Nucleic Acids Research

Articles:

Mitsuteru Nakao, Roberto A. Barrero, Yuri Mukai, Chie Motono, Makiko Suwa, and Kenta Nakai

Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals
Nucl. Acids Res. 2005 33: 2355-2363; doi:10.1093/nar/gki520 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tanushri Sengupta, Mandira Mukherjee, Rakhee Das, Aditi Das, and Hemanta K. Majumder

Characterization of the DNA-binding domain and identification of the active site residue in the ‘Gyr A’ half of Leishmania donovani topoisomerase II
Nucl. Acids Res. 2005 33: 2364-2373; doi:10.1093/nar/gki527 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Paul M. Harrison, Deyou Zheng, Zhaolei Zhang, Nicholas Carriero, and Mark Gerstein

Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability
Nucl. Acids Res. 2005 33: 2374-2383; doi:10.1093/nar/gki531 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Laurent Metzinger, Marc Hallier, and Brice Felden

Independent binding sites of small protein B onto transfer-messenger RNA during trans-translation
Nucl. Acids Res. 2005 33: 2384-2394; doi:10.1093/nar/gki534 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Aurélie Lescoute, Neocles B. Leontis, Christian Massire, and Eric Westhof

Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments
Nucl. Acids Res. 2005 33: 2395-2409; doi:10.1093/nar/gki535 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Conrad A. Nieduszynski, J. Julian Blow, and Anne D. Donaldson

The requirement of yeast replication origins for pre-replication complex proteins is modulated by transcription
Nucl. Acids Res. 2005 33: 2410-2420; doi:10.1093/nar/gki539 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Yoav Arava, F. Edward Boas, Patrick O. Brown, and Daniel Herschlag

Dissecting eukaryotic translation and its control by ribosome density mapping
Nucl. Acids Res. 2005 33: 2421-2432; doi:10.1093/nar/gki331 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Paul P. Gardner, Andreas Wilm, and Stefan Washietl

A benchmark of multiple sequence alignment programs upon structural RNAs
Nucl. Acids Res. 2005 33: 2433-2439; doi:10.1093/nar/gki541 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Lasse Sinkkonen, Marjo Malinen, Katri Saavalainen, Sami Väisänen, and Carsten Carlberg

Regulation of the human cyclin C gene via multiple vitamin D₃-responsive regions in its promoter
Nucl. Acids Res. 2005 33: 2440-2451; doi:10.1093/nar/gki502 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Koen Nauwelaerts, Eveline Lescrinier, Gert Sclep, and Piet Herdewijn

Cyclohexenyl nucleic acids: conformationally flexible oligonucleotides
Nucl. Acids Res. 2005 33: 2452-2463; doi:10.1093/nar/gki538 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Simona Cuzic and Roland K. Hartmann

Studies on Escherichia coli RNase P RNA with Zn²⁺ as the catalytic cofactor
Nucl. Acids Res. 2005 33: 2464-2474; doi:10.1093/nar/gki540 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Steven E. Bates, Ning Ye Zhou, Laura E. Federico, Liqun Xia, and Timothy R. O'Connor

Repair of cyclobutane pyrimidine dimers or dimethylsulfate damage in DNA is identical in normal or telomerase-immortalized human skin fibroblasts
Nucl. Acids Res. 2005 33: 2475-2485; doi:10.1093/nar/gki542 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Dan Su, Yehua Li, and Vadim N. Gladyshev

Selenocysteine insertion directed by the 3'-UTR SECIS element in Escherichia coli
Nucl. Acids Res. 2005 33: 2486-2492; doi:10.1093/nar/gki547 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Zsofia Palfi, Bernd Schimanski, Arthur Günzl, Stephan Lücke, and Albrecht Bindereif

U1 small nuclear RNP from Trypanosoma brucei: a minimal U1 snRNA with unusual protein components
Nucl. Acids Res. 2005 33: 2493-2503; doi:10.1093/nar/gki548 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Boris Görke, Jana Reinhardt, and Bodo Rak

Activity of Lac repressor anchored to the Escherichia coli inner membrane
Nucl. Acids Res. 2005 33: 2504-2511; doi:10.1093/nar/gki549 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Reto Brem and Janet Hall

