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Previous Next 		Contents: Volume 36, Number 14, August 2008   [Index by Author] 

Down Survey and Summary
Down Computational Biology
Down Gene Regulation, Chromatin and Epigenetics
Down Genomics
Down Molecular Biology
Down Nucleic Acid Enzymes
Down RNA
Down Structural Biology
Down Methods Online


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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

Nicolas J. Tourasse and Anne-Brit Kolstø
Survey of group I and group II introns in 29 sequenced genomes of the Bacillus cereus group: insights into their spread and evolution
Nucleic Acids Research Advance Access published on June 28, 2008
Nucl. Acids Res. 2008 36: 4529-4548; doi:10.1093/nar/gkn372 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Computational Biology Back

Hilda David-Eden and Yael Mandel-Gutfreund
Revealing unique properties of the ribosome using a network based analysis
Nucleic Acids Research Advance Access published on July 14, 2008
Nucl. Acids Res. 2008 36: 4641-4652; doi:10.1093/nar/gkn433 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Xiaohua Douglas Zhang, Pei Fen Kuan, Marc Ferrer, Xiaohua Shu, Yingxue C. Liu, Adam T. Gates, Priya Kunapuli, Erica M. Stec, Min Xu, Shane D. Marine, Daniel J. Holder, Berta Strulovici, Joseph F. Heyse, and Amy S. Espeseth
Hit selection with false discovery rate control in genome-scale RNAi screens
Nucleic Acids Research Advance Access published on July 15, 2008
Nucl. Acids Res. 2008 36: 4667-4679; doi:10.1093/nar/gkn435 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Gene Regulation, Chromatin and Epigenetics Back

Alicia Roque, Inma Ponte, José Luis R. Arrondo, and Pedro Suau
Phosphorylation of the carboxy-terminal domain of histone H1: effects on secondary structure and DNA condensation
Nucleic Acids Research Advance Access published on July 16, 2008
Nucl. Acids Res. 2008 36: 4719-4726; doi:10.1093/nar/gkn440 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genomics Back

Elizabeth D. Wederell, Mikhail Bilenky, Rebecca Cullum, Nina Thiessen, Melis Dagpinar, Allen Delaney, Richard Varhol, YongJun Zhao, Thomas Zeng, Bridget Bernier, Matthew Ingham, Martin Hirst, Gordon Robertson, Marco A. Marra, Steven Jones, and Pamela A. Hoodless
Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing
Nucleic Acids Research Advance Access published on July 8, 2008
Nucl. Acids Res. 2008 36: 4549-4564; doi:10.1093/nar/gkn382 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Alexey A. Gavrilov and Sergey V. Razin
Spatial configuration of the chicken {alpha}-globin gene domain: immature and active chromatin hubs
Nucleic Acids Research Advance Access published on July 11, 2008
Nucl. Acids Res. 2008 36: 4629-4640; doi:10.1093/nar/gkn429 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology Back

Youngran Cho, Sang-Hyun Song, Jong Joo Lee, Narae Choi, Chul Geun Kim, Ann Dean, and AeRi Kim
The role of transcriptional activator GATA-1 at human β-globin HS2
Nucleic Acids Research Advance Access published on June 27, 2008
Nucl. Acids Res. 2008 36: 4521-4528; doi:10.1093/nar/gkn368 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Gilles A. Robichaud, Jean-Pierre Perreault, and Rodney J. Ouellette
Development of an isoform-specific gene suppression system: the study of the human Pax-5B transcriptional element
Nucleic Acids Research Advance Access published on July 10, 2008
Nucl. Acids Res. 2008 36: 4609-4620; doi:10.1093/nar/gkn432 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yaobin Liu, Rodney S. Nairn, and Karen M. Vasquez
Processing of triplex-directed psoralen DNA interstrand crosslinks by recombination mechanisms
Nucleic Acids Research Advance Access published on July 15, 2008
Nucl. Acids Res. 2008 36: 4680-4688; doi:10.1093/nar/gkn438 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Daniel J. Weisenberger, Binh N. Trinh, Mihaela Campan, Shikhar Sharma, Tiffany I. Long, Suchitra Ananthnarayan, Gangning Liang, Francisco J. Esteva, Gabriel N. Hortobagyi, Frank McCormick, Peter A. Jones, and Peter W. Laird
DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight
Nucleic Acids Research Advance Access published on July 15, 2008
Nucl. Acids Res. 2008 36: 4689-4698; doi:10.1093/nar/gkn455 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yasuyo Johzuka-Hisatomi, Rie Terada, and Shigeru Iida
Efficient transfer of base changes from a vector to the rice genome by homologous recombination: involvement of heteroduplex formation and mismatch correction
Nucleic Acids Research Advance Access published on July 16, 2008
Nucl. Acids Res. 2008 36: 4727-4735; doi:10.1093/nar/gkn451 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ludovic Didierlaurent, Laurent Houzet, Zakia Morichaud, Jean-Luc Darlix, and Marylène Mougel
The conserved N-terminal basic residues and zinc-finger motifs of HIV-1 nucleocapsid restrict the viral cDNA synthesis during virus formation and maturation
Nucleic Acids Research Advance Access published on July 18, 2008
Nucl. Acids Res. 2008 36: 4745-4753; doi:10.1093/nar/gkn474 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Nucleic Acid Enzymes Back

