| | Articles SURVEY AND SUMMARY: Current methods of gene prediction, their strengths and weaknesses Catherine Mathé, Marie-France Sagot, Thomas Schiex, and Pierre Rouzé PMCID: PMC140543 SURVEY AND SUMMARY: Having it both ways: transcription factors that bind DNA and RNA Laura A. Cassiday and L. James Maher, III PMCID: PMC140532 Reversible inhibition of the second step of splicing suggests a possible role of zinc in the second step of splicing Noam Shomron, Hadar Malca, Ida Vig, and Gil Ast PMCID: PMC140552 RNA recognition site of PP7 coat protein Francis Lim and David S. Peabody PMCID: PMC140551 Sp1 and AP2 regulate but do not constitute TATA-less human TAFII55 core promoter activity Tianyuan Zhou and Cheng-Ming Chiang PMCID: PMC140537 Investigating the endonuclease activity of four Pyrococcus abyssi inteins Isabelle Saves, Cécile Morlot, Laurent Thion, Jean-Luc Rolland, Jacques Diétrich, and Jean-Michel Masson PMCID: PMC140554 Reconstitution of the signal recognition particle of the halophilic archaeon Haloferax volcanii Irit Tozik, Qiaojia Huang, Christian Zwieb, and Jerry Eichler PMCID: PMC140548 Human Mcm proteins at a replication origin during the G1 to S phase transition Daniel Schaarschmidt, Eva-Maria Ladenburger, Christian Keller, and Rolf Knippers PMCID: PMC140533 Temperature-sensitive mutants of the exosome subunit Rrp43p show a deficiency in mRNA degradation and no longer interact with the exosome Carla C. Oliveira, Fernando A. Gonzales, and Nilson I. T. Zanchin PMCID: PMC140545 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 Michaela Angermayr, Ulrich Oechsner, Kerstin Gregor, Gary P. Schroth, and Wolfhard Bandlow PMCID: PMC140550 Structure–function relationships of shared-stem and conventional molecular beacons Andrew Tsourkas, Mark A. Behlke, and Gang Bao PMCID: PMC140536 Frequent oligonucleotide motifs in genomes of three streptococci Jan Mrázek, Lisa H. Gaynon, and Samuel Karlin PMCID: PMC140534 Deletions in the S1 domain of Rrp5p cause processing at a novel site in ITS1 of yeast pre-rRNA that depends on Rex4p Noor A. Eppens, Alex W. Faber, Mariska Rondaij, Roshan S. Jahangir, Saskia van Hemert, Jan C. Vos, Jaap Venema, and Hendrik A. Raué PMCID: PMC140538 Structural variation and functional importance of a D-loop–T-loop interaction in valine-accepting tRNA-like structures of plant viral RNAs Maarten H. de Smit, Alexander P. Gultyaev, Mark Hilge, Hugo H. J. Bink, Sharief Barends, Barend Kraal, and Cornelis W. A. Pleij PMCID: PMC140539 The bulge region of HIV-1 TAR RNA binds metal ions in solution Mikołaj Olejniczak, Zofia Gdaniec, Artur Fischer, Tomasz Grabarkiewicz, Łukasz Bielecki, and Ryszard W. Adamiak PMCID: PMC140541 RNA canonical and non-canonical base pairing types: a recognition method and complete repertoire Sébastien Lemieux and François Major PMCID: PMC140540 Congruent evolution of different classes of non-coding DNA in prokaryotic genomes Igor B. Rogozin, Kira S. Makarova, Darren A. Natale, Alexey N. Spiridonov, Roman L. Tatusov, Yuri I. Wolf, Jodie Yin, and Eugene V. Koonin PMCID: PMC140549 Synonymous codon usage is subject to selection in thermophilic bacteria David J. Lynn, Gregory A. C. Singer, and Donal A. Hickey PMCID: PMC140546 Predicting transcription factor synergism Sridhar Hannenhalli and Samuel Levy PMCID: PMC140535 Engineered viruses to select genes encoding secreted and membrane-bound proteins in mammalian cells Pierre Moffatt, Patrick Salois, Marie-Hélène Gaumond, Natalie St-Amant, Éric Godin, and Christian Lanctôt PMCID: PMC140542 Artificial neural network prediction of antisense oligodeoxynucleotide activity Michael C. Giddings, Atul A. Shah, Sue Freier, John F. Atkins, Raymond F. Gesteland, and Olga V. Matveeva PMCID: PMC140555 Delineation of the high-affinity single-stranded telomeric DNA-binding domain of Saccharomyces cerevisiae Cdc13 Emily M. Anderson, Wayne A. Halsey, and Deborah S. Wuttke PMCID: PMC140553 Mutant Thermotoga neapolitana DNA polymerase I: altered catalytic properties for non-templated nucleotide addition and incorporation of correct nucleotides Shu-Wei Yang, Mekbib Astatke, Jason Potter, and Deb K. Chatterjee PMCID: PMC140547 A comparison of profile hidden Markov model procedures for remote homology detection Martin Madera and Julian Gough PMCID: PMC140544 NAR Methods Online Molecular haplotyping at high throughput Jörg Tost, Ole Brandt, Francis Boussicault, David Derbala, Christophe Caloustian, Doris Lechner, and Ivo Glynne Gut PMCID: PMC140556 MagiProbe: a novel fluorescence quenching-based oligonucleotide probe carrying a fluorophore and an intercalator Akio Yamane PMCID: PMC140557 PfoI, a unique type II restriction endonuclease that recognises the sequence 5′-T↓CCNGGA-3′ M. Gaigalas, Z. Manelienė, R. Kazlauskienė, M. Petrušytė, and A. Janulaitis PMCID: PMC140558 Effects of stray light on the fidelity of photodirected oligonucleotide array synthesis Peter B. Garland and Pawel J. Serafinowski PMCID: PMC140559 LNA-enhanced detection of single nucleotide polymorphisms in the apolipoprotein E Nana Jacobsen, Joan Bentzen, Michael Meldgaard, Mogens Havsteen Jakobsen, Mogens Fenger, Sakari Kauppinen, and Jan Skouv PMCID: PMC140560 An orthogonal oligonucleotide protecting group strategy that enables assembly of repetitive or highly structured DNAs Ulf M. Lindström and Eric T. Kool PMCID: PMC140561 Preferential hydrolysis of gap and bulge sites in DNA by Ce(IV)/EDTA complex Yoshihito Kitamura and Makoto Komiyama PMCID: PMC140562 Site-directed integration of the cre gene mediated by Cre recombinase using a combination of mutant lox sites Kimi Araki, Masatake Araki, and Ken-ichi Yamamura PMCID: PMC140563 |
