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Previous Next 		Contents: Volume 36, Number 12, July 2008   [Index by Author] 

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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

Rudy Juliano, Md. Rowshon Alam, Vidula Dixit, and Hyumin Kang
Mechanisms and strategies for effective delivery of antisense and siRNA oligonucleotides
Nucleic Acids Research Advance Access published on June 16, 2008
Nucl. Acids Res. 2008 36: 4158-4171; doi:10.1093/nar/gkn342 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Computational Biology Back

Mu Gao and Jeffrey Skolnick
DBD-Hunter: a knowledge-based method for the prediction of DNA–protein interactions
Nucleic Acids Research Advance Access published on May 31, 2008
Nucl. Acids Res. 2008 36: 3978-3992; doi:10.1093/nar/gkn332 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Lon M. Chubiz and Christopher V. Rao
Computational design of orthogonal ribosomes
Nucleic Acids Research Advance Access published on June 3, 2008
Nucl. Acids Res. 2008 36: 4038-4046; doi:10.1093/nar/gkn354 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Mikael Bodén and Timothy L. Bailey
Associating transcription factor-binding site motifs with target GO terms and target genes
Nucleic Acids Research Advance Access published on June 10, 2008
Nucl. Acids Res. 2008 36: 4108-4117; doi:10.1093/nar/gkn374 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Qing Zhou and Jun S. Liu
Extracting sequence features to predict protein–DNA interactions: a comparative study
Nucleic Acids Research Advance Access published on June 13, 2008
Nucl. Acids Res. 2008 36: 4137-4148; doi:10.1093/nar/gkn361 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genomics Back

Henri-Marc Bourbon
Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex
Nucleic Acids Research Advance Access published on May 31, 2008
Nucl. Acids Res. 2008 36: 3993-4008; doi:10.1093/nar/gkn349 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Geetu Tuteja, Shane T. Jensen, Peter White, and Klaus H. Kaestner
Cis-regulatory modules in the mammalian liver: composition depends on strength of Foxa2 consensus site
Nucleic Acids Research Advance Access published on June 13, 2008
Nucl. Acids Res. 2008 36: 4149-4157; doi:10.1093/nar/gkn366 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology Back

