Nucleic Acids Research

Articles:

Jaunius Urbonavicius, Stéphane Skouloubris, Hannu Myllykallio, and Henri Grosjean

Identification of a novel gene encoding a flavin-dependent tRNA:m⁵U methyltransferase in bacteria—evolutionary implications
Nucl. Acids Res. 2005 33: 3955-3964; doi:10.1093/nar/gki703 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Peter Haeberli, Imre Berger, Pradeep S. Pallan, and Martin Egli

Syntheses of 4'-thioribonucleosides and thermodynamic stability and crystal structure of RNA oligomers with incorporated 4'-thiocytosine
Nucl. Acids Res. 2005 33: 3965-3975; doi:10.1093/nar/gki704 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Miguel Landers, Margaret A. Calciano, Dan Colosi, Heather Glatt-Deeley, Joseph Wagstaff, and Marc Lalande

Maternal disruption of Ube3a leads to increased expression of Ube3a-ATS in trans
Nucl. Acids Res. 2005 33: 3976-3984; doi:10.1093/nar/gki705 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Dechen Fu and Jun Ma

Interplay between positive and negative activities that influence the role of Bicoid in transcription
Nucl. Acids Res. 2005 33: 3985-3993; doi:10.1093/nar/gki691 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

S. Balaji, M. Madan Babu, Lakshminarayan M. Iyer, and L. Aravind

Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains
Nucl. Acids Res. 2005 33: 3994-4006; doi:10.1093/nar/gki709 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Marzena A. Lewandowska, Cristiana Stuani, Alireza Parvizpur, Francisco E. Baralle, and Franco Pagani

Functional studies on the ATM intronic splicing processing element
Nucl. Acids Res. 2005 33: 4007-4015; doi:10.1093/nar/gki710 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Amit N. Khachane, Kenneth N. Timmis, and Vítor A. P. Martins dos Santos

Uracil content of 16S rRNA of thermophilic and psychrophilic prokaryotes correlates inversely with their optimal growth temperatures
Nucl. Acids Res. 2005 33: 4016-4022; doi:10.1093/nar/gki714 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Qi-En Wang, Qianzheng Zhu, Gulzar Wani, Mohamed A. El-Mahdy, Jinyou Li, and Altaf A. Wani

DNA repair factor XPC is modified by SUMO-1 and ubiquitin following UV irradiation
Nucl. Acids Res. 2005 33: 4023-4034; doi:10.1093/nar/gki684 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

M. L. Green and P. D. Karp

Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers
Nucl. Acids Res. 2005 33: 4035-4039; doi:10.1093/nar/gki711 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Kyudong Han, Shurjo K. Sen, Jianxin Wang, Pauline A. Callinan, Jungnam Lee, Richard Cordaux, Ping Liang, and Mark A. Batzer

Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages
Nucl. Acids Res. 2005 33: 4040-4052; doi:10.1093/nar/gki718 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Chun-Hua Hsu, Chinpan Chen, Maou-Lin Jou, Alan Yueh-Luen Lee, Yu-Ching Lin, Yi-Ping Yu, Wei-Ting Huang, and Shih-Hsiung Wu

Structural and DNA-binding studies on the bovine antimicrobial peptide, indolicidin: evidence for multiple conformations involved in binding to membranes and DNA
Nucl. Acids Res. 2005 33: 4053-4064; doi:10.1093/nar/gki725 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Samir Amrane, Barbara Saccà, Martin Mills, Madhu Chauhan, Horst H. Klump, and Jean-Louis Mergny

Length-dependent energetics of (CTG)_n and (CAG)_n trinucleotide repeats
Nucl. Acids Res. 2005 33: 4065-4077; doi:10.1093/nar/gki716 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jiyoung Kim, Kathryn Robertson, Katie J. L. Mylonas, Fiona C. Gray, Iryna Charapitsa, and Stuart A. MacNeill

Contrasting effects of Elg1–RFC and Ctf18–RFC inactivation in the absence of fully functional RFC in fission yeast
Nucl. Acids Res. 2005 33: 4078-4089; doi:10.1093/nar/gki728 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Justin S. Bois, Suvir Venkataraman, Harry M. T. Choi, Andrew J. Spakowitz, Zhen-Gang Wang, and Niles A. Pierce

Topological constraints in nucleic acid hybridization kinetics
Nucl. Acids Res. 2005 33: 4090-4095; doi:10.1093/nar/gki721 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jonathan Livny, Michael A. Fogel, Brigid M. Davis, and Matthew K. Waldor

sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes
Nucl. Acids Res. 2005 33: 4096-4105; doi:10.1093/nar/gki715 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kristie D. Goodwin, Eric C. Long, and Millie M. Georgiadis

