Nucleic Acids Research

Articles:

EDITORIAL
Nucl. Acids Res. 2003 31: 3869-3871; doi:10.1093/nar/gkg388 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

Claudio R. Alonso and Michael Akam

A Hox gene mutation that triggers nonsense-mediated RNA decay and affects alternative splicing during Drosophila development
Nucl. Acids Res. 2003 31: 3873-3880; doi:10.1093/nar/gkg482 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jianmin Zhou and Carol Prives

Replication of damaged DNA in vitro is blocked by p53
Nucl. Acids Res. 2003 31: 3881-3892; doi:10.1093/nar/gkg468 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ane Moe, Jeanette Ringvoll, Line M. Nordstrand, Lars Eide, Magnar Bjørås, Erling Seeberg, Torbjørn Rognes, and Arne Klungland

Incision at hypoxanthine residues in DNA by a mammalian homologue of the Escherichia coli antimutator enzyme endonuclease V
Nucl. Acids Res. 2003 31: 3893-3900; doi:10.1093/nar/gkg472 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Mu Xiao, Michael J. Leibowitz, and Yi Zhang

Concerted folding of a Candida ribozyme into the catalytically active structure posterior to a rapid RNA compaction
Nucl. Acids Res. 2003 31: 3901-3908; doi:10.1093/nar/gkg455 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Anne Karin Rasmussen, Aditi Chatterjee, Lene Juel Rasmussen, and Keshav K. Singh

Mitochondria-mediated nuclear mutator phenotype in Saccharomyces cerevisiae
Nucl. Acids Res. 2003 31: 3909-3917; doi:10.1093/nar/gkg446 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Marc Lemonnier, Günter Ziegelin, Tobias Reick, Ana Muñoz Gómez, Ramón Díaz-Orejas, and Erich Lanka

Bacteriophage P1 Ban protein is a hexameric DNA helicase that interacts with and substitutes for Escherichia coli DnaB
Nucl. Acids Res. 2003 31: 3918-3928; doi:10.1093/nar/gkg463 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ekaterina Protozanova, Vadim V. Demidov, Peter E. Nielsen, and Maxim D. Frank-Kamenetskii

Pseudocomplementary PNAs as selective modifiers of protein activity on duplex DNA: the case of type IIs restriction enzymes
Nucl. Acids Res. 2003 31: 3929-3935; doi:10.1093/nar/gkg450 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Andrea Kyburz, Martin Sadowski, Bernhard Dichtl, and Walter Keller

The role of the yeast cleavage and polyadenylation factor subunit Ydh1p/Cft2p in pre-mRNA 3'-end formation
Nucl. Acids Res. 2003 31: 3936-3945; doi:10.1093/nar/gkg478 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Ekaterina I. Zagryadskaya, Felix R. Doyon, and Sergey V. Steinberg

Importance of the reverse Hoogsteen base pair 54-58 for tRNA function
Nucl. Acids Res. 2003 31: 3946-3953; doi:10.1093/nar/gkg448 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jerzy Ostrowski, Yasunobu Kawata, Daniel S. Schullery, Oleg N. Denisenko, and Karol Bomsztyk

Transient recruitment of the hnRNP K protein to inducibly transcribed gene loci
Nucl. Acids Res. 2003 31: 3954-3962; doi:10.1093/nar/gkg452 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Pnina Weisman-Shomer, Esther Cohen, Inbal Hershco, Samer Khateb, Orit Wolfovitz-Barchad, Laurence H. Hurley, and Michael Fry

The cationic porphyrin TMPyP4 destabilizes the tetraplex form of the fragile X syndrome expanded sequence d(CGG)_n
Nucl. Acids Res. 2003 31: 3963-3970; doi:10.1093/nar/gkg453 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Patrick Trojer, Eva M. Brandtner, Gerald Brosch, Peter Loidl, Johannes Galehr, Roland Linzmaier, Hubertus Haas, Karin Mair, Martin Tribus, and Stefan Graessle

Histone deacetylases in fungi: novel members, new facts
Nucl. Acids Res. 2003 31: 3971-3981; doi:10.1093/nar/gkg473 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Bino John and Andrej Sali

Comparative protein structure modeling by iterative alignment, model building and model assessment
Nucl. Acids Res. 2003 31: 3982-3992; doi:10.1093/nar/gkg460 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Bill Wickstead, Klaus Ersfeld, and Keith Gull