Kumi Nakamura, Hiroyuki Ida, and Masamitsu Yamaguchi
Transcriptional regulation of the Drosophila moira and osa genes by the DREF pathway
Nucleic Acids Research Advance Access published on May 29, 2008
Nucl. Acids Res. 2008 36: 3905-3915; doi:10.1093/nar/gkn291 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Anat Yafe, Jeny Shklover, Pnina Weisman-Shomer, Eyal Bengal, and Michael Fry
Differential binding of quadruplex structures of muscle-specific genes regulatory sequences by MyoD, MRF4 and myogenin
Nucleic Acids Research Advance Access published on May 29, 2008
Nucl. Acids Res. 2008 36: 3916-3925; doi:10.1093/nar/gkn340 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Tomohiro Shimada, Akira Ishihama, Stephen J. W. Busby, and David C. Grainger
The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions
Nucleic Acids Research Advance Access published on May 30, 2008
Nucl. Acids Res. 2008 36: 3950-3955; doi:10.1093/nar/gkn339 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Anirban Mukherjee, Abimbola O. Sokunbi, and Anne Grove
DNA protection by histone-like protein HU from the hyperthermophilic eubacterium Thermotoga maritima
Nucleic Acids Research Advance Access published on May 30, 2008
Nucl. Acids Res. 2008 36: 3956-3968; doi:10.1093/nar/gkn348 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nicole A. Becker, Jason D. Kahn, and L. James Maher, III
Eukaryotic HMGB proteins as replacements for HU in E. coli repression loop formation
Nucleic Acids Research Advance Access published on May 31, 2008
Nucl. Acids Res. 2008 36: 4009-4021; doi:10.1093/nar/gkn353 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Harma Feitsma, Alper Akay, and Edwin Cuppen
Alkylation damage causes MMR-dependent chromosomal instability in vertebrate embryos
Nucleic Acids Research Advance Access published on June 3, 2008
Nucl. Acids Res. 2008 36: 4047-4056; doi:10.1093/nar/gkn341 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Sean D. Sheridan, Xiong Yu, Robyn Roth, John E. Heuser, Michael G. Sehorn, Patrick Sung, Edward H. Egelman, and Douglas K. Bishop
A comparative analysis of Dmc1 and Rad51 nucleoprotein filaments
Nucleic Acids Research Advance Access published on June 4, 2008
Nucl. Acids Res. 2008 36: 4057-4066; doi:10.1093/nar/gkn352 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Mohammad Shahidul Makki, Thorsten Heinzel, and Christoph Englert
TSA downregulates Wilms tumor gene 1 (Wt1) expression at multiple levels
Nucleic Acids Research Advance Access published on June 4, 2008
Nucl. Acids Res. 2008 36: 4067-4078; doi:10.1093/nar/gkn356 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Wael Y. Mansour, Sabine Schumacher, Raphael Rosskopf, Tim Rhein, Filip Schmidt-Petersen, Fruszina Gatzemeier, Friedrich Haag, Kerstin Borgmann, Henning Willers, and Jochen Dahm-Daphi
Hierarchy of nonhomologous end-joining, single-strand annealing and gene conversion at site-directed DNA double-strand breaks
Nucleic Acids Research Advance Access published on June 6, 2008
Nucl. Acids Res. 2008 36: 4088-4098; doi:10.1093/nar/gkn347 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Juri Hikiba, Kouji Hirota, Wataru Kagawa, Shukuko Ikawa, Takashi Kinebuchi, Isao Sakane, Yoshimasa Takizawa, Shigeyuki Yokoyama, Béatrice Mandon-Pépin, Alain Nicolas, Takehiko Shibata, Kunihiro Ohta, and Hitoshi Kurumizaka
Structural and functional analyses of the DMC1-M200V polymorphism found in the human population
Nucleic Acids Research Advance Access published on June 19, 2008
Nucl. Acids Res. 2008 36: 4181-4190; doi:10.1093/nar/gkn362 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Nucleic Acid Enzymes Back

Jessica A. Brown, Sean A. Newmister, Kevin A. Fiala, and Zucai Suo
Mechanism of double-base lesion bypass catalyzed by a Y-family DNA polymerase
Nucleic Acids Research Advance Access published on May 22, 2008
Nucl. Acids Res. 2008 36: 3867-3878; doi:10.1093/nar/gkn309 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Paul A. Rowley, Matthew C. A. Smith, Ellen Younger, and Margaret C. M. Smith
A motif in the C-terminal domain of {phi}C31 integrase controls the directionality of recombination
Nucleic Acids Research Advance Access published on May 23, 2008
Nucl. Acids Res. 2008 36: 3879-3891; doi:10.1093/nar/gkn269 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Xuejun Zhong, Lars C. Pedersen, and Thomas A. Kunkel
Characterization of a replicative DNA polymerase mutant with reduced fidelity and increased translesion synthesis capacity
Nucleic Acids Research Advance Access published on May 24, 2008
Nucl. Acids Res. 2008 36: 3892-3904; doi:10.1093/nar/gkn312 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Michal Minczuk, Monika A. Papworth, Jeffrey C. Miller, Michael P. Murphy, and Aaron Klug
Development of a single-chain, quasi-dimeric zinc-finger nuclease for the selective degradation of mutated human mitochondrial DNA
Nucleic Acids Research Advance Access published on May 29, 2008
Nucl. Acids Res. 2008 36: 3926-3938; doi:10.1093/nar/gkn313 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Eva Sisáková, Louise K. Stanley, Marie Weiserová, and Mark D. Szczelkun
A RecB-family nuclease motif in the Type I restriction endonuclease EcoR124I
Nucleic Acids Research Advance Access published on May 29, 2008
Nucl. Acids Res. 2008 36: 3939-3949; doi:10.1093/nar/gkn333 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Giedrius Sasnauskas, Bernard A. Connolly, Stephen E. Halford, and Virginijus Siksnys
Template-directed addition of nucleosides to DNA by the BfiI restriction enzyme
Nucleic Acids Research Advance Access published on May 30, 2008
Nucl. Acids Res. 2008 36: 3969-3977; doi:10.1093/nar/gkn343 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Katherine S. Pawelczak and John J. Turchi
A mechanism for DNA-PK activation requiring unique contributions from each strand of a DNA terminus and implications for microhomology-mediated nonhomologous DNA end joining
Nucleic Acids Research Advance Access published on May 31, 2008
Nucl. Acids Res. 2008 36: 4022-4031; doi:10.1093/nar/gkn344 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Isabelle Bonnet, Andreas Biebricher, Pierre-Louis Porté, Claude Loverdo, Olivier Bénichou, Raphaël Voituriez, Christophe Escudé, Wolfgang Wende, Alfred Pingoud, and Pierre Desbiolles
Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA
Nucleic Acids Research Advance Access published on June 10, 2008
Nucl. Acids Res. 2008 36: 4118-4127; doi:10.1093/nar/gkn376 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA Back

