Skip Navigation

Receive this page by email each issue: [Sign up for eTOCs]

Cover Image
[Cover Caption] 
Other Issues:
Previous Next 		Contents: Volume 34, Number 19, November 2006   [Index by Author] 

Down Survey and Summary
Down Chemistry
Down Computational Biology
Down Molecular Biology
Down Nucleic Acid Enzymes
Down RNA
Down Structural Biology
Down Methods Online


[Search ALL Issues]

Table of Contents (Print PDF)

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.

Survey and Summary Back

Sarah Burge, Gary N. Parkinson, Pascale Hazel, Alan K. Todd, and Stephen Neidle
Quadruplex DNA: sequence, topology and structure
Nucleic Acids Research Advance Access published on September 29, 2006
Nucl. Acids Res. 2006 34: 5402-5415; doi:10.1093/nar/gkl655 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Julien Häsler and Katharina Strub
Alu elements as regulators of gene expression
Nucleic Acids Research Advance Access published on October 4, 2006
Nucl. Acids Res. 2006 34: 5491-5497; doi:10.1093/nar/gkl706 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Caroline Jolly and Subhash C. Lakhotia
Human sat III and Drosophila hsr{omega} transcripts: a common paradigm for regulation of nuclear RNA processing in stressed cells
Nucleic Acids Research Advance Access published on October 4, 2006
Nucl. Acids Res. 2006 34: 5508-5514; doi:10.1093/nar/gkl711 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Chemistry Back

Brock Matter, Danuta Malejka-Giganti, A. Saari Csallany, and Natalia Tretyakova
Quantitative analysis of the oxidative DNA lesion, 2,2-diamino-4-(2-deoxy-ß-D-erythro-pentofuranosyl)amino]-5(2H)-oxazolone (oxazolone), in vitro and in vivo by isotope dilution-capillary HPLC-ESI-MS/MS
Nucleic Acids Research Advance Access published on October 4, 2006
Nucl. Acids Res. 2006 34: 5449-5460; doi:10.1093/nar/gkl596 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Computational Biology Back

Hideki Noguchi, Jungho Park, and Toshihisa Takagi
MetaGene: prokaryotic gene finding from environmental genome shotgun sequences
Nucleic Acids Research Advance Access published on October 5, 2006
Nucl. Acids Res. 2006 34: 5623-5630; doi:10.1093/nar/gkl723 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nils B. Becker, Lars Wolff, and Ralf Everaers
Indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials
Nucleic Acids Research Advance Access published on October 11, 2006
Nucl. Acids Res. 2006 34: 5638-5649; doi:10.1093/nar/gkl683 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Yu Shao, Yan Wu, Chi Yu Chan, Kathleen McDonough, and Ye Ding
Rational design and rapid screening of antisense oligonucleotides for prokaryotic gene modulation
Nucleic Acids Research Advance Access published on October 11, 2006
Nucl. Acids Res. 2006 34: 5660-5669; doi:10.1093/nar/gkl715 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Molecular Biology Back

