Nucleic Acids Research

Articles:

Marek Napierala, Daniel Michalowski, Mateusz de Mezer, and Wlodzimierz J. Krzyzosiak

Facile FMR1 mRNA structure regulation by interruptions in CGG repeats
Nucl. Acids Res. 2005 33: 451-463; doi:10.1093/nar/gki186 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Benoit St-Pierre, Xudong Liu, Lan-Chau T. Kha, Xudong Zhu, Owen Ryan, Zhe Jiang, and Eldad Zacksenhaus

Conserved and specific functions of mammalian ssu72
Nucl. Acids Res. 2005 33: 464-477; doi:10.1093/nar/gki171 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Natalia Nevskaya, Svetlana Tishchenko, Azat Gabdoulkhakov, Ekaterina Nikonova, Oleg Nikonov, Alexei Nikulin, Olga Platonova, Maria Garber, Stanislav Nikonov, and Wolfgang Piendl

Ribosomal protein L1 recognizes the same specific structural motif in its target sites on the autoregulatory mRNA and 23S rRNA
Nucl. Acids Res. 2005 33: 478-485; doi:10.1093/nar/gki194 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kim Moran-Jones, Lyndal Wayman, Derek D. Kennedy, Roger R. Reddel, Sergio Sara, Mark J. Snee, and Ross Smith

hnRNP A2, a potential ssDNA/RNA molecular adapter at the telomere
Nucl. Acids Res. 2005 33: 486-496; doi:10.1093/nar/gki203 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Priyamvada Rai, David E. Wemmer, and Stuart Linn

Preferential binding and structural distortion by Fe²⁺ at RGGG-containing DNA sequences correlates with enhanced oxidative cleavage at such sequences
Nucl. Acids Res. 2005 33: 497-510; doi:10.1093/nar/gki192 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Kazutaka Katoh, Kei-ichi Kuma, Hiroyuki Toh, and Takashi Miyata

MAFFT version 5: improvement in accuracy of multiple sequence alignment
Nucl. Acids Res. 2005 33: 511-518; doi:10.1093/nar/gki198 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

D. M. Layton and R. Bundschuh

A statistical analysis of RNA folding algorithms through thermodynamic parameter perturbation
Nucl. Acids Res. 2005 33: 519-524; doi:10.1093/nar/gkh983 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alexander B. Kotlyar, Natalia Borovok, Tatiana Molotsky, Ludmila Fadeev, and Michael Gozin

In vitro synthesis of uniform poly(dG)–poly(dC) by Klenow exo^– fragment of polymerase I
Nucl. Acids Res. 2005 33: 525-535; doi:10.1093/nar/gki178 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kelly S. Trego, Yali Zhu, and Deborah S. Parris

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
Nucl. Acids Res. 2005 33: 536-545; doi:10.1093/nar/gki196 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Zhijie Liu, Fenglou Mao, Jun-tao Guo, Bo Yan, Peng Wang, Youxing Qu, and Ying Xu

Quantitative evaluation of protein–DNA interactions using an optimized knowledge-based potential
Nucl. Acids Res. 2005 33: 546-558; doi:10.1093/nar/gki204 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alexander E. Vinogradov

Noncoding DNA, isochores and gene expression: nucleosome formation potential
Nucl. Acids Res. 2005 33: 559-563; doi:10.1093/nar/gki184 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alessandra Napoli, Anna Valenti, Vincenzo Salerno, Marc Nadal, Florence Garnier, Mosè Rossi, and Maria Ciaramella

Functional interaction of reverse gyrase with single-strand binding protein of the archaeon Sulfolobus
Nucl. Acids Res. 2005 33: 564-576; doi:10.1093/nar/gki202 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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

The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice
Nucl. Acids Res. 2005 33: 577-586; doi:10.1093/nar/gki206 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Joydeep Basu, Gregory Stromberg, George Compitello, Huntington F. Willard, and Gil Van Bokkelen

Rapid creation of BAC-based human artificial chromosome vectors by transposition with synthetic alpha-satellite arrays
Nucl. Acids Res. 2005 33: 587-596; doi:10.1093/nar/gki207 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Haibo Bai, Siân Jones, Xin Guan, Teresa M. Wilson, Julian R. Sampson, Jeremy P. Cheadle, and A-Lien Lu

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
Nucl. Acids Res. 2005 33: 597-604; doi:10.1093/nar/gki209 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yael Garten, Shai Kaplan, and Yitzhak Pilpel