Rita Lózsa, Tibor Csorba, Lóránt Lakatos, and József Burgyán
Inhibition of 3' modification of small RNAs in virus-infected plants require spatial and temporal co-expression of small RNAs and viral silencing-suppressor proteins
Nucleic Acids Research Advance Access published on June 6, 2008
Nucl. Acids Res. 2008 36: 4099-4107; doi:10.1093/nar/gkn365 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Dileep K. Pulukkunat and Venkat Gopalan
Studies on Methanocaldococcus jannaschii RNase P reveal insights into the roles of RNA and protein cofactors in RNase P catalysis
Nucleic Acids Research Advance Access published on June 16, 2008
Nucl. Acids Res. 2008 36: 4172-4180; doi:10.1093/nar/gkn360 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Elke Duchardt, Lennart Nilsson, and Jürgen Schleucher
Cytosine ribose flexibility in DNA: a combined NMR 13C spin relaxation and molecular dynamics simulation study
Nucleic Acids Research Advance Access published on June 25, 2008
Nucl. Acids Res. 2008 36: 4211-4219; doi:10.1093/nar/gkn375 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology Back

David J. Wilton, Mahua Ghosh, K. V. A. Chary, Kazuyuki Akasaka, and Mike P. Williamson
Structural change in a B-DNA helix with hydrostatic pressure
Nucleic Acids Research Advance Access published on May 31, 2008
Nucl. Acids Res. 2008 36: 4032-4037; doi:10.1093/nar/gkn350 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Timur I. Gaynutdinov, Ronald D. Neumann, and Igor G. Panyutin
Structural polymorphism of intramolecular quadruplex of human telomeric DNA: effect of cations, quadruplex-binding drugs and flanking sequences
Nucleic Acids Research Advance Access published on June 4, 2008
Nucl. Acids Res. 2008 36: 4079-4087; doi:10.1093/nar/gkn351 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Thomas S. Dexheimer, Albena Kozekova, Carmelo J. Rizzo, Michael P. Stone, and Yves Pommier
The modulation of topoisomerase I-mediated DNA cleavage and the induction of DNA–topoisomerase I crosslinks by crotonaldehyde-derived DNA adducts
Nucleic Acids Research Advance Access published on June 10, 2008
Nucl. Acids Res. 2008 36: 4128-4136; doi:10.1093/nar/gkn334 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Robert D. Gray and Jonathan B. Chaires
Kinetics and mechanism of K+- and Na+-induced folding of models of human telomeric DNA into G-quadruplex structures
Nucleic Acids Research Advance Access published on June 21, 2008
Nucl. Acids Res. 2008 36: 4191-4203; doi:10.1093/nar/gkn379 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Giuseppe Lia, Szabolcs Semsey, Dale E. A. Lewis, Sankar Adhya, David Bensimon, David Dunlap, and Laura Finzi
The antiparallel loops in gal DNA
Nucleic Acids Research Advance Access published on June 23, 2008
Nucl. Acids Res. 2008 36: 4204-4210; doi:10.1093/nar/gkn389 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online Back