Beata Kosmider and Robert D. Wells
Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli
Nucleic Acids Research Advance Access published on September 29, 2006
Nucl. Acids Res. 2006 34: 5369-5382; doi:10.1093/nar/gkl612 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Masayasu Kuwahara, Jun-ichi Nagashima, Masatoshi Hasegawa, Takehiro Tamura, Rina Kitagata, Kazuo Hanawa, Shin-ichi Hososhima, Toshiyuki Kasamatsu, Hiroaki Ozaki, and Hiroaki Sawai
Systematic characterization of 2'-deoxynucleoside- 5'-triphosphate analogs as substrates for DNA polymerases by polymerase chain reaction and kinetic studies on enzymatic production of modified DNA
Nucleic Acids Research Advance Access published on September 29, 2006
Nucl. Acids Res. 2006 34: 5383-5394; doi:10.1093/nar/gkl637 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Michael McArthur and Mervyn Bibb
In vivo DNase I sensitivity of the Streptomyces coelicolor chromosome correlates with gene expression: implications for bacterial chromosome structure
Nucleic Acids Research Advance Access published on September 29, 2006
Nucl. Acids Res. 2006 34: 5395-5401; doi:10.1093/nar/gkl649 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Francesco Chiani, Francesca Di Felice, and Giorgio Camilloni
SIR2 modifies histone H4-K16 acetylation and affects superhelicity in the ARS region of plasmid chromatin in Saccharomyces cerevisiae
Nucleic Acids Research Advance Access published on September 29, 2006
Nucl. Acids Res. 2006 34: 5426-5437; doi:10.1093/nar/gkl678 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jörg Tost, Hélène Jammes, Jean-Michel Dupont, Christophe Buffat, Brigitte Robert, Thérèse-Marie Mignot, Françoise Mondon, Bruno Carbonne, Umberto Siméoni, Gilles Grangé, Antoine Kerjean, Françoise Ferré, Ivo Glynne Gut, and Daniel Vaiman
Non-random, individual-specific methylation profiles are present at the sixth CTCF binding site in the human H19/IGF2 imprinting control region
Nucleic Acids Research Advance Access published on September 29, 2006
Nucl. Acids Res. 2006 34: 5438-5448; doi:10.1093/nar/gkl657 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Tage Thorstensen, Andreas Fischer, Silje V. Sandvik, Sylvia S. Johnsen, Paul E. Grini, Gunter Reuter, and Reidunn B. Aalen
The Arabidopsis SUVR4 protein is a nucleolar histone methyltransferase with preference for monomethylated H3K9
Nucleic Acids Research Advance Access published on October 4, 2006
Nucl. Acids Res. 2006 34: 5461-5470; doi:10.1093/nar/gkl687 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Patrick H. Maxwell, John M. Belote, and Robert W. Levis
Identification of multiple transcription initiation, polyadenylation, and splice sites in the Drosophila melanogaster TART family of telomeric retrotransposons
Nucleic Acids Research Advance Access published on October 4, 2006
Nucl. Acids Res. 2006 34: 5498-5507; doi:10.1093/nar/gkl709 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Paola Sacchetti, Rodolphe Carpentier, Pascaline Ségard, Cécile Olivé-Cren, and Philippe Lefebvre
Multiple signaling pathways regulate the transcriptional activity of the orphan nuclear receptor NURR1
Nucleic Acids Research Advance Access published on October 4, 2006
Nucl. Acids Res. 2006 34: 5515-5527; doi:10.1093/nar/gkl712 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Minghua Nie and Han Htun
Different modes and potencies of translational repression by sequence-specific RNA–protein interaction at the 5'-UTR
Nucleic Acids Research Advance Access published on October 5, 2006
Nucl. Acids Res. 2006 34: 5528-5540; doi:10.1093/nar/gkl584 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jiang-Hong Man, Hui-Yan Li, Pei-Jing Zhang, Tao Zhou, Kun He, Xin Pan, Bing Liang, Ai-Ling Li, Jie Zhao, Wei-Li Gong, Bao-Feng Jin, Qing Xia, Ming Yu, Bei-Fen Shen, and Xue-Min Zhang
PIAS3 induction of PRB sumoylation represses PRB transactivation by destabilizing its retention in the nucleus
Nucleic Acids Research Advance Access published on October 4, 2006
Nucl. Acids Res. 2006 34: 5552-5566; doi:10.1093/nar/gkl691 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nick D. Tsihlis and Anne Grove
The Saccharomyces cerevisiae RNA polymerase III recruitment factor subunits Brf1 and Bdp1 impose a strict sequence preference for the downstream half of the TATA box
Nucleic Acids Research Advance Access published on October 6, 2006
Nucl. Acids Res. 2006 34: 5585-5593; doi:10.1093/nar/gkl534 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

David Goldschneider, Emilie Horvilleur, Louis-François Plassa, Marine Guillaud-Bataille, Karine Million, Evelyne Wittmer-Dupret, Gisèle Danglot, Hughes de Thé, Jean Bénard, Evelyne May, and Sétha Douc-Rasy
Expression of C-terminal deleted p53 isoforms in neuroblastoma
Nucleic Acids Research Advance Access published on October 5, 2006
Nucl. Acids Res. 2006 34: 5603-5612; doi:10.1093/nar/gkl619 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Alessandra Mescalchin, Winfried Wünsche, Sandra D. Laufer, Dina Grohmann, Tobias Restle, and Georg Sczakiel
Specific binding of a hexanucleotide to HIV-1 reverse transcriptase: a novel class of bioactive molecules
Nucleic Acids Research Advance Access published on October 12, 2006
Nucl. Acids Res. 2006 34: 5631-5637; doi:10.1093/nar/gkl533 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes Back

Litao Yang, Janet R. Mullen, and Steven J. Brill
Purification of the yeast Slx5–Slx8 protein complex and characterization of its DNA-binding activity
Nucleic Acids Research Advance Access published on October 4, 2006
Nucl. Acids Res. 2006 34: 5541-5551; doi:10.1093/nar/gkl685 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Sugopa Sengupta, Meera Shah, and Valakunja Nagaraja
Glutamate racemase from Mycobacterium tuberculosis inhibits DNA gyrase by affecting its DNA-binding
Nucleic Acids Research Advance Access published on October 4, 2006
Nucl. Acids Res. 2006 34: 5567-5576; doi:10.1093/nar/gkl704 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Megan P. Hall and C. Kiong Ho
Functional characterization of a 48 kDa Trypanosoma brucei cap 2 RNA methyltransferase
Nucleic Acids Research Advance Access published on October 5, 2006
Nucl. Acids Res. 2006 34: 5594-5602; doi:10.1093/nar/gkl573 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

