Nucleic Acids Research

Articles:

Zhongxin Yu, Li-Jyun Syu, and Dervla M. Mellerick

Contextual interactions determine whether the Drosophila homeodomain protein, Vnd, acts as a repressor or activator
Nucl. Acids Res. 2005 33: 1-12; doi:10.1093/nar/gki140 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Luke Gaughan, Ian R. Logan, David E. Neal, and Craig N. Robson

Regulation of androgen receptor and histone deacetylase 1 by Mdm2-mediated ubiquitylation
Nucl. Acids Res. 2005 33: 13-26; doi:10.1093/nar/gki141 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

John J. Turner, Andrey A. Arzumanov, and Michael J. Gait

Synthesis, cellular uptake and HIV-1 Tat-dependent trans-activation inhibition activity of oligonucleotide analogues disulphide-conjugated to cell-penetrating peptides
Nucl. Acids Res. 2005 33: 27-42; doi:10.1093/nar/gki142 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

R. Thenmalarchelvi and N. Yathindra

New insights into DNA triplexes: residual twist and radial difference as measures of base triplet non-isomorphism and their implication to sequence-dependent non-uniform DNA triplex
Nucl. Acids Res. 2005 33: 43-55; doi:10.1093/nar/gki143 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Yongxi Tan, Leming Shi, Weida Tong, and Charles Wang

Multi-class cancer classification by total principal component regression (TPCR) using microarray gene expression data
Nucl. Acids Res. 2005 33: 56-65; doi:10.1093/nar/gki144 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Antonia Patsialou, Deborah Wilsker, and Elizabeth Moran

DNA-binding properties of ARID family proteins
Nucl. Acids Res. 2005 33: 66-80; doi:10.1093/nar/gki145 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jean-Louis Mergny, Anne De Cian, Amar Ghelab, Barbara Saccŕ, and Laurent Lacroix

Kinetics of tetramolecular quadruplexes
Nucl. Acids Res. 2005 33: 81-94; doi:10.1093/nar/gki148 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Mingyi Liu, Heiko Walch, Shaoping Wu, and Andrei Grigoriev

Significant expansion of exon-bordering protein domains during animal proteome evolution
Nucl. Acids Res. 2005 33: 95-105; doi:10.1093/nar/gki152 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Sandrine Jacob, Catherine Miquel, Alain Sarasin, and Françoise Praz

Effects of camptothecin on double-strand break repair by non-homologous end-joining in DNA mismatch repair-deficient human colorectal cancer cell lines
Nucl. Acids Res. 2005 33: 106-113; doi:10.1093/nar/gki154 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Peter Hasselblatt, Birgit Hockenjos, Christian Thoma, Hubert E. Blum, and Wolf-Bernhard Offensperger

Translation of stable hepadnaviral mRNA cleavage fragments induced by the action of phosphorothioate-modified antisense oligodeoxynucleotides
Nucl. Acids Res. 2005 33: 114-125; doi:10.1093/nar/gki155 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Laura Pérez-Lago, Margarita Salas, and Ana Camacho

A precise DNA bend angle is essential for the function of the phage 29 transcriptional regulator
Nucl. Acids Res. 2005 33: 126-134; doi:10.1093/nar/gki146 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Thorarinn Blondal, Audur Thorisdottir, Unnur Unnsteinsdottir, Sigridur Hjorleifsdottir, Arnthor Ćvarsson, Sveinn Ernstsson, Olafur H. Fridjonsson, Sigurlaug Skirnisdottir, Jon Oskar Wheat, Anna Gudny Hermannsdottir, Snorri Th. Sigurdsson, Gudmundur O. Hreggvidsson, Albert Vernon Smith, and Jakob K. Kristjansson

Isolation and characterization of a thermostable RNA ligase 1 from a Thermus scotoductus bacteriophage TS2126 with good single-stranded DNA ligation properties
Nucl. Acids Res. 2005 33: 135-142; doi:10.1093/nar/gki149 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tumpa Sarkar, Christine C. Conwell, Lilia C. Harvey, Catherine T. Santai, and Nicholas V. Hud

