Controlling gene expression in mycobacteria with anhydrotetracycline and Tet repressor Sabine Ehrt, Xinzheng V. Guo, Christopher M. Hickey, Marvin Ryou, Mercedes Monteleone, Lee W. Riley, and Dirk Schnappinger PMCID: PMC548372 Tetracycline-inducible gene regulation in mycobacteria Marian C. J. Blokpoel, Helen N. Murphy, Ronan O'Toole, Siouxsie Wiles, Ellen S. C. Runn, Graham R. Stewart, Douglas B. Young, and Brian D. Robertson PMCID: PMC548381 Exonuclease III protection assay with FRET probe for detecting DNA-binding proteins Jinke Wang, Tongxiang Li, Xiaoying Guo, and Zuhong Lu PMCID: PMC548379 Corrigendum The histone deacetylase inhibitor trichostatin A alters the pattern of DNA replication origin activity in human cells Michael G. Kemp, Maloy Ghosh, Guoqi Liu, and Michael Leffak PMCID: PMC548368 Corrects: Michael G. Kemp, et al. The histone deacetylase inhibitor trichostatin A alters the pattern of DNA replication origin activity in human cells. Nucleic Acids Res. 2005; 33(1): 325–336. |