You-Yi Huang, Jiao-Yu Deng, Jing Gu, Zhi-Ping Zhang, Anthony Maxwell, Li-Jun Bi, Yuan-Yuan Chen, Ya-Feng Zhou, Zi-Niu Yu, and Xian-En Zhang
The key DNA-binding residues in the C-terminal domain of Mycobacterium tuberculosis DNA gyrase A subunit (GyrA)
Nucleic Acids Research Advance Access published on October 11, 2006
Nucl. Acids Res. 2006 34: 5650-5659; doi:10.1093/nar/gkl695 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Stefán R. Jónsson, Guylaine Haché, Mark D. Stenglein, Scott C. Fahrenkrug, Valgerdur Andrésdóttir, and Reuben S. Harris
Evolutionarily conserved and non-conserved retrovirus restriction activities of artiodactyl APOBEC3F proteins
Nucleic Acids Research Advance Access published on October 11, 2006
Nucl. Acids Res. 2006 34: 5683-5694; doi:10.1093/nar/gkl721 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA Back

Nina E. McCrate, Mychel E. Varner, Kenneth I. Kim, and Maria C. Nagan
Molecular dynamics simulations of human Formula: the role of modified bases in mRNA recognition
Nucleic Acids Research Advance Access published on September 29, 2006
Nucl. Acids Res. 2006 34: 5361-5368; doi:10.1093/nar/gkl580 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Jianhe Sun, Ying Cai, Wulf-Dieter Moll, and Peixuan Guo
Controlling bacteriophage phi29 DNA-packaging motor by addition or discharge of a peptide at N-terminus of connector protein that interacts with pRNA
Nucleic Acids Research Advance Access published on October 4, 2006
Nucl. Acids Res. 2006 34: 5482-5490; doi:10.1093/nar/gkl701 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Alberto Carbonell, Marcos De la Peña, Ricardo Flores, and Selma Gago
Effects of the trinucleotide preceding the self-cleavage site on eggplant latent viroid hammerheads: differences in co- and post-transcriptional self-cleavage may explain the lack of trinucleotide AUC in most natural hammerheads
Nucleic Acids Research Advance Access published on October 5, 2006
Nucl. Acids Res. 2006 34: 5613-5622; doi:10.1093/nar/gkl717 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Maung Nyan Win, Joshua S. Klein, and Christina D. Smolke
Codeine-binding RNA aptamers and rapid determination of their binding constants using a direct coupling surface plasmon resonance assay
Nucleic Acids Research Advance Access published on October 11, 2006
Nucl. Acids Res. 2006 34: 5670-5682; doi:10.1093/nar/gkl718 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Bijoy K. Mohanty and Sidney R. Kushner
The majority of Escherichia coli mRNAs undergo post-transcriptional modification in exponentially growing cells
Nucleic Acids Research Advance Access published on October 12, 2006
Nucl. Acids Res. 2006 34: 5695-5704; doi:10.1093/nar/gkl684 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Hee Kyu Lee and Sunjoo Jeong
ß-Catenin stabilizes Cyclooxygenase-2 mRNA by interacting with AU-rich elements of 3'-UTR
Nucleic Acids Research Advance Access published on October 12, 2006
Nucl. Acids Res. 2006 34: 5705-5714; doi:10.1093/nar/gkl698 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Structural Biology Back

Sherwin P. Montaño, Marie L. Coté, Monica J. Roth, and Millie M. Georgiadis
Crystal structures of oligonucleotides including the integrase processing site of the Moloney murine leukemia virus
Nucleic Acids Research Advance Access published on September 26, 2006
Nucl. Acids Res. 2006 34: 5353-5360; doi:10.1093/nar/gkl693 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Neal Crampton, William A. Bonass, Jennifer Kirkham, Claudio Rivetti, and Neil H. Thomson
Collision events between RNA polymerases in convergent transcription studied by atomic force microscopy
Nucleic Acids Research Advance Access published on September 29, 2006
Nucl. Acids Res. 2006 34: 5416-5425; doi:10.1093/nar/gkl668 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Björn Voß
Structural analysis of aligned RNAs
Nucleic Acids Research Advance Access published on October 4, 2006
Nucl. Acids Res. 2006 34: 5471-5481; doi:10.1093/nar/gkl692 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Rachel Macmaster, Svetlana Sedelnikova, Patrick J. Baker, Edward L. Bolt, Robert G. Lloyd, and John B. Rafferty
RusA Holliday junction resolvase: DNA complex structure—insights into selectivity and specificity
Nucleic Acids Research Advance Access published on October 5, 2006
Nucl. Acids Res. 2006 34: 5577-5584; doi:10.1093/nar/gkl447 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Anh Tuân Phan, Kim Ngoc Luu, and Dinshaw J. Patel
Different loop arrangements of intramolecular human telomeric (3+1) G-quadruplexes in K+ solution
Nucleic Acids Research Advance Access published on October 12, 2006
Nucl. Acids Res. 2006 34: 5715-5719; doi:10.1093/nar/gkl726 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online Back