Condensation of oligonucleotides assembled into nicked and gapped duplexes: potential structures for oligonucleotide delivery
Nucl. Acids Res. 2005 33: 143-151; doi:10.1093/nar/gki156 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Katherine S. Pawelczak, Brooke J. Andrews, and John J. Turchi

Differential activation of DNA-PK based on DNA strand orientation and sequence bias
Nucl. Acids Res. 2005 33: 152-161; doi:10.1093/nar/gki157 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Liang Ye and Xiaoqiu Huang

MAP2: multiple alignment of syntenic genomic sequences
Nucl. Acids Res. 2005 33: 162-170; doi:10.1093/nar/gki159 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Arkadiusz Bibillo, Daniela Lener, George J. Klarmann, and Stuart F. J. Le Grice

Functional roles of carboxylate residues comprising the DNA polymerase active site triad of Ty3 reverse transcriptase
Nucl. Acids Res. 2005 33: 171-181; doi:10.1093/nar/gki150 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Magdalena Dorywalska, Scott C. Blanchard, Ruben L. Gonzalez, Harold D. Kim, Steven Chu, and Joseph D. Puglisi

Site-specific labeling of the ribosome for single-molecule spectroscopy
Nucl. Acids Res. 2005 33: 182-189; doi:10.1093/nar/gki151 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tamaki Hori, Yusuke Taguchi, Seiichi Uesugi, and Yasuyuki Kurihara

The RNA ligands for mouse proline-rich RNA-binding protein (mouse Prrp) contain two consensus sequences in separate loop structure
Nucl. Acids Res. 2005 33: 190-200; doi:10.1093/nar/gki153 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Bin Tian, Jun Hu, Haibo Zhang, and Carol S. Lutz

A large-scale analysis of mRNA polyadenylation of human and mouse genes
Nucl. Acids Res. 2005 33: 201-212; doi:10.1093/nar/gki158 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Narcisse Esmaili and Jean Louis Leroy

i-motif solution structure and dynamics of the d(AACCCC) and d(CCCCAA) tetrahymena telomeric repeats
Nucl. Acids Res. 2005 33: 213-224; doi:10.1093/nar/gki160 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kate H. Brettingham-Moore, Sudha Rao, Torsten Juelich, M. Frances Shannon, and Adele F. Holloway

GM-CSF promoter chromatin remodelling and gene transcription display distinct signal and transcription factor requirements
Nucl. Acids Res. 2005 33: 225-234; doi:10.1093/nar/gki161 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yuichiro Habu, Naoko Miyano-Kurosaki, Michiko Kitano, Yumihiko Endo, Masakazu Yukita, Shigeru Ohira, Hiroaki Takaku, Masayuki Nashimoto, and Hiroshi Takaku

Inhibition of HIV-1 gene expression by retroviral vector-mediated small-guide RNAs that direct specific RNA cleavage by tRNase ZL
Nucl. Acids Res. 2005 33: 235-243; doi:10.1093/nar/gki164 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Suvobrata Chakravarty, Lei Wang, and Roberto Sanchez

Accuracy of structure-derived properties in simple comparative models of protein structures
Nucl. Acids Res. 2005 33: 244-259; doi:10.1093/nar/gki162 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Grégory Eot-Houllier, Séverine Eon-Marchais, Didier Gasparutto, and Evelyne Sage

Processing of a complex multiply damaged DNA site by human cell extracts and purified repair proteins
Nucl. Acids Res. 2005 33: 260-271; doi:10.1093/nar/gki165 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Nils Blüthgen, Szymon M. Kielbasa, and Hanspeter Herzel

Inferring combinatorial regulation of transcription in silico
Nucl. Acids Res. 2005 33: 272-279; doi:10.1093/nar/gki167 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Barbara Pascucci, Maria Teresa Russo, Marco Crescenzi, Margherita Bignami, and Eugenia Dogliotti

The accumulation of MMS-induced single strand breaks in G₁ phase is recombinogenic in DNA polymerase ß defective mammalian cells
Nucl. Acids Res. 2005 33: 280-288; doi:10.1093/nar/gki168 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tong Zhou, Jae Wan Lee, Haritha Tatavarthi, James R. Lupski, Kristoffer Valerie, and Lawrence F. Povirk

