Nucleic Acids Research

Semi-automated, single-band peak-fitting analysis of hydroxyl radical nucleic acid footprint autoradiograms for the quantitative analysis of transitions
pp. e119-e119(1)
Authors: Takamoto, Keiji; Chance, Mark R.; Brenowitz, Michael

RNA expression microarrays (REMs), a high-throughput method to measure differences in gene expression in diverse biological samples
pp. e120-e120(1)
Authors: Rogler, Charles E.; Tchaikovskaya, Tatyana; Norel, Raquel; Massimi, Aldo; Plescia, Christopher; Rubashevsky, Eugeny; Siebert, Paul; Rogler, Leslie E.

Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments
pp. e121-e121(1)
Authors: Tengs, Torstein; LaFramboise, Thomas; Den, Robert B.; Hayes, David N.; Zhang, Jianhua; DebRoy, Saikat; Gentleman, Robert C.; O'Neill, Keith; Birren, Bruce; Meyerson, Matthew

A `one-pot' assay for the accessibility of DNA in a nucleosome core particle
pp. e122-e122(1)
Authors: Wu, Chenyi; Travers, Andrew

Quantitative assessment of a novel flow-through porous microarray for the rapid analysis of gene expression profiles
pp. e123-e123(1)
Authors: Wu, Ying; de Kievit, Peggy; Vahlkamp, Lars; Pijnenburg, Dirk; Smit, Maarten; Dankers, Martijn; Melchers, Diana; Stax, Martijn; Boender, Piet J.; Ingham, Colin; Bastiaensen, Niek; de Wijn, Rik; van Alewijk, Dirk; van Damme, Henk; Raap, Anton K.; Chan, Alan B.; van Beuningen, Rinie

Comprehensive comparison of six microarray technologies
pp. e124-e124(1)
Authors: Yauk, Carole L.; Berndt, M. Lynn; Williams, Andrew; Douglas, George R.

A novel type of silencing factor, Clr2, is necessary for transcriptional silencing at various chromosomal locations in the fission yeast Schizosaccharomyces pombe
pp. 4421-4428(8)
Authors: Bjerling, Pernilla; Ekwall, Karl; Egel, Richard; Thon, Geneviève

The N-terminal half-domain of the long form of tRNase Z is required for the RNase 65 activity
pp. 4429-4438(10)
Authors: Takaku, Hiroaki; Minagawa, Asako; Takagi, Masamichi; Nashimoto, Masayuki

Selectivity and affinity of triplex-forming oligonucleotides containing 2′-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine for recognizing AT base pairs in duplex DNA
pp. 4439-4447(9)
Authors: Osborne, Sadie D.; Powers, Vicki E. C.; Rusling, David A.; Lack, Oliver; Fox, Keith R.; Brown, Tom

tRNA^Ser(CGA) differentially regulates expression of wild-type and codon-modified papillomavirus L1 genes
pp. 4448-4461(14)
Authors: Gu, Wenyi; Li, Mengrong; Zhao, Wei Ming; Fang, Ning Xia; Bu, Shurui; Frazer, Ian H.; Zhao, Kong-Nan

Ribosome stalling and peptidyl-tRNA drop-off during translational delay at AGA codons
pp. 4462-4468(7)
Authors: Cruz-Vera, Luis Rogelio; Magos-Castro, Marco Antonio; Zamora-Romo, Efraín; Guarneros, Gabriel

Transcription influences the types of deletion and expansion products in an orientation-dependent manner from GAC•GTC repeats
pp. 4469-4479(11)
Authors: Mochmann, Liliana H.; Wells, Robert D.

Transcriptional repression by p53 promotes a Bcl-2-insensitive and mitochondria-independent pathway of apoptosis
pp. 4480-4490(11)
Authors: Godefroy, Nelly; Bouleau, Sylvina; Gruel, Gaëtan; Renaud, Flore; Rincheval, Vincent; Mignotte, Bernard; Tronik-Le Roux, Diana; Vayssière, Jean-Luc

The effect of eukaryotic release factor depletion on translation termination in human cell lines
pp. 4491-4502(12)
Authors: Janzen, Deanna M.; Geballe, Adam P.

DNA ligases ensure fidelity by interrogating minor groove contacts
pp. 4503-4511(9)
Authors: Liu, Pingfang; Burdzy, Artur; Sowers, Lawrence C.

Comparative analysis of dioxin response elements in human, mouse and rat genomic sequences
pp. 4512-4523(12)
Authors: Sun, Y. V.; Boverhof, D. R.; Burgoon, L. D.; Fielden, M. R.; Zacharewski, T. R.