A host–guest approach for determining drug–DNA interactions: an example using netropsin
Nucl. Acids Res. 2005 33: 4106-4116; doi:10.1093/nar/gki717 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Emmanuele Crespan, Samantha Zanoli, Anastasiya Khandazhinskaya, Igor Shevelev, Maxim Jasko, Ludmila Alexandrova, Marina Kukhanova, Giuseppina Blanca, Giuseppe Villani, Ulrich Hübscher, Silvio Spadari, and Giovanni Maga

Incorporation of non-nucleoside triphosphate analogues opposite to an abasic site by human DNA polymerases ß and
Nucl. Acids Res. 2005 33: 4117-4127; doi:10.1093/nar/gki723 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Orly Laufman, Ron Ben Yosef, Noam Adir, and Haim Manor

Cloning and characterization of the Schizosaccharomyces pombe homologs of the human protein Translin and the Translin-associated protein TRAX
Nucl. Acids Res. 2005 33: 4128-4139; doi:10.1093/nar/gki727 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Scott D. Rose, Dong-Ho Kim, Mohammed Amarzguioui, Jeremy D. Heidel, Michael A. Collingwood, Mark E. Davis, John J. Rossi, and Mark A. Behlke

Functional polarity is introduced by Dicer processing of short substrate RNAs
Nucl. Acids Res. 2005 33: 4140-4156; doi:10.1093/nar/gki732 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Olga V. Iarovaia, Sergey B. Akopov, Lev G. Nikolaev, Eugene D. Sverdlov, and Sergey V. Razin

Induction of transcription within chromosomal DNA loops flanked by MAR elements causes an association of loop DNA with the nuclear matrix
Nucl. Acids Res. 2005 33: 4157-4163; doi:10.1093/nar/gki733 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Julie D. Thompson, Stephen R. Holbrook, Kazutaka Katoh, Patrice Koehl, Dino Moras, Eric Westhof, and Olivier Poch

MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences
Nucl. Acids Res. 2005 33: 4164-4171; doi:10.1093/nar/gki735 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Chin-Ju Park, Joon-Hwa Lee, and Byong-Seok Choi

Solution structure of the DNA-binding domain of RPA from Saccharomyces cerevisiae and its interaction with single-stranded DNA and SV40 T antigen
Nucl. Acids Res. 2005 33: 4172-4181; doi:10.1093/nar/gki736 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Christine Granotier, Gaëlle Pennarun, Lydia Riou, Françoise Hoffschir, Laurent R. Gauthier, Anne De Cian, Dennis Gomez, Eliane Mandine, Jean-François Riou, Jean-Louis Mergny, Patrick Mailliet, Bernard Dutrillaux, and François D. Boussin

Preferential binding of a G-quadruplex ligand to human chromosome ends
Nucl. Acids Res. 2005 33: 4182-4190; doi:10.1093/nar/gki722 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Takatoshi Morinaga, Atsushi Enomoto, Yohei Shimono, Fumiko Hirose, Naoyuki Fukuda, Atsushi Dambara, Mayumi Jijiwa, Kumi Kawai, Katsunori Hashimoto, Masatoshi Ichihara, Naoya Asai, Yoshiki Murakumo, Seiichi Matsuo, and Masahide Takahashi

GDNF-inducible zinc finger protein 1 is a sequence-specific transcriptional repressor that binds to the HOXA10 gene regulatory region
Nucl. Acids Res. 2005 33: 4191-4201; doi:10.1093/nar/gki734 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Vasily Sosunov, Savva Zorov, Ekaterina Sosunova, Anatoly Nikolaev, Irina Zakeyeva, Irina Bass, Alex Goldfarb, Vadim Nikiforov, Konstantin Severinov, and Arkady Mustaev

The involvement of the aspartate triad of the active center in all catalytic activities of multisubunit RNA polymerase
Nucl. Acids Res. 2005 33: 4202-4211; doi:10.1093/nar/gki688 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Bahru Habtemariam, Victor M. Anisimov, and Alexander D. MacKerell, Jr

Cooperative binding of DNA and CBFß to the Runt domain of the CBF studied via MD simulations
Nucl. Acids Res. 2005 33: 4212-4222; doi:10.1093/nar/gki724 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Erika Brunet, Maddalena Corgnali, Loïc Perrouault, Victoria Roig, Ulysse Asseline, Mads D. Sørensen, B. Ravindra Babu, Jesper Wengel, and Carine Giovannangeli

