Nucleic Acids Research

Articles:

Joachim Forner, Bärbel Weber, Caterina Wiethölter, Rhonda C. Meyer, and Stefan Binder

Distant sequences determine 5' end formation of cox3 transcripts in Arabidopsis thaliana ecotype C24
Nucl. Acids Res. 2005 33: 4673-4682; doi:10.1093/nar/gki774 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Takuma Suematsu, Aya Sato, Masayuki Sakurai, Kimitsuna Watanabe, and Takashi Ohtsuki

A unique tRNA recognition mechanism of Caenorhabditis elegans mitochondrial EF-Tu2
Nucl. Acids Res. 2005 33: 4683-4691; doi:10.1093/nar/gki784 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Gargi Ghosal and K. Muniyappa

Saccharomyces cerevisiae Mre11 is a high-affinity G4 DNA-binding protein and a G-rich DNA-specific endonuclease: implications for replication of telomeric DNA
Nucl. Acids Res. 2005 33: 4692-4703; doi:10.1093/nar/gki777 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Torgeir Holen, Svein Erik Moe, Jan Gunnar Sørbø, Trine J. Meza, Ole Petter Ottersen, and Arne Klungland

Tolerated wobble mutations in siRNAs decrease specificity, but can enhance activity in vivo
Nucl. Acids Res. 2005 33: 4704-4710; doi:10.1093/nar/gki785 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Srinivasan Madhusudan, Fiona Smart, Paul Shrimpton, Jason L. Parsons, Laurence Gardiner, Sue Houlbrook, Denis C. Talbot, Timothy Hammonds, Paul A. Freemont, Michael J. E. Sternberg, Grigory L. Dianov, and Ian D. Hickson

Isolation of a small molecule inhibitor of DNA base excision repair
Nucl. Acids Res. 2005 33: 4711-4724; doi:10.1093/nar/gki781 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Hwa Dai, Yih-Shan Lo, Alexandra Litvinchuk, Yuh-Tai Wang, Wann-Neng Jane, Lin-June Hsiao, and Kwen-Sheng Chiang

Structural and functional characterizations of mung bean mitochondrial nucleoids
Nucl. Acids Res. 2005 33: 4725-4739; doi:10.1093/nar/gki783 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sara Rodriguez-Jato, Robert D. Nicholls, Daniel J. Driscoll, and Thomas P. Yang

Characterization of cis- and trans-acting elements in the imprinted human SNURF-SNRPN locus
Nucl. Acids Res. 2005 33: 4740-4753; doi:10.1093/nar/gki786 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Loreto Suay, Maria L. Salvador, Emnet Abesha, and Uwe Klein

Specific roles of 5' RNA secondary structures in stabilizing transcripts in chloroplasts
Nucl. Acids Res. 2005 33: 4754-4761; doi:10.1093/nar/gki760 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sergio González-Barrera, Arancha Sánchez, José F. Ruiz, Raquel Juárez, Angel J. Picher, Gloria Terrados, Paula Andrade, and Luis Blanco

Characterization of SpPol4, a unique X-family DNA polymerase in Schizosaccharomyces pombe
Nucl. Acids Res. 2005 33: 4762-4774; doi:10.1093/nar/gki780 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Alice Sears, Luke J. Peakman, Geoffrey G. Wilson, and Mark D. Szczelkun

Characterization of the Type III restriction endonuclease PstII from Providencia stuartii
Nucl. Acids Res. 2005 33: 4775-4787; doi:10.1093/nar/gki787 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alice Sears and Mark D. Szczelkun

Subunit assembly modulates the activities of the Type III restriction–modification enzyme PstII in vitro
Nucl. Acids Res. 2005 33: 4788-4796; doi:10.1093/nar/gki788 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Samuel Dugré-Brisson, George Elvira, Karine Boulay, Laurent Chatel-Chaix, Andrew J. Mouland, and Luc DesGroseillers

Interaction of Staufen1 with the 5' end of mRNA facilitates translation of these RNAs
Nucl. Acids Res. 2005 33: 4797-4812; doi:10.1093/nar/gki794 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Katrin Linker, Andrea Pautz, Marcel Fechir, Thomas Hubrich, Jobst Greeve, and Hartmut Kleinert

