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Previous Next 		Contents: Volume 36, Number 11, June 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

Jerzy Orlowski and Janusz M. Bujnicki
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses
Nucleic Acids Research Advance Access published on May 2, 2008
Nucl. Acids Res. 2008 36: 3552-3569; doi:10.1093/nar/gkn175 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Chemistry Back

Joel R. Morgan, Robert P. Lyon, Dean Y. Maeda, and John A. Zebala
Snap-to-it probes: chelate-constrained nucleobase oligomers with enhanced binding specificity
Nucleic Acids Research Advance Access published on April 29, 2008
Nucl. Acids Res. 2008 36: 3522-3530; doi:10.1093/nar/gkn219 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Jaroslav Malina, Michael J. Hannon, and Viktor Brabec
DNA binding of dinuclear iron(II) metallosupramolecular cylinders. DNA unwinding and sequence preference
Nucleic Acids Research Advance Access published on May 8, 2008
Nucl. Acids Res. 2008 36: 3630-3638; doi:10.1093/nar/gkn244 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jingyang Chen, Manas K. Ghorai, Grace Kenney, and JoAnne Stubbe
Mechanistic studies on bleomycin-mediated DNA damage: multiple binding modes can result in double-stranded DNA cleavage
Nucleic Acids Research Advance Access published on May 20, 2008
Nucl. Acids Res. 2008 36: 3781-3790; doi:10.1093/nar/gkn302 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Computational Biology Back

I. K. Darcy, R. G. Scharein, and A. Stasiak
3D visualization software to analyze topological outcomes of topoisomerase reactions
Nucleic Acids Research Advance Access published on April 24, 2008
Nucl. Acids Res. 2008 36: 3515-3521; doi:10.1093/nar/gkn192 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Zeba Wunderlich and Leonid A. Mirny
Spatial effects on the speed and reliability of protein–DNA search
Nucleic Acids Research Advance Access published on May 3, 2008
Nucl. Acids Res. 2008 36: 3570-3578; doi:10.1093/nar/gkn173 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Daniel Aguilar, Lucy Skrabanek, Steven S. Gross, Baldo Oliva, and Fabien Campagne
Beyond tissueInfo: functional prediction using tissue expression profile similarity searches
Nucleic Acids Research Advance Access published on May 15, 2008
Nucl. Acids Res. 2008 36: 3728-3737; doi:10.1093/nar/gkn233 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Zhi John Lu and David H. Mathews
Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design
Nucleic Acids Research Advance Access published on May 15, 2008
Nucl. Acids Res. 2008 36: 3738-3745; doi:10.1093/nar/gkn266 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Morten Kloster and Chao Tang
SCUMBLE: a method for systematic and accurate detection of codon usage bias by maximum likelihood estimation
Nucleic Acids Research Advance Access published on May 21, 2008
Nucl. Acids Res. 2008 36: 3819-3827; doi:10.1093/nar/gkn288 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genomics Back

Riu Yamashita, Yutaka Suzuki, Nono Takeuchi, Hiroyuki Wakaguri, Takuya Ueda, Sumio Sugano, and Kenta Nakai
Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics
Nucleic Acids Research Advance Access published on May 14, 2008
Nucl. Acids Res. 2008 36: 3707-3715; doi:10.1093/nar/gkn248 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Vincent Miele, Cédric Vaillant, Yves d'Aubenton-Carafa, Claude Thermes, and Thierry Grange
DNA physical properties determine nucleosome occupancy from yeast to fly
Nucleic Acids Research Advance Access published on May 17, 2008
Nucl. Acids Res. 2008 36: 3746-3756; doi:10.1093/nar/gkn262 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology Back