Intercalator conjugates of pyrimidine locked nucleic acid-modified triplex-forming oligonucleotides: improving DNA binding properties and reaching cellular activities
Nucl. Acids Res. 2005 33: 4223-4234; doi:10.1093/nar/gki726 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Aviad Zick, Itay Onn, Rachel Bezalel, Hanah Margalit, and Joseph Shlomai

Assigning functions to genes: identification of S-phase expressed genes in Leishmania major based on post-transcriptional control elements
Nucl. Acids Res. 2005 33: 4235-4242; doi:10.1093/nar/gki742 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Emilie Auriol, Lise-Marie Billard, Frédérique Magdinier, and Robert Dante

Specific binding of the methyl binding domain protein 2 at the BRCA1-NBR2 locus
Nucl. Acids Res. 2005 33: 4243-4254; doi:10.1093/nar/gki729 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Kobe Florquin, Yvan Saeys, Sven Degroeve, Pierre Rouzé, and Yves Van de Peer

Large-scale structural analysis of the core promoter in mammalian and plant genomes
Nucl. Acids Res. 2005 33: 4255-4264; doi:10.1093/nar/gki737 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Mei-Chi Su, Chung-Te Chang, Chiu-Hui Chu, Ching-Hsiu Tsai, and Kung-Yao Chang

An atypical RNA pseudoknot stimulator and an upstream attenuation signal for –1 ribosomal frameshifting of SARS coronavirus
Nucl. Acids Res. 2005 33: 4265-4275; doi:10.1093/nar/gki731 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Pierre de la Grange, Martin Dutertre, Natalia Martin, and Didier Auboeuf

FAST DB: a website resource for the study of the expression regulation of human gene products
Nucl. Acids Res. 2005 33: 4276-4284; doi:10.1093/nar/gki738 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Véronique Goffin, Dominique Demonté, Caroline Vanhulle, Stéphane de Walque, Yvan de Launoit, Arsène Burny, Yves Collette, and Carine Van Lint

Transcription factor binding sites in the pol gene intragenic regulatory region of HIV-1 are important for virus infectivity
Nucl. Acids Res. 2005 33: 4285-4310; doi:10.1093/nar/gki720 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Perrine J. Martin, Virginie Lardeux, and Philippe Lefebvre

The proliferating cell nuclear antigen regulates retinoic acid receptor transcriptional activity through direct protein–protein interaction
Nucl. Acids Res. 2005 33: 4311-4321; doi:10.1093/nar/gki745 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yong Yang, Lauryn E. Sass, Chunwei Du, Peggy Hsieh, and Dorothy A. Erie

Determination of protein–DNA binding constants and specificities from statistical analyses of single molecules: MutS–DNA interactions
Nucl. Acids Res. 2005 33: 4322-4334; doi:10.1093/nar/gki708 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

You Jung Kim, Andrew Boyd, Brian D. Athey, and Jignesh M. Patel

miBLAST: scalable evaluation of a batch of nucleotide sequence queries with BLAST
Nucl. Acids Res. 2005 33: 4335-4344; doi:10.1093/nar/gki739 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Snehlata Tripathi, Binay Chaubey, Sabyasachi Ganguly, Dylan Harris, Ralph A Casale, and Virendra N. Pandey

Anti-HIV-1 activity of anti-TAR polyamide nucleic acid conjugated with various membrane transducing peptides
Nucl. Acids Res. 2005 33: 4345-4356; doi:10.1093/nar/gki743 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tal Oren, Ingrid Torregroza, and Todd Evans

An Oct-1 binding site mediates activation of the gata2 promoter by BMP signaling
Nucl. Acids Res. 2005 33: 4357-4367; doi:10.1093/nar/gki746 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Frédéric Allemand, Nathalie Mathy, Dominique Brechemier-Baey, and Ciarán Condon

The 5S rRNA maturase, ribonuclease M5, is a Toprim domain family member
Nucl. Acids Res. 2005 33: 4368-4376; doi:10.1093/nar/gki752 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Corrigendum:

Anil G. Jegga, Ashima Gupta, Sivakumar Gowrisankar, Mrunal A. Deshmukh, Steven Connolly, Kevin Finley, and Bruce J. Aronow

CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes
Nucl. Acids Res. 2005 33: 4377; doi:10.1093/nar/gki740 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Rajeev Gangal and Pankaj Sharma