The human Rad9 checkpoint protein stimulates the carbamoyl phosphate synthetase activity of the multifunctional protein CAD
pp. 4524-4530(7)
Authors: Lindsey-Boltz, Laura A.; Wauson, Eric M.; Graves, Lee M.; Sancar, Aziz

A third lineage with two-piece tmRNA
pp. 4531-4538(8)
Authors: Sharkady, Stephen M.; Williams, Kelly P.

Increased frequency of aberrant V(D)J recombination products in core RAG-expressing mice
pp. 4539-4549(11)
Authors: Talukder, Sadiqur R.; Dudley, Darryll D.; Alt, Frederick W.; Takahama, Yousuke; Akamatsu, Yoshiko

Redefining the structure of the mouse connexin43 gene: selective promoter usage and alternative splicing mechanisms yield transcripts with different translational efficiencies
pp. 4550-4562(13)
Authors: Pfeifer, Ingrid; Anderson, Curtis; Werner, Rudolf; Oltra, Elisa

Thioredoxin can influence gene expression by affecting gyrase activity
pp. 4563-4575(13)
Authors: Li, Kuanyu; Pasternak, Cécile; Härtig, Elisabeth; Haberzettl, Kerstin; Maxwell, Anthony; Klug, Gabriele

RNA binding and R-loop formation by the herpes simplex virus type-1 single-stranded DNA-binding protein (ICP8)
pp. 4576-4584(9)
Author: Boehmer, Paul E.

Splicing affects presentation of RNA dimerization signals in HIV-2 in vitro
pp. 4585-4595(11)
Authors: Lanchy, Jean-Marc; Szafran, Quenna N.; Lodmell, J. Stephen

Nucleotide-dependent interactions between a fork junction-RNA polymerase complex and an AAA+ transcriptional activator protein
pp. 4596-4608(13)
Authors: Cannon, W. V.; Schumacher, J.; Buck, M.

Relative gene-silencing efficiencies of small interfering RNAs targeting sense and antisense transcripts from the same genetic locus
pp. 4609-4617(9)
Authors: Hu, Xiuyuan; Hipolito, Sharlene; Lynn, Rebecca; Abraham, Violet; Ramos, Silvester; Wong-Staal, Flossie

Phosphorylation at 5′ end of guanosine stretches inhibits dimerization of G-quadruplexes and formation of a G-quadruplex interferes with the enzymatic activities of DNA enzymes
pp. 4618-4629(12)
Authors: Uddin, M. Khabir; Kato, Yoshio; Takagi, Yasuomi; Mikuma, Toshiyasu; Taira, Kazunari

Rational design of DNA sequences for nanotechnology, microarrays and molecular computers using Eulerian graphs
pp. 4630-4645(16)
Authors: Pancoska, Petr; Moravek, Zdenek; Moll, Ute M.

Novel non-coding RNAs in Dictyostelium discoideum and their expression during development
pp. 4646-4656(11)
Authors: Aspegren, Anders; Hinas, Andrea; Larsson, Pontus; Larsson, Anders; Söderbom, Fredrik

Design and synthesis of fluorescent substrates for human tyrosyl-DNA phosphodiesterase I
pp. 4657-4664(8)
Authors: Rideout, Marc C.; Raymond, Amy C.; Burgin, Alex B.

Enzymatic switching for efficient and accurate translesion DNA replication
pp. 4665-4675(11)
Authors: McCulloch, Scott D.; Kokoska, Robert J.; Chilkova, Olga; Welch, Carrie M.; Johansson, Erik; Burgers, Peter M. J.; Kunkel, Thomas A.

Alternative splicing generates multiple SMRT transcripts encoding conserved repressor domains linked to variable transcription factor interaction domains
pp. 4676-4686(11)
Authors: Malartre, Marianne; Short, Stephen; Sharpe, Colin

Synthetic tRNA^Lys,3 as the replication primer for the HIV-1_HXB2 and HIV-1_Mal genomes
pp. 4687-4695(9)
Authors: Miller, Jennifer T.; Khvorova, Anastasia; Scaringe, Stephen A.; Le Grice, Stuart F. J.

Cooperative effects on the formation of intercalation sites
pp. 4696-4703(8)
Authors: Trieb, Michael; Rauch, Christine; Wibowo, Fajar R.; Wellenzohn, Bernd; Liedl, Klaus R.

Interaction of the Zα domain of human ADAR1 with a negatively supercoiled plasmid visualized by atomic force microscopy
pp. 4704-4712(9)
Authors: Lushnikov, Alexander Y.; Brown, Bernard A.; Oussatcheva, Elena A.; Potaman, Vladimir N.; Sinden, Richard R.; Lyubchenko, Yuri L.

Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics
pp. 4713-4713(1)
Authors: McCutcheon, John P.; Eddy, Sean R.