Malali Gowda, Haumeng Li, Joe Alessi, Feng Chen, Richard Pratt, and Guo-Liang Wang
Robust analysis of 5'-transcript ends (5'-RATE): a novel technique for transcriptome analysis and genome annotation
Nucleic Acids Research Advance Access published on September 29, 2006
Nucl. Acids Res. 2006 34: e126; doi:10.1093/nar/gkl522 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Isao Fukuda, Kanehisa Kojoh, Noriko Tabata, Nobuhide Doi, Hideaki Takashima, Etsuko Miyamoto-Sato, and Hiroshi Yanagawa
In vitro evolution of single-chain antibodies using mRNA display
Nucleic Acids Research Advance Access published on September 29, 2006
Nucl. Acids Res. 2006 34: e127; doi:10.1093/nar/gkl618 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Igor V. Kutyavin, Dave Milesi, Yevgeniy Belousov, Mikhail Podyminogin, Alexei Vorobiev, Vladimir Gorn, Eugeny A. Lukhtanov, Nicolaas M. J. Vermeulen, and Walt Mahoney
A novel endonuclease IV post-PCR genotyping system
Nucleic Acids Research Advance Access published on September 29, 2006
Nucl. Acids Res. 2006 34: e128; doi:10.1093/nar/gkl679 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Kenneth B. Beckman, Kenneth J. Abel, Andreas Braun, and Eran Halperin
Using DNA pools for genotyping trios
Nucleic Acids Research Advance Access published on October 4, 2006
Nucl. Acids Res. 2006 34: e129; doi:10.1093/nar/gkl700 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Richard A. George, Jason Y. Liu, Lina L. Feng, Robert J. Bryson-Richardson, Diane Fatkin, and Merridee A. Wouters
Analysis of protein sequence and interaction data for candidate disease gene prediction
Nucleic Acids Research Advance Access published on October 4, 2006
Nucl. Acids Res. 2006 34: e130; doi:10.1093/nar/gkl707 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Holly K. Dressman, Lise Barley-Maloney, Laura-Leigh Rowlette, Paul F. Agris, and Mariano A. Garcia-Blanco
Assessing incomplete deprotection of microarray oligonucleotides in situ
Nucleic Acids Research Advance Access published on October 4, 2006
Nucl. Acids Res. 2006 34: e131; doi:10.1093/nar/gkl713 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Csaba Kiss, Hugh Fisher, Emanuele Pesavento, Minghua Dai, Rosa Valero, Milan Ovecka, Rhiannon Nolan, M. Lisa Phipps, Nileena Velappan, Leslie Chasteen, Jennifer S. Martinez, Geoffrey S. Waldo, Peter Pavlik, and Andrew R.M. Bradbury
Antibody binding loop insertions as diversity elements
Nucleic Acids Research Advance Access published on October 5, 2006
Nucl. Acids Res. 2006 34: e132; doi:10.1093/nar/gkl681 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Kåre L. Nielsen, Annabeth Laursen Høgh, and Jeppe Emmersen
DeepSAGE—digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples
Nucleic Acids Research Advance Access published on October 5, 2006
Nucl. Acids Res. 2006 34: e133; doi:10.1093/nar/gkl714 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Julie Mantovani, Nathalie Holic, Kelly Martinez, Olivier Danos, and Javier Perea
A high throughput method for genome-wide analysis of retroviral integration
Nucleic Acids Research Advance Access published on October 5, 2006
Nucl. Acids Res. 2006 34: e134; doi:10.1093/nar/gkl716 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Madina B. Iskakova, Witold Szaflarski, Marc Dreyfus, Jaanus Remme, and Knud H. Nierhaus
Troubleshooting coupled in vitro transcription–translation system derived from Escherichia coli cells: synthesis of high-yield fully active proteins
Nucleic Acids Research Advance Access published on October 11, 2006
Nucl. Acids Res. 2006 34: e135; doi:10.1093/nar/gkl462 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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.