The frequency of gene targeting in Trypanosoma brucei is independent of target site copy number
Nucl. Acids Res. 2003 31: 3993-4000; doi:10.1093/nar/gkg445 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Hosam G. Abdelhady, Stephanie Allen, Martyn C. Davies, Clive J. Roberts, Saul J. B. Tendler, and Philip M. Williams

Direct real-time molecular scale visualisation of the degradation of condensed DNA complexes exposed to DNase I
Nucl. Acids Res. 2003 31: 4001-4005; doi:10.1093/nar/gkg462 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Heather L. Heikkinen, Sara A. Llewellyn, and Christine A. Barnes

Initiation-mediated mRNA decay in yeast affects heat-shock mRNAs, and works through decapping and 5'-to-3' hydrolysis
Nucl. Acids Res. 2003 31: 4006-4016; doi:10.1093/nar/gkg474 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jacques Le Derout, Marc Folichon, Federica Briani, Gianni Dehò, Philippe Régnier, and Eliane Hajnsdorf

Hfq affects the length and the frequency of short oligo(A) tails at the 3' end of Escherichia coli rpsO mRNAs
Nucl. Acids Res. 2003 31: 4017-4023; doi:10.1093/nar/gkg456 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Petr Grúz, Masatomi Shimizu, Francesca M. Pisani, Mariarita De Felice, Yusuke Kanke, and Takehiko Nohmi

Processing of DNA lesions by archaeal DNA polymerases from Sulfolobus solfataricus
Nucl. Acids Res. 2003 31: 4024-4030; doi:10.1093/nar/gkg447 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Paola B. Arimondo, Stéphane Angenault, Ludovic Halby, Alexandre Boutorine, Frédéric Schmidt, Claude Monneret, Thérèse Garestier, Jian-Sheng Sun, Christian Bailly, and Claude Hélène

Spatial organization of topoisomerase I-mediated DNA cleavage induced by camptothecin–oligonucleotide conjugates
Nucl. Acids Res. 2003 31: 4031-4040; doi:10.1093/nar/gkg457 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Hitoshi Kurumizaka, Rima Enomoto, Maki Nakada, Keiko Eda, Shigeyuki Yokoyama, and Takehiko Shibata

Region and amino acid residues required for Rad51C binding in the human Xrcc3 protein
Nucl. Acids Res. 2003 31: 4041-4050; doi:10.1093/nar/gkg442 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jodi M. Maglich, Justin A. Caravella, Millard H. Lambert, Timothy M. Willson, John T. Moore, and Lakshman Ramamurthy

The first completed genome sequence from a teleost fish (Fugu rubripes) adds significant diversity to the nuclear receptor superfamily
Nucl. Acids Res. 2003 31: 4051-4058; doi:10.1093/nar/gkg444 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Sylvain Huard, Tara J. Moriarty, and Chantal Autexier

The C terminus of the human telomerase reverse transcriptase is a determinant of enzyme processivity
Nucl. Acids Res. 2003 31: 4059-4070; doi:10.1093/nar/gkg437 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hiroyuki Kurata, Nana Matoba, and Natsumi Shimizu

CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle
Nucl. Acids Res. 2003 31: 4071-4084; doi:10.1093/nar/gkg461 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hajime Murakami, Valerie Borde, Takehiko Shibata, Michael Lichten, and Kunihiro Ohta

Correlation between premeiotic DNA replication and chromatin transition at yeast recombination initiation sites
Nucl. Acids Res. 2003 31: 4085-4090; doi:10.1093/nar/gkg441 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Claude Sauter, Jérôme Basquin, and Dietrich Suck

Sm-like proteins in Eubacteria: the crystal structure of the Hfq protein from Escherichia coli
Nucl. Acids Res. 2003 31: 4091-4098; doi:10.1093/nar/gkg480 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Rachel A. Cassidy, Nitin Puri, and Paul S. Miller

Effect of DNA target sequence on triplex formation by oligo-2'-deoxy- and 2'-O-methylribonucleotides
Nucl. Acids Res. 2003 31: 4099-4108; doi:10.1093/nar/gkg436 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

David Sheehan, Benjamin Lunstad, Christina M. Yamada, Brian G. Stell, Marvin H. Caruthers, and Douglas J. Dellinger

Biochemical properties of phosphonoacetate and thiophosphonoacetate oligodeoxyribonucleotides
Nucl. Acids Res. 2003 31: 4109-4118; doi:10.1093/nar/gkg439 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