Philippe Simon, Fabio Cannata, Loïc Perrouault, Ludovic Halby, Jean-Paul Concordet, Alexandre Boutorine, Vladimir Ryabinin, Alexandre Sinyakov, and Carine Giovannangeli
Sequence-specific DNA cleavage mediated by bipyridine polyamide conjugates
Nucleic Acids Research Advance Access published on May 1, 2008
Nucl. Acids Res. 2008 36: 3531-3538; doi:10.1093/nar/gkn231 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Xudong Wu, Yanhua Gong, Jiping Yue, Boqin Qiang, Jiangang Yuan, and Xiaozhong Peng
Cooperation between EZH2, NSPc1-mediated histone H2A ubiquitination and Dnmt1 in HOX gene silencing
Nucleic Acids Research Advance Access published on May 6, 2008
Nucl. Acids Res. 2008 36: 3590-3599; doi:10.1093/nar/gkn243 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Keren Weidenfeld-Baranboim, Keren Bitton-Worms, and Ami Aronheim
TRE-dependent transcription activation by JDP2–CHOP10 association
Nucleic Acids Research Advance Access published on May 7, 2008
Nucl. Acids Res. 2008 36: 3608-3619; doi:10.1093/nar/gkn268 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Leonie Smeenk, Simon J. van Heeringen, Max Koeppel, Marc A. van Driel, Stefanie J. J. Bartels, Robert C. Akkers, Sergei Denissov, Hendrik G. Stunnenberg, and Marion Lohrum
Characterization of genome-wide p53-binding sites upon stress response
Nucleic Acids Research Advance Access published on May 12, 2008
Nucl. Acids Res. 2008 36: 3639-3654; doi:10.1093/nar/gkn232 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Sarah C. Roemer, James Adelman, Mair E. A. Churchill, and Dean P. Edwards
Mechanism of high-mobility group protein B enhancement of progesterone receptor sequence-specific DNA binding
Nucleic Acids Research Advance Access published on May 12, 2008
Nucl. Acids Res. 2008 36: 3655-3666; doi:10.1093/nar/gkn249 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Wichai Pornthanakasem, Narisorn Kongruttanachok, Chutipa Phuangphairoj, Chotika Suyarnsestakorn, Taweap Sanghangthum, Sornjarod Oonsiri, Wanpen Ponyeam, Thatchawan Thanasupawat, Oranart Matangkasombut, and Apiwat Mutirangura
LINE-1 methylation status of endogenous DNA double-strand breaks
Nucleic Acids Research Advance Access published on May 12, 2008
Nucl. Acids Res. 2008 36: 3667-3675; doi:10.1093/nar/gkn261 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Florencia Pratto, Aslan Cicek, Wilhelm A. Weihofen, Rudi Lurz, Wolfram Saenger, and Juan C. Alonso
Streptococcus pyogenes pSM19035 requires dynamic assembly of ATP-bound ParA and ParB on parS DNA during plasmid segregation
Nucleic Acids Research Advance Access published on May 13, 2008
Nucl. Acids Res. 2008 36: 3676-3689; doi:10.1093/nar/gkn170 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Susan Woods, Alexandra Farrall, Carl Procko, and Murray L. Whitelaw
The bHLH/Per-Arnt-Sim transcription factor SIM2 regulates muscle transcript myomesin2 via a novel, non-canonical E-box sequence
Nucleic Acids Research Advance Access published on May 14, 2008
Nucl. Acids Res. 2008 36: 3716-3727; doi:10.1093/nar/gkn247 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Niall S. Kenneth, Lynne Marshall, and Robert J. White
Recruitment of RNA polymerase III in vivo
Nucleic Acids Research Advance Access published on May 17, 2008
Nucl. Acids Res. 2008 36: 3757-3764; doi:10.1093/nar/gkn272 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Susanna Cogoi, Manikandan Paramasivam, Barbara Spolaore, and Luigi E. Xodo
Structural polymorphism within a regulatory element of the human KRAS promoter: formation of G4-DNA recognized by nuclear proteins
Nucleic Acids Research Advance Access published on May 19, 2008
Nucl. Acids Res. 2008 36: 3765-3780; doi:10.1093/nar/gkn120 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

L. Bouillaut, S. Perchat, S. Arold, S. Zorrilla, L. Slamti, C. Henry, M. Gohar, N. Declerck, and D. Lereclus
Molecular basis for group-specific activation of the virulence regulator PlcR by PapR heptapeptides
Nucleic Acids Research Advance Access published on May 20, 2008
Nucl. Acids Res. 2008 36: 3791-3801; doi:10.1093/nar/gkn149 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Beth Basham, Manjiri Sathe, Jeffrey Grein, Terrill McClanahan, Annalisa D’Andrea, Emma Lees, and Anne Rascle
In vivo identification of novel STAT5 target genes
Nucleic Acids Research Advance Access published on May 20, 2008
Nucl. Acids Res. 2008 36: 3802-3818; doi:10.1093/nar/gkn271 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ilya G. Lyakhov, Annangarachari Krishnamachari, and Thomas D. Schneider
Discovery of novel tumor suppressor p53 response elements using information theory
Nucleic Acids Research Advance Access published on May 21, 2008
Nucl. Acids Res. 2008 36: 3828-3833; doi:10.1093/nar/gkn189 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Steffen Wolfgang Schubert, Alexandra Abendroth, Karin Kilian, Tina Vogler, Bernhard Mayr, Ina Knerr, and Said Hashemolhosseini
bZIP-Type transcription factors CREB and OASIS bind and stimulate the promoter of the mammalian transcription factor GCMa/Gcm1 in trophoblast cells
Nucleic Acids Research Advance Access published on May 21, 2008
Nucl. Acids Res. 2008 36: 3834-3846; doi:10.1093/nar/gkn306 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Ronita Nag, Feng Gong, Deirdre Fahy, and Michael J. Smerdon
A single amino acid change in histone H4 enhances UV survival and DNA repair in yeast
Nucleic Acids Research Advance Access published on May 28, 2008
Nucl. Acids Res. 2008 36: 3857-3866; doi:10.1093/nar/gkn311 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Nucleic Acid Enzymes Back

