Nucleic Acids Research

Articles:

Catherine Mathé, Marie-France Sagot, Thomas Schiex, and Pierre Rouzé

Current methods of gene prediction, their strengths and weaknesses
Nucl. Acids Res. 2002 30: 4103-4117; doi:10.1093/nar/gkf543 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Laura A. Cassiday and L. James Maher III

Having it both ways: transcription factors that bind DNA and RNA
Nucl. Acids Res. 2002 30: 4118-4126; doi:10.1093/nar/gkf512 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Noam Shomron, Hadar Malca, Ida Vig, and Gil Ast

Reversible inhibition of the second step of splicing suggests a possible role of zinc in the second step of splicing
Nucl. Acids Res. 2002 30: 4127-4137; doi:10.1093/nar/gkf553 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Francis Lim and David S. Peabody

RNA recognition site of PP7 coat protein
Nucl. Acids Res. 2002 30: 4138-4144; doi:10.1093/nar/gkf552 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Tianyuan Zhou and Cheng-Ming Chiang

Sp1 and AP2 regulate but do not constitute TATA-less human TAF_II55 core promoter activity
Nucl. Acids Res. 2002 30: 4145-4157; doi:10.1093/nar/gkf537 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Isabelle Saves, Cécile Morlot, Laurent Thion, Jean-Luc Rolland, Jacques Diétrich, and Jean-Michel Masson

Investigating the endonuclease activity of four Pyrococcus abyssi inteins
Nucl. Acids Res. 2002 30: 4158-4165; doi:10.1093/nar/gkf556 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Irit Tozik, Qiaojia Huang, Christian Zwieb, and Jerry Eichler

Reconstitution of the signal recognition particle of the halophilic archaeon Haloferax volcanii
Nucl. Acids Res. 2002 30: 4166-4175; doi:10.1093/nar/gkf548 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Daniel Schaarschmidt, Eva-Maria Ladenburger, Christian Keller, and Rolf Knippers

Human Mcm proteins at a replication origin during the G₁ to S phase transition
Nucl. Acids Res. 2002 30: 4176-4185; doi:10.1093/nar/gkf532 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Carla C. Oliveira, Fernando A. Gonzales, and Nilson I. T. Zanchin

Temperature-sensitive mutants of the exosome subunit Rrp43p show a deficiency in mRNA degradation and no longer interact with the exosome
Nucl. Acids Res. 2002 30: 4186-4198; doi:10.1093/nar/gkf545 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Michaela Angermayr, Ulrich Oechsner, Kerstin Gregor, Gary P. Schroth, and Wolfhard Bandlow

Transcription initiation in vivo without classical transactivators: DNA kinks flanking the core promoter of the housekeeping yeast adenylate kinase gene, AKY2, position nucleosomes and constitutively activate transcription
Nucl. Acids Res. 2002 30: 4199-4207; doi:10.1093/nar/gkf551 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Andrew Tsourkas, Mark A. Behlke, and Gang Bao

Structure–function relationships of shared-stem and conventional molecular beacons
Nucl. Acids Res. 2002 30: 4208-4215; doi:10.1093/nar/gkf536 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jan Mrázek, Lisa H. Gaynon, and Samuel Karlin

Frequent oligonucleotide motifs in genomes of three streptococci
Nucl. Acids Res. 2002 30: 4216-4221; doi:10.1093/nar/gkf534 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Noor A. Eppens, Alex W. Faber, Mariska Rondaij, Roshan S. Jahangir, Saskia van Hemert, Jan C. Vos, Jaap Venema, and Hendrik A. Raué

Deletions in the S1 domain of Rrp5p cause processing at a novel site in ITS1 of yeast pre-rRNA that depends on Rex4p
Nucl. Acids Res. 2002 30: 4222-4231; doi:10.1093/nar/gkf538 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Maarten H. de Smit, Alexander P. Gultyaev, Mark Hilge, Hugo H. J. Bink, Sharief Barends, Barend Kraal, and Cornelis W. A. Pleij

Structural variation and functional importance of a D-loop–T-loop interaction in valine-accepting tRNA-like structures of plant viral RNAs
Nucl. Acids Res. 2002 30: 4232-4240; doi:10.1093/nar/gkf539 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Mikolaj Olejniczak, Zofia Gdaniec, Artur Fischer, Tomasz Grabarkiewicz, Lukasz Bielecki, and Ryszard W. Adamiak

The bulge region of HIV-1 TAR RNA binds metal ions in solution
Nucl. Acids Res. 2002 30: 4241-4249; doi:10.1093/nar/gkf541 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Sébastien Lemieux and François Major