Katherine Hekman, Kip Guja, Chris Larkin, and Joel F. Schildbach
An intrastrand three-DNA-base interaction is a key specificity determinant of F transfer initiation and of F TraI relaxase DNA recognition and cleavage
Nucleic Acids Research Advance Access published on July 8, 2008
Nucl. Acids Res. 2008 36: 4565-4572; doi:10.1093/nar/gkn422 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Anna Valenti, Giuseppe Perugino, Anna D’Amaro, Andrea Cacace, Alessandra Napoli, Mosè Rossi, and Maria Ciaramella
Dissection of reverse gyrase activities: insight into the evolution of a thermostable molecular machine
Nucleic Acids Research Advance Access published on July 9, 2008
Nucl. Acids Res. 2008 36: 4587-4597; doi:10.1093/nar/gkn418 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Debbie Sommer, Carrie M. Stith, Peter M. J. Burgers, and Robert S. Lahue
Partial reconstitution of DNA large loop repair with purified proteins from Saccharomyces cerevisiae
Nucleic Acids Research Advance Access published on July 15, 2008
Nucl. Acids Res. 2008 36: 4699-4707; doi:10.1093/nar/gkn446 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Elena P. Sorokin, Bokun Cheng, Siddarth Rathi, Sandra J. Aedo, Maria V. Abrenica, and Yuk-Ching Tse-Dinh
Inhibition of Mg2+ binding and DNA religation by bacterial topoisomerase I via introduction of an additional positive charge into the active site region
Nucleic Acids Research Advance Access published on July 24, 2008
Nucl. Acids Res. 2008 36: 4788-4796; doi:10.1093/nar/gkn460 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA Back

Antonio M. Estévez
The RNA-binding protein TbDRBD3 regulates the stability of a specific subset of mRNAs in trypanosomes
Nucleic Acids Research Advance Access published on July 8, 2008
Nucl. Acids Res. 2008 36: 4573-4586; doi:10.1093/nar/gkn406 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Rui Zhang and Bing Su
MicroRNA regulation and the variability of human cortical gene expression
Nucleic Acids Research Advance Access published on July 10, 2008
Nucl. Acids Res. 2008 36: 4621-4628; doi:10.1093/nar/gkn431 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Laurie James and Bruno Sargueil
RNA secondary structure of the feline immunodeficiency virus 5'UTR and Gag coding region
Nucleic Acids Research Advance Access published on July 14, 2008
Nucl. Acids Res. 2008 36: 4653-4666; doi:10.1093/nar/gkn447 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Chung-Sheng Lee, Anusha P. Dias, Mark Jedrychowski, Arvind H. Patel, Jeanne L. Hsu, and Robin Reed
Human DDX3 functions in translation and interacts with the translation initiation factor eIF3
Nucleic Acids Research Advance Access published on July 15, 2008
Nucl. Acids Res. 2008 36: 4708-4718; doi:10.1093/nar/gkn454 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Tatyana V. Budkevich, Anna V. El'skaya, and Knud H. Nierhaus
Features of 80S mammalian ribosome and its subunits
Nucleic Acids Research Advance Access published on July 16, 2008
Nucl. Acids Res. 2008 36: 4736-4744; doi:10.1093/nar/gkn424 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Kenny Schlosser, Jimmy Gu, Jeffrey C. F. Lam, and Yingfu Li
In vitro selection of small RNA-cleaving deoxyribozymes that cleave pyrimidine–pyrimidine junctions
Nucleic Acids Research Advance Access published on July 21, 2008
Nucl. Acids Res. 2008 36: 4768-4777; doi:10.1093/nar/gkn396 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology Back