Mercedes E. Arana, Mineaki Seki, Richard D. Wood, Igor B. Rogozin, and Thomas A. Kunkel
Low-fidelity DNA synthesis by human DNA polymerase theta
Nucleic Acids Research Advance Access published on May 24, 2008
Nucl. Acids Res. 2008 36: 3847-3856; doi:10.1093/nar/gkn310 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

RNA Back

Takeshi Yokoyama and Tsutomu Suzuki
Ribosomal RNAs are tolerant toward genetic insertions: evolutionary origin of the expansion segments
Nucleic Acids Research Advance Access published on May 2, 2008
Nucl. Acids Res. 2008 36: 3539-3551; doi:10.1093/nar/gkn224 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Shoji P. Ohuchi, Yoshiya Ikawa, and Yoshikazu Nakamura
Selection of a novel class of RNA–RNA interaction motifs based on the ligase ribozyme with defined modular architecture
Nucleic Acids Research Advance Access published on May 6, 2008
Nucl. Acids Res. 2008 36: 3600-3607; doi:10.1093/nar/gkn206 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology Back

Chia-Lung Li, Wei-Zen Yang, Yi-Ping Chen, and Hanna S. Yuan
Structural and functional insights into human Tudor-SN, a key component linking RNA interference and editing
Nucleic Acids Research Advance Access published on May 3, 2008
Nucl. Acids Res. 2008 36: 3579-3589; doi:10.1093/nar/gkn236 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

C. Gondeau, L. Chaloin, P. Lallemand, B. Roy, C. Périgaud, T. Barman, A. Varga, M. Vas, C. Lionne, and S. T. Arold
Molecular basis for the lack of enantioselectivity of human 3-phosphoglycerate kinase
Nucleic Acids Research Advance Access published on May 7, 2008
Nucl. Acids Res. 2008 36: 3620-3629; doi:10.1093/nar/gkn212 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Daniel Svozil, Jan Kalina, Marek Omelka, and Bohdan Schneider
DNA conformations and their sequence preferences
Nucleic Acids Research Advance Access published on May 13, 2008
Nucl. Acids Res. 2008 36: 3690-3706; doi:10.1093/nar/gkn260 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Methods Online Back

Somdeb Mitra, Inna V. Shcherbakova, Russ B. Altman, Michael Brenowitz, and Alain Laederach
High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis
Nucleic Acids Research Advance Access published on May 13, 2008
Nucl. Acids Res. 2008 36: e63; doi:10.1093/nar/gkn267 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Tatiana I. Leakey, Jerzy Zielinski, Rachel N. Siegfried, Eric R. Siegel, Chun-Yang Fan, and Craig A. Cooney
A simple algorithm for quantifying DNA methylation levels on multiple independent CpG sites in bisulfite genomic sequencing electropherograms
Nucleic Acids Research Advance Access published on May 14, 2008
Nucl. Acids Res. 2008 36: e64; doi:10.1093/nar/gkn210 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Fang Wei, Jianghua Wang, Wei Liao, Bernhard G. Zimmermann, David T. Wong, and Chih-Ming Ho
Electrochemical detection of low-copy number salivary RNA based on specific signal amplification with a hairpin probe
Nucleic Acids Research Advance Access published on May 17, 2008
Nucl. Acids Res. 2008 36: e65; doi:10.1093/nar/gkn299 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Reidar Andreson, Tõnu Möls, and Maido Remm
Predicting failure rate of PCR in large genomes
Nucleic Acids Research Advance Access published on May 20, 2008
Nucl. Acids Res. 2008 36: e66; doi:10.1093/nar/gkn290 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nynne Sharma, Brian Moldt, Trine Dalsgaard, Thomas G. Jensen, and Jacob Giehm Mikkelsen
Regulated gene insertion by steroid-induced {Phi}C31 integrase
Nucleic Acids Research Advance Access published on May 22, 2008
Nucl. Acids Res. 2008 36: e67; doi:10.1093/nar/gkn298 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yuko Osawa, Kazunori Ikebukuro, Hiroaki Motoki, Takafumi Matsuo, Michio Horiuchi, and Koji Sode
The simple and rapid detection of specific PCR products from bacterial genomes using Zn finger proteins
Nucleic Acids Research Advance Access published on May 23, 2008
Nucl. Acids Res. 2008 36: e68; doi:10.1093/nar/gkn274 [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.