Involvement of KSRP in the post-transcriptional regulation of human iNOS expression–complex interplay of KSRP with TTP and HuR
Nucl. Acids Res. 2005 33: 4813-4827; doi:10.1093/nar/gki797 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Nobuyoshi Nagamine, Yuji Kawada, and Yasubumi Sakakibara

Identifying cooperative transcriptional regulations using protein–protein interactions
Nucl. Acids Res. 2005 33: 4828-4837; doi:10.1093/nar/gki793 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Karsten Siegmund, Shruti Maheshwary, Sukunath Narayanan, William Connors, Matthias Riedrich, Michael Printz, and Clemens Richert

Molecular details of quinolone–DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it
Nucl. Acids Res. 2005 33: 4838-4848; doi:10.1093/nar/gki795 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jason L. Parsons, Dmitry O. Zharkov, and Grigory L. Dianov

NEIL1 excises 3' end proximal oxidative DNA lesions resistant to cleavage by NTH1 and OGG1
Nucl. Acids Res. 2005 33: 4849-4856; doi:10.1093/nar/gki816 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Silvia Canudas, Silvia Pérez, Laura Fanti, Sergio Pimpinelli, Navjot Singh, Steven D. Hanes, Fernando Azorín, and M. Lluïsa Espinás

dSAP18 and dHDAC1 contribute to the functional regulation of the Drosophila Fab-7 element
Nucl. Acids Res. 2005 33: 4857-4864; doi:10.1093/nar/gki776 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Brent A. Mulder, Steve Anaya, Peilin Yu, Keun Woo Lee, Anvy Nguyen, Jason Murphy, Richard Willson, James M. Briggs, Xiaolian Gao, and Susan H. Hardin

Nucleotide modification at the -phosphate leads to the improved fidelity of HIV-1 reverse transcriptase
Nucl. Acids Res. 2005 33: 4865-4873; doi:10.1093/nar/gki779 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Subash C. B. Gopinath, Akimasa Matsugami, Masato Katahira, and Penmetcha K. R. Kumar

Human vault-associated non-coding RNAs bind to mitoxantrone, a chemotherapeutic compound
Nucl. Acids Res. 2005 33: 4874-4881; doi:10.1093/nar/gki809 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jana Královicová, Mikkel B. Christensen, and Igor Vorechovsky

Biased exon/intron distribution of cryptic and de novo 3' splice sites
Nucl. Acids Res. 2005 33: 4882-4898; doi:10.1093/nar/gki811 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jianjun Hu, Bin Li, and Daisuke Kihara

Limitations and potentials of current motif discovery algorithms
Nucl. Acids Res. 2005 33: 4899-4913; doi:10.1093/nar/gki791 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kevin T. Duffy, Mary Frances McAleer, William R. Davidson, Laszlo Kari, Csaba Kari, Chang-Gong Liu, Steven A. Farber, Keith C. Cheng, Jason R. Mest, Eric Wickstrom, Adam P. Dicker, and Ulrich Rodeck

Coordinate control of cell cycle regulatory genes in zebrafish development tested by cyclin D1 knockdown with morpholino phosphorodiamidates and hydroxyprolyl-phosphono peptide nucleic acids
Nucl. Acids Res. 2005 33: 4914-4921; doi:10.1093/nar/gki799 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jörg S. Hartig and Eric T. Kool

Efficient isothermal expansion of human telomeric and minisatellite repeats by Thermococcus litoralis DNA polymerase
Nucl. Acids Res. 2005 33: 4922-4927; doi:10.1093/nar/gki803 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

L. Kevin Lewis, G. Karthikeyan, Jared Cassiano, and Michael A. Resnick

Reduction of nucleosome assembly during new DNA synthesis impairs both major pathways of double-strand break repair
Nucl. Acids Res. 2005 33: 4928-4939; doi:10.1093/nar/gki806 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Rajesh Kasiviswanathan, Jae-Ho Shin, and Zvi Kelman