Antony K. Chen, Mark A. Behlke, and Andrew Tsourkas
Efficient cytosolic delivery of molecular beacon conjugates and flow cytometric analysis of target RNA
Nucleic Acids Research Advance Access published on May 24, 2008
Nucl. Acids Res. 2008 36: e69; doi:10.1093/nar/gkn331 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Sotaro Uemura, Ryo Iizuka, Taro Ueno, Yoshihiro Shimizu, Hideki Taguchi, Takuya Ueda, Joseph D. Puglisi, and Takashi Funatsu
Single-molecule imaging of full protein synthesis by immobilized ribosomes
Nucleic Acids Research Advance Access published on May 29, 2008
Nucl. Acids Res. 2008 36: e70; doi:10.1093/nar/gkn338 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Gilles Breuzard, Magdalena Tertil, Cristine Gonçalves, Hervé Cheradame, Philippe Géguan, Chantal Pichon, and Patrick Midoux
Nuclear delivery of NF{kappa}B-assisted DNA/polymer complexes: plasmid DNA quantitation by confocal laser scanning microscopy and evidence of nuclear polyplexes by FRET imaging
Nucleic Acids Research Advance Access published on May 30, 2008
Nucl. Acids Res. 2008 36: e71; doi:10.1093/nar/gkn287 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Rodolphe Suspène, Myrtille Renard, Michel Henry, Denise Guétard, David Puyraimond-Zemmour, Agnès Billecocq, Michèle Bouloy, Frederic Tangy, Jean-Pierre Vartanian, and Simon Wain-Hobson
Inversing the natural hydrogen bonding rule to selectively amplify GC-rich ADAR-edited RNAs
Nucleic Acids Research Advance Access published on May 30, 2008
Nucl. Acids Res. 2008 36: e72; doi:10.1093/nar/gkn295 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Calin C. Guet, Luke Bruneaux, Taejin L. Min, Dan Siegal-Gaskins, Israel Figueroa, Thierry Emonet, and Philippe Cluzel
Minimally invasive determination of mRNA concentration in single living bacteria
Nucleic Acids Research Advance Access published on May 30, 2008
Nucl. Acids Res. 2008 36: e73; doi:10.1093/nar/gkn329 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Jason D. Gans and Murray Wolinsky
Improved assay-dependent searching of nucleic acid sequence databases
Nucleic Acids Research Advance Access published on May 31, 2008
Nucl. Acids Res. 2008 36: e74; doi:10.1093/nar/gkn301 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Kaarel Krjutskov, Reidar Andreson, Reedik Mägi, Tiit Nikopensius, Andrey Khrunin, Evelin Mihailov, Veronika Tammekivi, Helena Sork, Maido Remm, and Andres Metspalu
Development of a single tube 640-plex genotyping method for detection of nucleic acid variations on microarrays
Nucleic Acids Research Advance Access published on June 5, 2008
Nucl. Acids Res. 2008 36: e75; doi:10.1093/nar/gkn357 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Franz S. Hartner, Claudia Ruth, David Langenegger, Sabrina N. Johnson, Petr Hyka, Geoffrey P. Lin-Cereghino, Joan Lin-Cereghino, Karin Kovar, James M. Cregg, and Anton Glieder
Promoter library designed for fine-tuned gene expression in Pichia pastoris
Nucleic Acids Research Advance Access published on June 6, 2008
Nucl. Acids Res. 2008 36: e76; doi:10.1093/nar/gkn369 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

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.