XRCC1 is required for DNA single-strand break repair in human cells
Nucl. Acids Res. 2005 33: 2512-2520; doi:10.1093/nar/gki543 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sarath Chandra Janga, Julio Collado-Vides, and Gabriel Moreno-Hagelsieb

Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons
Nucl. Acids Res. 2005 33: 2521-2530; doi:10.1093/nar/gki545 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

C. P. Diggle, J. Bentley, M. A. Knowles, and A. E. Kiltie

Inhibition of double-strand break non-homologous end-joining by cisplatin adducts in human cell extracts
Nucl. Acids Res. 2005 33: 2531-2539; doi:10.1093/nar/gki528 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Xiao-Chun Chen, Jie Feng, Bi-He Hou, Feng-Qing Li, Qiang Li, and Guo-Fan Hong

Modulating DNA bending affects NodD-mediated transcriptional control in Rhizobium leguminosarum
Nucl. Acids Res. 2005 33: 2540-2548; doi:10.1093/nar/gki537 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Mim A. Bower, Matthew Spencer, Shuichi Matsumura, R. Ellen R. Nisbet, and Christopher J. Howe

How many clones need to be sequenced from a single forensic or ancient DNA sample in order to determine a reliable consensus sequence?
Nucl. Acids Res. 2005 33: 2549-2556; doi:10.1093/nar/gki550 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sylvia Tobé, Thomas Heams, Jacques Vergne, Guy Hervé, and Marie-Christine Maurel

The catalytic mechanism of hairpin ribozyme studied by hydrostatic pressure
Nucl. Acids Res. 2005 33: 2557-2564; doi:10.1093/nar/gki552 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tyra Hall-Pogar, Haibo Zhang, Bin Tian, and Carol S. Lutz

Alternative polyadenylation of cyclooxygenase-2
Nucl. Acids Res. 2005 33: 2565-2579; doi:10.1093/nar/gki544 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Christopher E. Hart, Lucas Sharenbroich, Benjamin J. Bornstein, Diane Trout, Brandon King, Eric Mjolsness, and Barbara J. Wold

A mathematical and computational framework for quantitative comparison and integration of large-scale gene expression data
Nucl. Acids Res. 2005 33: 2580-2594; doi:10.1093/nar/gki536 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Hamid Fauzi, Karen D. Jack, and Jennifer V. Hines

In vitro selection to identify determinants in tRNA for Bacillus subtilis tyrS T box antiterminator mRNA binding
Nucl. Acids Res. 2005 33: 2595-2602; doi:10.1093/nar/gki546 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Rodrigo S. Galhardo, Raquel P. Rocha, Marilis V. Marques, and Carlos F. M. Menck

An SOS-regulated operon involved in damage-inducible mutagenesis in Caulobacter crescentus
Nucl. Acids Res. 2005 33: 2603-2614; doi:10.1093/nar/gki551 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

James G. Wetmur, Madhu Kumar, Li Zhang, Caroline Palomeque, Sylvan Wallenstein, and Jia Chen

Molecular haplotyping by linking emulsion PCR: analysis of paraoxonase 1 haplotypes and phenotypes
Nucl. Acids Res. 2005 33: 2615-2619; doi:10.1093/nar/gki556 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kristi Kincaid, Jeff Beckman, Aleksandra Zivkovic, Randall L. Halcomb, Joachim W. Engels, and Robert D. Kuchta

Exploration of factors driving incorporation of unnatural dNTPS into DNA by Klenow fragment (DNA polymerase I) and DNA polymerase
Nucl. Acids Res. 2005 33: 2620-2628; doi:10.1093/nar/gki563 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Marie-France Langelier, Dania Baali, Vincent Trinh, Jack Greenblatt, Jacques Archambault, and Benoit Coulombe

The highly conserved glutamic acid 791 of Rpb2 is involved in the binding of NTP and Mg(B) in the active center of human RNA polymerase II
Nucl. Acids Res. 2005 33: 2629-2639; doi:10.1093/nar/gki570 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Feng Xiao, Wulf-Dieter Moll, Songchuan Guo, and Peixuan Guo