Interactions between the archaeal Cdc6 and MCM proteins modulate their biochemical properties
Nucl. Acids Res. 2005 33: 4940-4950; doi:10.1093/nar/gki807 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Dan Tulpan, Mirela Andronescu, Seo Bong Chang, Michael R. Shortreed, Anne Condon, Holger H. Hoos, and Lloyd M. Smith

Thermodynamically based DNA strand design
Nucl. Acids Res. 2005 33: 4951-4964; doi:10.1093/nar/gki773 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Michael R. Shortreed, Seo Bong Chang, DongGee Hong, Maggie Phillips, Bridget Campion, Dan C. Tulpan, Mirela Andronescu, Anne Condon, Holger H. Hoos, and Lloyd M. Smith

A thermodynamic approach to designing structure-free combinatorial DNA word sets
Nucl. Acids Res. 2005 33: 4965-4977; doi:10.1093/nar/gki812 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Adam P. Silverman and Eric T. Kool

Quenched autoligation probes allow discrimination of live bacterial species by single nucleotide differences in rRNA
Nucl. Acids Res. 2005 33: 4978-4986; doi:10.1093/nar/gki814 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Sergey Sheetlin, Yonil Park, and John L. Spouge

The Gumbel pre-factor k for gapped local alignment can be estimated from simulations of global alignment
Nucl. Acids Res. 2005 33: 4987-4994; doi:10.1093/nar/gki800 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Anton V. Borovjagin and Susan A. Gerbi

An evolutionary intra-molecular shift in the preferred U3 snoRNA binding site on pre-ribosomal RNA
Nucl. Acids Res. 2005 33: 4995-5005; doi:10.1093/nar/gki815 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Gali Golan, Dmitry O. Zharkov, Hadar Feinberg, Andrea S. Fernandes, Elena I. Zaika, Jadwiga H. Kycia, Arthur P. Grollman, and Gil Shoham

Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility
Nucl. Acids Res. 2005 33: 5006-5016; doi:10.1093/nar/gki796 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Corrigendum:

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: 5017; doi:10.1093/nar/gki798 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Kei Moriyama, Michiko Kimoto, Tsuneo Mitsui, Shigeyuki Yokoyama, and Ichiro Hirao

Site-specific biotinylation of RNA molecules by transcription using unnatural base pairs
Nucl. Acids Res. 2005 33: e129; doi:10.1093/nar/gni128 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Tom Ebersole, Yasuhide Okamoto, Vladimir N. Noskov, Natalay Kouprina, Jung-Hyun Kim, Sun-Hee Leem, J. Carl Barrett, Hiroshi Masumoto, and Vladimir Larionov

Rapid generation of long synthetic tandem repeats and its application for analysis in human artificial chromosome formation
Nucl. Acids Res. 2005 33: e130; doi:10.1093/nar/gni129 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Amarsanaa Jazag, Fumihiko Kanai, Hideaki Ijichi, Keisuke Tateishi, Tsuneo Ikenoue, Yasuo Tanaka, Miki Ohta, Jun Imamura, Bayasi Guleng, Yoshinari Asaoka, Takao Kawabe, Makoto Miyagishi, Kazunari Taira, and Masao Omata

Single small-interfering RNA expression vector for silencing multiple transforming growth factor-ß pathway components
Nucl. Acids Res. 2005 33: e131; doi:10.1093/nar/gni130 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ding-Gan Liu and Li Sun

Direct isolation of specific RNA-interacting proteins using a novel affinity medium
Nucl. Acids Res. 2005 33: e132; doi:10.1093/nar/gni133 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Guo-Hua Zhou, Mari Gotou, Tomoharu Kajiyama, and Hideki Kambara

Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation (BATI)
Nucl. Acids Res. 2005 33: e133; doi:10.1093/nar/gni132 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

David S. H. Chew, Kwok Pui Choi, and Ming-Ying Leung

Scoring schemes of palindrome clusters for more sensitive prediction of replication origins in herpesviruses
Nucl. Acids Res. 2005 33: e134; doi:10.1093/nar/gni135 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Cinzia Pizzi, Stefania Bortoluzzi, Andrea Bisognin, Alessandro Coppe, and Gian Antonio Danieli

Detecting seeded motifs in DNA sequences
Nucl. Acids Res. 2005 33: e135; doi:10.1093/nar/gni131 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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