Human POL II promoter prediction: time series descriptors and machine learning
Nucl. Acids Res. 2005 33: 4378; doi:10.1093/nar/gki753 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Wu Wu, Zongchao Jia, Ping Liu, Zhigang Xie, and Qun Wei

A novel PCR strategy for high-efficiency, automated site-directed mutagenesis
Nucl. Acids Res. 2005 33: e110; doi:10.1093/nar/gni115 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Felix Naef and Joerg Huelsken

Cell-type-specific transcriptomics in chimeric models using transcriptome-based masks
Nucl. Acids Res. 2005 33: e111; doi:10.1093/nar/gni104 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ken Ishikawa, Miki Watanabe, Toshihiro Kuroita, Ikuo Uchiyama, Janusz M. Bujnicki, Bunsei Kawakami, Masaru Tanokura, and Ichizo Kobayashi

Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (5'-GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi
Nucl. Acids Res. 2005 33: e112; doi:10.1093/nar/gni113 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jin-Woo Bae, Sung-Keun Rhee, Young-Do Nam, and Yong-Ha Park

Generation of subspecies level-specific microbial diagnostic microarrays using genes amplified from subtractive suppression hybridization as microarray probes
Nucl. Acids Res. 2005 33: e113; doi:10.1093/nar/gni112 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Julie K. A. Kasarjian, Yoshiaki Kodama, Masatake Iida, Katsura Matsuda, and Junichi Ryu

Four new type I restriction enzymes identified in Escherichia coli clinical isolates
Nucl. Acids Res. 2005 33: e114; doi:10.1093/nar/gni114 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Heikki Hyyrö, Martti Juhola, and Mauno Vihinen

Genome-wide selection of unique and valid oligonucleotides
Nucl. Acids Res. 2005 33: e115; doi:10.1093/nar/gni110 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Norimichi Nomura, Yayoi Morinaga, Nobuaki Shirai, and Yoshihiko Sako

I-ApeI: a novel intron-encoded LAGLIDADG homing endonuclease from the archaeon, Aeropyrum pernix K1
Nucl. Acids Res. 2005 33: e116; doi:10.1093/nar/gni118 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kristian M. Müller, Sabine C. Stebel, Susanne Knall, Gregor Zipf, Hubert S. Bernauer, and Katja M. Arndt

Nucleotide exchange and excision technology (NExT) DNA shuffling: a robust method for DNA fragmentation and directed evolution
Nucl. Acids Res. 2005 33: e117; doi:10.1093/nar/gni116 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Leighcraft A. Shakes, Douglas M. Garland, Deepak K. Srivastava, Ken R. Harewood, and Pradeep K. Chatterjee

Minimal cross-recombination between wild-type and loxP511 sites in vivo facilitates truncating both ends of large DNA inserts in pBACe3.6 and related vectors
Nucl. Acids Res. 2005 33: e118; doi:10.1093/nar/gni119 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Peter A. Dickson, Grant W. Montgomery, Anjali Henders, Megan J. Campbell, Nicholas G. Martin, and Michael R. James

Evaluation of multiple displacement amplification in a 5 cM STR genome-wide scan
Nucl. Acids Res. 2005 33: e119; doi:10.1093/nar/gni126 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nobuhiro Takahashi and Igor B. Dawid

Characterization of zebrafish Rad52 and replication protein A for oligonucleotide-mediated mutagenesis
Nucl. Acids Res. 2005 33: e120; doi:10.1093/nar/gni122 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Xiao-bo Zhong, Lin Leng, Anna Beitin, Rui Chen, Courtney McDonald, Betty Hsiao, Robert D. Jenison, Insoo Kang, Sung-Hwan Park, Annette Lee, Peter Gregersen, Philip Thuma, Patricia Bray-Ward, David C. Ward, and Richard Bucala

Simultaneous detection of microsatellite repeats and SNPs in the macrophage migration inhibitory factor (MIF) gene by thin-film biosensor chips and application to rural field studies
Nucl. Acids Res. 2005 33: e121; doi:10.1093/nar/gni123 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Guihong Tan, Yin Gao, Miao Shi, Xinyue Zhang, Shanping He, Zhangliang Chen, and Chengcai An

SiteFinding-PCR: a simple and efficient PCR method for chromosome walking
Nucl. Acids Res. 2005 33: e122; doi:10.1093/nar/gni124 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Zhiqiang Gao and Natalia C. Tansil

An ultrasensitive photoelectrochemical nucleic acid biosensor
Nucl. Acids Res. 2005 33: e123; doi:10.1093/nar/gni125 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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