RNA canonical and non-canonical base pairing types: a recognition method and complete repertoire
Nucl. Acids Res. 2002 30: 4250-4263; doi:10.1093/nar/gkf540 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Igor B. Rogozin, Kira S. Makarova, Darren A. Natale, Alexey N. Spiridonov, Roman L. Tatusov, Yuri I. Wolf, Jodie Yin, and Eugene V. Koonin

Congruent evolution of different classes of non-coding DNA in prokaryotic genomes
Nucl. Acids Res. 2002 30: 4264-4271; doi:10.1093/nar/gkf549 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

David J. Lynn, Gregory A. C. Singer, and Donal A. Hickey

Synonymous codon usage is subject to selection in thermophilic bacteria
Nucl. Acids Res. 2002 30: 4272-4277; doi:10.1093/nar/gkf546 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Sridhar Hannenhalli and Samuel Levy

Predicting transcription factor synergism
Nucl. Acids Res. 2002 30: 4278-4284; doi:10.1093/nar/gkf535 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Pierre Moffatt, Patrick Salois, Marie-Hélène Gaumond, Natalie St-Amant, Éric Godin, and Christian Lanctôt

Engineered viruses to select genes encoding secreted and membrane-bound proteins in mammalian cells
Nucl. Acids Res. 2002 30: 4285-4294; doi:10.1093/nar/gkf542 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Michael C. Giddings, Atul A. Shah, Sue Freier, John F. Atkins, Raymond F. Gesteland, and Olga V. Matveeva

Artificial neural network prediction of antisense oligodeoxynucleotide activity
Nucl. Acids Res. 2002 30: 4295-4304; doi:10.1093/nar/gkf557 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Emily M. Anderson, Wayne A. Halsey, and Deborah S. Wuttke

Delineation of the high-affinity single-stranded telomeric DNA-binding domain of Saccharomyces cerevisiae Cdc13
Nucl. Acids Res. 2002 30: 4305-4313; doi:10.1093/nar/gkf554 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Shu-Wei Yang, Mekbib Astatke, Jason Potter, and Deb K. Chatterjee

Mutant Thermotoga neapolitana DNA polymerase I: altered catalytic properties for non-templated nucleotide addition and incorporation of correct nucleotides
Nucl. Acids Res. 2002 30: 4314-4320; doi:10.1093/nar/gkf547 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Martin Madera and Julian Gough

A comparison of profile hidden Markov model procedures for remote homology detection
Nucl. Acids Res. 2002 30: 4321-4328; doi:10.1093/nar/gkf544 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

NAR Methods Online:

Jörg Tost, Ole Brandt, Francis Boussicault, David Derbala, Christophe Caloustian, Doris Lechner, and Ivo Glynne Gut

Molecular haplotyping at high throughput
Nucl. Acids Res. 2002 30: e96; doi:10.1093/nar/gnf095 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Akio Yamane

MagiProbe: a novel fluorescence quenching-based oligonucleotide probe carrying a fluorophore and an intercalator
Nucl. Acids Res. 2002 30: e97; doi:10.1093/nar/gnf096 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

M. Gaigalas, Z. Maneliene, R. Kazlauskiene, M. Petrusyte, and A. Janulaitis

PfoI, a unique type II restriction endonuclease that recognises the sequence 5'-TCCNGGA-3'
Nucl. Acids Res. 2002 30: e98; doi:10.1093/nar/gnf097 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Peter B. Garland and Pawel J. Serafinowski

Effects of stray light on the fidelity of photodirected oligonucleotide array synthesis
Nucl. Acids Res. 2002 30: e99; doi:10.1093/nar/gnf098 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Nana Jacobsen, Joan Bentzen, Michael Meldgaard, Mogens Havsteen Jakobsen, Mogens Fenger, Sakari Kauppinen, and Jan Skouv

LNA-enhanced detection of single nucleotide polymorphisms in the apolipoprotein E
Nucl. Acids Res. 2002 30: e100; doi:10.1093/nar/gnf099 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ulf M. Lindström and Eric T. Kool

An orthogonal oligonucleotide protecting group strategy that enables assembly of repetitive or highly structured DNAs
Nucl. Acids Res. 2002 30: e101; doi:10.1093/nar/gnf100 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yoshihito Kitamura and Makoto Komiyama

Preferential hydrolysis of gap and bulge sites in DNA by Ce(IV)/EDTA complex
Nucl. Acids Res. 2002 30: e102; doi:10.1093/nar/gnf101 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Kimi Araki, Masatake Araki, and Ken-ichi Yamamura

Site-directed integration of the cre gene mediated by Cre recombinase using a combination of mutant lox sites
Nucl. Acids Res. 2002 30: e103; doi:10.1093/nar/gnf102 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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