John P. McCutcheon and Sean R. Eddy

Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics
Nucl. Acids Res. 2003 31: 4119-4128; doi:10.1093/nar/gkg438 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Angela M. DeLucia, Nigel D. F. Grindley, and Catherine M. Joyce

An error-prone family Y DNA polymerase (DinB homolog from Sulfolobus solfataricus) uses a ‘steric gate’ residue for discrimination against ribonucleotides
Nucl. Acids Res. 2003 31: 4129-4137; doi:10.1093/nar/gkg417 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hemanta Baruah and Ulrich Bierbach

Unusual intercalation of acridin-9-ylthiourea into the 5'-GA/TC DNA base step from the minor groove: implications for the covalent DNA adduct profile of a novel platinum–intercalator conjugate
Nucl. Acids Res. 2003 31: 4138-4146; doi:10.1093/nar/gkg465 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Tokameh Mahmoudi, Lobke M. P. Zuijderduijn, Adone Mohd-Sarip, and C. Peter Verrijzer

GAGA facilitates binding of Pleiohomeotic to a chromatinized Polycomb response element
Nucl. Acids Res. 2003 31: 4147-4156; doi:10.1093/nar/gkg479 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Andrei Grigoriev

On the number of protein–protein interactions in the yeast proteome
Nucl. Acids Res. 2003 31: 4157-4161; doi:10.1093/nar/gkg466 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Laurent Miccoli, Denis S. F. Biard, Isabelle Frouin, Francis Harper, Giovanni Maga, and Jaime F. Angulo

Selective interactions of human kin17 and RPA proteins with chromatin and the nuclear matrix in a DNA damage- and cell cycle-regulated manner
Nucl. Acids Res. 2003 31: 4162-4175; doi:10.1093/nar/gkg459 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Gary W. Daughdrill, Garry W. Buchko, Maria V. Botuyan, Cheryl Arrowsmith, Marc S. Wold, Michael A. Kennedy, and David F. Lowry

Chemical shift changes provide evidence for overlapping single-stranded DNA- and XPA-binding sites on the 70 kDa subunit of human replication protein A
Nucl. Acids Res. 2003 31: 4176-4183; doi:10.1093/nar/gkg451 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

N. Guhan and K. Muniyappa

Mycobacterium tuberculosis RecA intein, a LAGLIDADG homing endonuclease, displays Mn²⁺ and DNA-dependent ATPase activity
Nucl. Acids Res. 2003 31: 4184-4191; doi:10.1093/nar/gkg475 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ofer Peleg, Edward N. Trifonov, and Alexander Bolshoy

Hidden messages in the nef gene of human immunodeficiency virus type 1 suggest a novel RNA secondary structure
Nucl. Acids Res. 2003 31: 4192-4200; doi:10.1093/nar/gkg454 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

E. A. Worthey, Santiago Martinez-Calvillo, Achim Schnaufer, Gautam Aggarwal, Jason Cawthra, Gholam Fazelinia, Chris Fong, Guoliang Fu, Melissa Hassebrock, Greg Hixson, Alasdair C. Ivens, Patti Kiser, Felicia Marsolini, Erica Rickell, Reza Salavati, Ellen Sisk, Susan M. Sunkin, Kenneth D. Stuart, and Peter J. Myler

Leishmania major chromosome 3 contains two long convergent polycistronic gene clusters separated by a tRNA gene
Nucl. Acids Res. 2003 31: 4201-4210; doi:10.1093/nar/gkg469 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

O. V. Matveeva, S. A. Shabalina, V. A. Nemtsov, A. D. Tsodikov, R. F. Gesteland, and J. F. Atkins

Thermodynamic calculations and statistical correlations for oligo-probes design
Nucl. Acids Res. 2003 31: 4211-4217; doi:10.1093/nar/gkg476 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Emeline Teyssier, Go Hirokawa, Anna Tretiakova, Bradford Jameson, Akira Kaji, and Hideko Kaji

Temperature-sensitive mutation in yeast mitochondrial ribosome recycling factor (RRF)
Nucl. Acids Res. 2003 31: 4218-4226; doi:10.1093/nar/gkg449 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yuji Inagaki, Christian Blouin, Edward Susko, and Andrew J. Roger

Assessing functional divergence in EF-1 and its paralogs in eukaryotes and archaebacteria
Nucl. Acids Res. 2003 31: 4227-4237; doi:10.1093/nar/gkg440 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Fu-Ming Chen, Feng Sha, Ko-Hsin Chin, and Shan-Ho Chou