Deficiency in 3'-phosphoglycolate processing in human cells with a hereditary mutation in tyrosyl-DNA phosphodiesterase (TDP1)
Nucl. Acids Res. 2005 33: 289-297; doi:10.1093/nar/gki170 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Marguerite Sossou, Claudia Flohr-Beckhaus, Ina Schulz, Fayza Daboussi, Bernd Epe, and J. Pablo Radicella

APE1 overexpression in XRCC1-deficient cells complements the defective repair of oxidative single strand breaks but increases genomic instability
Nucl. Acids Res. 2005 33: 298-306; doi:10.1093/nar/gki173 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Egle Merkiene and Saulius Klimasauskas

Probing a rate-limiting step by mutational perturbation of AdoMet binding in the HhaI methyltransferase
Nucl. Acids Res. 2005 33: 307-315; doi:10.1093/nar/gki175 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Andrew Ferenbach, Anatoliy Li, Marta Brito-Martins, and J. Julian Blow

Functional domains of the Xenopus replication licensing factor Cdt1
Nucl. Acids Res. 2005 33: 316-324; doi:10.1093/nar/gki176 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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: 325-336; doi:10.1093/nar/gki177 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kristina Kühn, Andreas Weihe, and Thomas Börner

Multiple promoters are a common feature of mitochondrial genes in Arabidopsis
Nucl. Acids Res. 2005 33: 337-346; doi:10.1093/nar/gki179 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Bastiaan B. J. Tops, Hiroaki Tabara, Titia Sijen, Femke Simmer, Craig C. Mello, Ronald H. A. Plasterk, and René F. Ketting

RDE-2 interacts with MUT-7 to mediate RNA interference in Caenorhabditis elegans
Nucl. Acids Res. 2005 33: 347-355; doi:10.1093/nar/gki183 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jacob G. Jansen, Anastasia Tsaalbi-Shtylik, Petra Langerak, Fabienne Calléja, Caro M. Meijers, Heinz Jacobs, and Niels de Wind

The BRCT domain of mammalian Rev1 is involved in regulating DNA translesion synthesis
Nucl. Acids Res. 2005 33: 356-365; doi:10.1093/nar/gki189 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Michael M. A. Sekar, Will Bloch, and Pamela M. St John

Comparative study of sequence-dependent hybridization kinetics in solution and on microspheres
Nucl. Acids Res. 2005 33: 366-375; doi:10.1093/nar/gki163 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ruth Seal, Richard Temperley, Jeffrey Wilusz, Robert N. Lightowlers, and Zofia M. A. Chrzanowska-Lightowlers

Serum-deprivation stimulates cap-binding by PARN at the expense of eIF4E, consistent with the observed decrease in mRNA stability
Nucl. Acids Res. 2005 33: 376-387; doi:10.1093/nar/gki169 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Markus Englert and Hildburg Beier

Plant tRNA ligases are multifunctional enzymes that have diverged in sequence and substrate specificity from RNA ligases of other phylogenetic origins
Nucl. Acids Res. 2005 33: 388-399; doi:10.1093/nar/gki174 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Christopher D. Bayliss, Wendy A. Sweetman, and E. Richard Moxon

Destabilization of tetranucleotide repeats in Haemophilus influenzae mutants lacking RnaseHI or the Klenow domain of PolI
Nucl. Acids Res. 2005 33: 400-408; doi:10.1093/nar/gki180 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yee Leng Yap, Maria P. Wong, Xue Wu Zhang, David Hernandez, Robin Gras, David K. Smith, and Antoine Danchin

Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays
Nucl. Acids Res. 2005 33: 409-421; doi:10.1093/nar/gki188 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Satoshi Okano, Li Lan, Alan E. Tomkinson, and Akira Yasui

Translocation of XRCC1 and DNA ligase III from centrosomes to chromosomes in response to DNA damage in mitotic human cells
Nucl. Acids Res. 2005 33: 422-429; doi:10.1093/nar/gki190 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Chin-Yu Chen, Tzu-Ping Ko, Ting-Wan Lin, Chia-Cheng Chou, Chun-Jung Chen, and Andrew H.-J. Wang

Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d
Nucl. Acids Res. 2005 33: 430-438; doi:10.1093/nar/gki191 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Joacim Elmén, Hĺkan Thonberg, Karl Ljungberg, Miriam Frieden, Majken Westergaard, Yunhe Xu, Britta Wahren, Zicai Liang, Henrik Řrum, Troels Koch, and Claes Wahlestedt

Locked nucleic acid (LNA) mediated improvements in siRNA stability and functionality
Nucl. Acids Res. 2005 33: 439-447; doi:10.1093/nar/gki193 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Corrigendum:

Khelifi Adel, Durent Laurent, and Mouchiroud Dominique

HOPPSIGEN: a database of human and mouse processed pseudogenes
Nucl. Acids Res. 2005 33: 448; doi:10.1093/nar/gki217 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Erratum:

Hyo Jin Kang, Kyoung Oak Choi, Byung-Dong Kim, Sangsoo Kim, and Young Joo Kim

FESD: a Functional Element SNPs Database in human
Nucl. Acids Res. 2005 33: 449; doi:10.1093/nar/gki216 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Richard Ingram, Hiromi Tagoh, Arthur D. Riggs, and Constanze Bonifer

Rapid, solid-phase based automated analysis of chromatin structure and transcription factor occupancy in living eukaryotic cells
Nucl. Acids Res. 2005 33: e1; doi:10.1093/nar/gni001 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Shawna L. Hiley, Jane Jackman, Tomas Babak, Miles Trochesset, Quaid D. Morris, Eric Phizicky, and Timothy R. Hughes

Detection and discovery of RNA modifications using microarrays
Nucl. Acids Res. 2005 33: e2; doi:10.1093/nar/gni002 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Hong-Yu Ou, Rebecca Smith, Sacha Lucchini, Jay Hinton, Roy R. Chaudhuri, Mark Pallen, Michael R. Barer, and Kumar Rajakumar

ArrayOme: a program for estimating the sizes of microarray-visualized bacterial genomes
Nucl. Acids Res. 2005 33: e3; doi:10.1093/nar/gni005 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Kae Sato, Kazuo Hosokawa, and Mizuo Maeda

Non-cross-linking gold nanoparticle aggregation as a detection method for single-base substitutions
Nucl. Acids Res. 2005 33: e4; doi:10.1093/nar/gni007 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Karel Nejedlý, Jana Chládková, Michaela Vorlícková, Iva Hrabcová, and Jaroslav Kypr

Mapping the B-A conformational transition along plasmid DNA
Nucl. Acids Res. 2005 33: e5; doi:10.1093/nar/gni008 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Christine Dufraigne, Bernard Fertil, Sylvain Lespinats, Alain Giron, and Patrick Deschavanne

Detection and characterization of horizontal transfers in prokaryotes using genomic signature
Nucl. Acids Res. 2005 33: e6; doi:10.1093/nar/gni004 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Alberto Pascual, Kai-Lian Huang, and Thomas Preat

Conditional UAS-targeted repression in Drosophila
Nucl. Acids Res. 2005 33: e7; doi:10.1093/nar/gni006 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jae-Ho Shin, John N. Reeve, and Zvi Kelman

Use of a restriction enzyme-digested PCR product as substrate for helicase assays
Nucl. Acids Res. 2005 33: e8; doi:10.1093/nar/gni009 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Gábor E. Tusnády, István Simon, András Váradi, and Tamás Arányi

BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes
Nucl. Acids Res. 2005 33: e9; doi:10.1093/nar/gni012 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Herald Reiersen, Inger Lřbersli, Geir Ĺ. Lřset, Else Hvattum, Bjřrg Simonsen, John E. Stacy, Duncan McGregor, Kevin FitzGerald, Martin Welschof, Ole H. Brekke, and Ole J. Marvik

Covalent antibody display—an in vitro antibody-DNA library selection system
Nucl. Acids Res. 2005 33: e10; doi:10.1093/nar/gni010 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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