Extraction of transcription regulatory signals from genome-wide DNA–protein interaction data
Nucl. Acids Res. 2005 33: 605-615; doi:10.1093/nar/gki166 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Victor Kunin, Dag Ahren, Leon Goldovsky, Paul Janssen, and Christos A. Ouzounis

Measuring genome conservation across taxa: divided strains and united kingdoms
Nucl. Acids Res. 2005 33: 616-621; doi:10.1093/nar/gki181 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Maris Zivarts, Yong Liu, and Ronald R. Breaker

Engineered allosteric ribozymes that respond to specific divalent metal ions
Nucl. Acids Res. 2005 33: 622-631; doi:10.1093/nar/gki182 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Peter Gill, James Curran, and Keith Elliot

A graphical simulation model of the entire DNA process associated with the analysis of short tandem repeat loci
Nucl. Acids Res. 2005 33: 632-643; doi:10.1093/nar/gki205 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jane Kawaoka and Anna Marie Pyle

Choosing between DNA and RNA: the polymer specificity of RNA helicase NPH-II
Nucl. Acids Res. 2005 33: 644-649; doi:10.1093/nar/gki208 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Neil P. Shull, Sherry L. Spinelli, and Eric M. Phizicky

A highly specific phosphatase that acts on ADP-ribose 1''-phosphate, a metabolite of tRNA splicing in Saccharomyces cerevisiae
Nucl. Acids Res. 2005 33: 650-660; doi:10.1093/nar/gki211 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sebastian D. Pawlak, Monika Radlinska, Agnieszka A. Chmiel, Janusz M. Bujnicki, and Krzysztof J. Skowronek

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
Nucl. Acids Res. 2005 33: 661-671; doi:10.1093/nar/gki213 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Yasuhiro Ushijima, Yohei Tominaga, Tomofumi Miura, Daisuke Tsuchimoto, Kunihiko Sakumi, and Yusaku Nakabeppu

A functional analysis of the DNA glycosylase activity of mouse MUTYH protein excising 2-hydroxyadenine opposite guanine in DNA
Nucl. Acids Res. 2005 33: 672-682; doi:10.1093/nar/gki214 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kunio Kikuchi, Takuya Umehara, Kotaro Fukuda, Atsushi Kuno, Tsunemi Hasegawa, and Satoshi Nishikawa

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
Nucl. Acids Res. 2005 33: 683-692; doi:10.1093/nar/gki215 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Mariola Dutkiewicz and Jerzy Ciesiolka

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
Nucl. Acids Res. 2005 33: 693-703; doi:10.1093/nar/gki218 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Martin Toussaint, Isabelle Dionne, and Raymund J. Wellinger

Limited TTP supply affects telomere length regulation in a telomerase-independent fashion
Nucl. Acids Res. 2005 33: 704-713; doi:10.1093/nar/gki219 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Simon Minovitsky, Sherry L. Gee, Shiruyeh Schokrpur, Inna Dubchak, and John G. Conboy

The splicing regulatory element, UGCAUG, is phylogenetically and spatially conserved in introns that flank tissue-specific alternative exons
Nucl. Acids Res. 2005 33: 714-724; doi:10.1093/nar/gki210 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jozica Dolenc, Chris Oostenbrink, Joze Koller, and Wilfred F. van Gunsteren

Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site
Nucl. Acids Res. 2005 33: 725-733; doi:10.1093/nar/gki195 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Elias Seif, Jessica Leigh, Yu Liu, Ingeborg Roewer, Lise Forget, and B. Franz Lang

Comparative mitochondrial genomics in zygomycetes: bacteria-like RNase P RNAs, mobile elements and a close source of the group I intron invasion in angiosperms
Nucl. Acids Res. 2005 33: 734-744; doi:10.1093/nar/gki199 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Taiichi Sakamoto, Akihiro Oguro, Gota Kawai, Takashi Ohtsu, and Yoshikazu Nakamura

NMR structures of double loops of an RNA aptamer against mammalian initiation factor 4A
Nucl. Acids Res. 2005 33: 745-754; doi:10.1093/nar/gki222 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

A. J. Smith and N. J. Savery

RNA polymerase mutants defective in the initiation of transcription-coupled DNA repair
Nucl. Acids Res. 2005 33: 755-764; doi:10.1093/nar/gki225 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Takashi Tsuyama, Shusuke Tada, Saori Watanabe, Masayuki Seki, and Takemi Enomoto

Licensing for DNA replication requires a strict sequential assembly of Cdc6 and Cdt1 onto chromatin in Xenopus egg extracts
Nucl. Acids Res. 2005 33: 765-775; doi:10.1093/nar/gki226 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Maria del Carmen Seleme, Olivier Disson, Stéphanie Robin, Christine Brun, Danielle Teninges, and Alain Bucheton