Unique actinomycin D binding to self-complementary d(CXYGGCCY'X'G) sequences: duplex disruption and binding to a nominally base-paired hairpin
Nucl. Acids Res. 2003 31: 4238-4246; doi:10.1093/nar/gkg477 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Haico van Attikum, Paul Bundock, René M. Overmeer, Lan-Ying Lee, Stanton B. Gelvin, and Paul J. J. Hooykaas

The Arabidopsis AtLIG4 gene is required for the repair of DNA damage, but not for the integration of Agrobacterium T-DNA
Nucl. Acids Res. 2003 31: 4247-4255; doi:10.1093/nar/gkg458 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Sergei Ivanov, Yakov Alekseev, Jean-Remi Bertrand, Claude Malvy, and Marina B. Gottikh

Formation of stable triplexes between purine RNA and pyrimidine oligodeoxyxylonucleotides
Nucl. Acids Res. 2003 31: 4256-4263; doi:10.1093/nar/gkg443 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

M. M. Srinivas Bharath, Nagasuma R. Chandra, and M. R. S. Rao

Molecular modeling of the chromatosome particle
Nucl. Acids Res. 2003 31: 4264-4274; doi:10.1093/nar/gkg481 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

François Beaurain, Carmelo Di Primo, Jean Jacques Toulmé, and Michel Laguerre

Molecular dynamics reveals the stabilizing role of loop closing residues in kissing interactions: comparison between TAR–TAR* and TAR–aptamer
Nucl. Acids Res. 2003 31: 4275-4284; doi:10.1093/nar/gkg467 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

NAR Methods Online:

H. Q. Xu, A. H. Zhang, C. Auclair, and X. G. Xi

Simultaneously monitoring DNA binding and helicase-catalyzed DNA unwinding by fluorescence polarization
Nucl. Acids Res. 2003 31: e70; doi:10.1093/nar/gng070 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Wilfried Weber, Ronald Schoenmakers, Manuela Spielmann, Marie Daoud El-Baba, Marc Folcher, Bettina Keller, Cornelia C. Weber, Nils Link, Petra van de Wetering, Christoph Heinzen, Benoît Jolivet, Urs Séquin, Dominique Aubel, Charles J. Thompson, and Martin Fussenegger

Streptomyces-derived quorum-sensing systems engineered for adjustable transgene expression in mammalian cells and mice
Nucl. Acids Res. 2003 31: e71; doi:10.1093/nar/gng071 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Hong-Yan Zhang, Jianping Mao, Daixing Zhou, Yunhe Xu, Håkan Thonberg, Zicai Liang, and Claes Wahlestedt

mRNA accessible site tagging (MAST): a novel high throughput method for selecting effective antisense oligonucleotides
Nucl. Acids Res. 2003 31: e72; doi:10.1093/nar/gng072 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Stuart N. Peirson, Jason N. Butler, and Russell G. Foster

Experimental validation of novel and conventional approaches to quantitative real-time PCR data analysis
Nucl. Acids Res. 2003 31: e73; doi:10.1093/nar/gng073 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Piotr M. Skowron, Jaroslaw Majewski, Agnieszka Zylicz-Stachula, Sylwia M. Rutkowska, Izabela Jaworowska, and Renata I. Harasimowicz-Slowinska

A new Thermus sp. class-IIS enzyme sub-family: isolation of a ‘twin’ endonuclease TspDTI with a novel specificity 5'-ATGAA(N_11/9)-3', related to TspGWI, TaqII and Tth111II
Nucl. Acids Res. 2003 31: e74; doi:10.1093/nar/gng074 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Irma Lemmens, Sven Eyckerman, Lennart Zabeau, Dominiek Catteeuw, Els Vertenten, Kristin Verschueren, Danny Huylebroeck, Joël Vandekerckhove, and Jan Tavernier

Heteromeric MAPPIT: a novel strategy to study modification-dependent protein–protein interactions in mammalian cells
Nucl. Acids Res. 2003 31: e75; doi:10.1093/nar/gng075 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Saki Kondo, Aya Okuda, Hiromi Sato, Naoto Tachikawa, Miho Terashima, Yumi Kanegae, and Izumu Saito

Simultaneous on/off regulation of transgenes located on a mammalian chromosome with Cre-expressing adenovirus and a mutant loxP
Nucl. Acids Res. 2003 31: e76; doi:10.1093/nar/gng076 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

To see an article, click its [Full Text] or [PDF] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.