Binding of pRNA to the N-terminal 14 amino acids of connector protein of bacteriophage phi29
Nucl. Acids Res. 2005 33: 2640-2649; doi:10.1093/nar/gki554 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Takahiro Arima, Tetsuya Kamikihara, Toshirou Hayashida, Kiyoko Kato, Toshiaki Inoue, Yasuaki Shirayoshi, Mitsuo Oshimura, Hidenobu Soejima, Tunehiro Mukai, and Norio Wake

ZAC, LIT1 (KCNQ1OT1) and p57^KIP2 (CDKN1C) are in an imprinted gene network that may play a role in Beckwith–Wiedemann syndrome
Nucl. Acids Res. 2005 33: 2650-2660; doi:10.1093/nar/gki555 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jack-Ansgar Bruun, Ernst Ivan Simon Thomassen, Kurt Kristiansen, Garth Tylden, Turid Holm, Ingvild Mikkola, Geir Bjørkøy, and Terje Johansen

The third helix of the homeodomain of paired class homeodomain proteins acts as a recognition helix both for DNA and protein interactions
Nucl. Acids Res. 2005 33: 2661-2675; doi:10.1093/nar/gki562 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Bram van den Broek, Maarten C. Noom, and Gijs J. L. Wuite

DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway
Nucl. Acids Res. 2005 33: 2676-2684; doi:10.1093/nar/gki565 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Janina Lisso, Dirk Steinhauser, Thomas Altmann, Joachim Kopka, and Carsten Müssig

Identification of brassinosteroid-related genes by means of transcript co-response analyses
Nucl. Acids Res. 2005 33: 2685-2696; doi:10.1093/nar/gki566 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Yael Altuvia, Pablo Landgraf, Gila Lithwick, Naama Elefant, Sébastien Pfeffer, Alexei Aravin, Michael J. Brownstein, Thomas Tuschl, and Hanah Margalit

Clustering and conservation patterns of human microRNAs
Nucl. Acids Res. 2005 33: 2697-2706; doi:10.1093/nar/gki567 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Praveen Kumar, Anjali Verma, Adesh Kumar Saini, Puneet Chopra, Pradip K. Chakraborti, Yogendra Singh, and Shantanu Chowdhury

Nucleoside diphosphate kinase from Mycobacterium tuberculosis cleaves single strand DNA within the human c-myc promoter in an enzyme-catalyzed reaction
Nucl. Acids Res. 2005 33: 2707-2714; doi:10.1093/nar/gki568 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Zizheng Dong, Yang Liu, and Jian-Ting Zhang

Regulation of ribonucleotide reductase M2 expression by the upstream AUGs
Nucl. Acids Res. 2005 33: 2715-2725; doi:10.1093/nar/gki569 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Svetlana Nikolajewa, Andreas Beyer, Maik Friedel, Jens Hollunder, and Thomas Wilhelm

Common patterns in type II restriction enzyme binding sites
Nucl. Acids Res. 2005 33: 2726-2733; doi:10.1093/nar/gki575 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Peik Haugen, Odd-Gunnar Wikmark, Anna Vader, Dag H. Coucheron, Eva Sjøttem, and Steinar D. Johansen

The recent transfer of a homing endonuclease gene
Nucl. Acids Res. 2005 33: 2734-2741; doi:10.1093/nar/gki564 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Shigehiro Osada, Mitsumasa Kurita, Jun-ichi Nishikawa, and Tsutomu Nishihara

Chromatin assembly factor Asf1p-dependent occupancy of the SAS histone acetyltransferase complex at the silent mating-type locus HML
Nucl. Acids Res. 2005 33: 2742-2750; doi:10.1093/nar/gki560 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Thomas J. Bollenbach, Heike Lange, Ryan Gutierrez, Mathieu Erhardt, David B. Stern, and Dominique Gagliardi

RNR1, a 3'–5' exoribonuclease belonging to the RNR superfamily, catalyzes 3' maturation of chloroplast ribosomal RNAs in Arabidopsis thaliana
Nucl. Acids Res. 2005 33: 2751-2763; doi:10.1093/nar/gki576 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Corrigendum:

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: 2764; doi:10.1093/nar/gki558 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Gusztav Belteki, Jody Haigh, Nikolett Kabacs, Katharina Haigh, Karen Sison, Frank Costantini, Jeff Whitsett, Susan E. Quaggin, and Andras Nagy

Conditional and inducible transgene expression in mice through the combinatorial use of Cre-mediated recombination and tetracycline induction
Nucl. Acids Res. 2005 33: 2765; doi:10.1093/nar/gki559 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Thijn van der Heijden, John van Noort, Hendrikje van Leest, Roland Kanaar, Claire Wyman, Nynke Dekker, and Cees Dekker

Torque-limited RecA polymerization on dsDNA
Nucl. Acids Res. 2005 33: 2766; doi:10.1093/nar/gki571 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Erratum:

Remus T. Dame, Joost van Mameren, Martijn S. Luijsterburg, Monika E. Mysiak, Ana Janicijevic, Grzegorz Pazdzior, Peter C. van der Vliet, Claire Wyman, and Gijs J.L. Wuite

Analysis of scanning force microscopy images of protein-induced DNA bending using simulations
Nucl. Acids Res. 2005 33: 2767; doi:10.1093/nar/gki577 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Marianna Szemes, Peter Bonants, Marjanne de Weerdt, Johan Baner, Ulf Landegren, and Cor D. Schoen

Diagnostic application of padlock probes—multiplex detection of plant pathogens using universal microarrays
Nucl. Acids Res. 2005 33: e70; doi:10.1093/nar/gni069 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Fredrik Dahl, Mats Gullberg, Johan Stenberg, Ulf Landegren, and Mats Nilsson

Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments
Nucl. Acids Res. 2005 33: e71; doi:10.1093/nar/gni070 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Johan Stenberg, Fredrik Dahl, Ulf Landegren, and Mats Nilsson

PieceMaker: selection of DNA fragments for selector-guided multiplex amplification
Nucl. Acids Res. 2005 33: e72; doi:10.1093/nar/gni071 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Cora Mund, Verena Beier, Peter Bewerunge, Michael Dahms, Frank Lyko, and Jörg D. Hoheisel

Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16^INK4A promoter in colon carcinoma cell lines
Nucl. Acids Res. 2005 33: e73; doi:10.1093/nar/gni072 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Heung-Sun Kwon, Hyun-Chul Shin, and Jin-Soo Kim

Suppression of vascular endothelial growth factor expression at the transcriptional and post-transcriptional levels
Nucl. Acids Res. 2005 33: e74; doi:10.1093/nar/gni068 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Matthew J. Moorcroft, Wouter R. A. Meuleman, Steven G. Latham, Thomas J. Nicholls, Ryan D. Egeland, and Edwin M. Southern

In situ oligonucleotide synthesis on poly(dimethylsiloxane): a flexible substrate for microarray fabrication
Nucl. Acids Res. 2005 33: e75; doi:10.1093/nar/gni075 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Masakazu Nakano, Kazuhiko Odaka, Yuzuka Takahashi, Masakazu Ishimura, Izumu Saito, and Yumi Kanegae

Production of viral vectors using recombinase-mediated cassette exchange
Nucl. Acids Res. 2005 33: e76; doi:10.1093/nar/gni074 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Caroline Crey-Desbiolles, Dae-Ro Ahn, and Christian J. Leumann

Molecular beacons with a homo-DNA stem: improving target selectivity
Nucl. Acids Res. 2005 33: e77; doi:10.1093/nar/gni076 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Cheng-Wey Wei, Ji-Yen Cheng, Chih-Ting Huang, Meng-Hua Yen, and Tai-Horng Young

Using a microfluidic device for 1 µl DNA microarray hybridization in 500 s
Nucl. Acids Res. 2005 33: e78; doi:10.1093/nar/gni078 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tanja Egener, Emmanuelle Roulet, Marc Zehnder, Philipp Bucher, and Nicolas Mermod

Proof of concept for microarray-based detection of DNA-binding oncogenes in cell extracts
Nucl. Acids Res. 2005 33: e79; doi:10.1093/nar/gni079 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

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