In vivo RNA localization of I factor, a non-LTR retrotransposon, requires a cis-acting signal in ORF2 and ORF1 protein
Nucl. Acids Res. 2005 33: 776-785; doi:10.1093/nar/gki221 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Shigeharu Takiya, Tetsurou Ishikawa, Katsuya Ohtsuka, Yoshinori Nishita, and Yoshiaki Suzuki

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
Nucl. Acids Res. 2005 33: 786-795; doi:10.1093/nar/gki228 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ellen M. Westerhout, Marcel Ooms, Monique Vink, Atze T. Das, and Ben Berkhout

HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome
Nucl. Acids Res. 2005 33: 796-804; doi:10.1093/nar/gki220 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Corrigendum:

Michael G. Kemp, Maloy Ghosh, Guoqi Liu, and Michael Leffak

The histone deacetylase inhibitor trichostatin A alters the pattern of DNA replication origin activity in human cells
Nucl. Acids Res. 2005 33: 805; doi:10.1093/nar/gki229 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

A. Pemov, H. Modi, D. P. Chandler, and S. Bavykin

DNA analysis with multiplex microarray-enhanced PCR
Nucl. Acids Res. 2005 33: e11; doi:10.1093/nar/gnh184 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jongmin Nam, Kerstin Kaufmann, Günter Theißen, and Masatoshi Nei

A simple method for predicting the functional differentiation of duplicate genes and its application to MIKC-type MADS-box genes
Nucl. Acids Res. 2005 33: e12; doi:10.1093/nar/gni003 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Douglas Horejsh, Federico Martini, Fabrizio Poccia, Giuseppe Ippolito, Antonino Di Caro, and Maria R. Capobianchi

A molecular beacon, bead-based assay for the detection of nucleic acids by flow cytometry
Nucl. Acids Res. 2005 33: e13; doi:10.1093/nar/gni015 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

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

Gene trap and gene inversion methods for conditional gene inactivation in the mouse
Nucl. Acids Res. 2005 33: e14; doi:10.1093/nar/gni016 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Y. Paul Bao, Martin Huber, Tai-Fen Wei, Sudhakar S. Marla, James J. Storhoff, and Uwe R. Müller

SNP identification in unamplified human genomic DNA with gold nanoparticle probes
Nucl. Acids Res. 2005 33: e15; doi:10.1093/nar/gni017 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ilgar Z. Mamedov, Elena S. Arzumanyan, Anna L. Amosova, Yuri B. Lebedev, and Eugene D. Sverdlov

Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach
Nucl. Acids Res. 2005 33: e16; doi:10.1093/nar/gni018 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Ru-Qiang Liang, Wei Li, Yang Li, Cui-yan Tan, Jian-Xun Li, You-Xin Jin, and Kang-Cheng Ruan

An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe
Nucl. Acids Res. 2005 33: e17; doi:10.1093/nar/gni019 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Paul Clarke, Páraic Ó Cuív, and Michael O'Connell

Novel mobilizable prokaryotic two-hybrid system vectors for high-throughput protein interaction mapping in Escherichia coli by bacterial conjugation
Nucl. Acids Res. 2005 33: e18; doi:10.1093/nar/gni011 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jae Yang Song, Hyun Gyu Park, Sung-Ouk Jung, and JaeChan Park

Diagnosis of HNF-1 mutations on a PNA zip-code microarray by single base extension
Nucl. Acids Res. 2005 33: e19; doi:10.1093/nar/gni020 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Toshiaki Shigeoka, Masashi Kawaichi, and Yasumasa Ishida

Suppression of nonsense-mediated mRNA decay permits unbiased gene trapping in mouse embryonic stem cells
Nucl. Acids Res. 2005 33: e20; doi:10.1093/nar/gni022 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Sabine Ehrt, Xinzheng V. Guo, Christopher M. Hickey, Marvin Ryou, Mercedes Monteleone, Lee W. Riley, and Dirk Schnappinger

Controlling gene expression in mycobacteria with anhydrotetracycline and Tet repressor
Nucl. Acids Res. 2005 33: e21; doi:10.1093/nar/gni013 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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

Tetracycline-inducible gene regulation in mycobacteria
Nucl. Acids Res. 2005 33: e22; doi:10.1093/nar/gni023 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jinke Wang, Tongxiang Li, Xiaoying Guo, and Zuhong Lu

Exonuclease III protection assay with FRET probe for detecting DNA-binding proteins
Nucl. Acids Res. 2005 33: e23; doi:10.1093/nar/gni021 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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