Kexiao Guo, Vijay Gokhale, Laurence H. Hurley, and Daekyu Sun
Intramolecularly folded G-quadruplex and i-motif structures in the proximal promoter of the vascular endothelial growth factor gene
Nucleic Acids Research Advance Access published on July 9, 2008
Nucl. Acids Res. 2008 36: 4598-4608; doi:10.1093/nar/gkn380 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Takashi Nagata, Sakura Suzuki, Ryuta Endo, Mikako Shirouzu, Takaho Terada, Makoto Inoue, Takanori Kigawa, Naohiro Kobayashi, Peter Güntert, Akiko Tanaka, Yoshihide Hayashizaki, Yutaka Muto, and Shigeyuki Yokoyama
The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition
Nucleic Acids Research Advance Access published on July 19, 2008
Nucl. Acids Res. 2008 36: 4754-4767; doi:10.1093/nar/gkn458 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

John E. McGeehan, Simon D. Streeter, Sarah -J. Thresh, Neil Ball, Raimond B. G. Ravelli, and G. Geoff Kneale
Structural analysis of the genetic switch that regulates the expression of restriction-modification genes
Nucleic Acids Research Advance Access published on July 21, 2008
Nucl. Acids Res. 2008 36: 4778-4787; doi:10.1093/nar/gkn448 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Søren Lindemose, Peter Eigil Nielsen, and Niels Erik Møllegaard
Dissecting direct and indirect readout of cAMP receptor protein DNA binding using an inosine and 2,6-diaminopurine in vitro selection system
Nucleic Acids Research Advance Access published on July 24, 2008
Nucl. Acids Res. 2008 36: 4797-4807; doi:10.1093/nar/gkn452 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Thirumananseri Kumarevel, Noboru Nakano, Karthe Ponnuraj, Subash C. B. Gopinath, Keiko Sakamoto, Akeo Shinkai, Penmetcha K. R. Kumar, and Shigeyuki Yokoyama
Crystal structure of glutamine receptor protein from Sulfolobus tokodaii strain 7 in complex with its effector L-glutamine: implications of effector binding in molecular association and DNA binding
Nucleic Acids Research Advance Access published on July 24, 2008
Nucl. Acids Res. 2008 36: 4808-4820; doi:10.1093/nar/gkn456 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Methods Online Back

Byung Jo Yu, Kui Hyeon Kang, Jun Hyoung Lee, Bong Hyun Sung, Mi Sun Kim, and Sun Chang Kim
Rapid and efficient construction of markerless deletions in the Escherichia coli genome
Nucleic Acids Research Advance Access published on June 21, 2008
Nucl. Acids Res. 2008 36: e84; doi:10.1093/nar/gkn359 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Wei Wang, Gil Jun Lee, Kyeung Joo Jang, Tae Sub Cho, and Seog K. Kim
Real-time detection of Fe·EDTA/H2O2-induced DNA cleavage by linear dichroism
Nucleic Acids Research Advance Access published on June 21, 2008
Nucl. Acids Res. 2008 36: e85; doi:10.1093/nar/gkn370 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Anna-Maria Anesti, Pieter J. Peeters, Ines Royaux, and Robert S. Coffin
Efficient delivery of RNA Interference to peripheral neurons in vivo using herpes simplex virus
Nucleic Acids Research Advance Access published on June 25, 2008
Nucl. Acids Res. 2008 36: e86; doi:10.1093/nar/gkn371 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jing Chen, Jean Lozach, Eliza Wickham Garcia, Bret Barnes, Shujun Luo, Ivan Mikoulitch, Lixin Zhou, Gary Schroth, and Jian-Bing Fan
Highly sensitive and specific microRNA expression profiling using BeadArray technology
Nucleic Acids Research Advance Access published on June 25, 2008
Nucl. Acids Res. 2008 36: e87; doi:10.1093/nar/gkn387 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Marc van Dijk and Alexandre M. J. J. Bonvin
A protein–DNA docking benchmark
Nucleic Acids Research Advance Access published on June 26, 2008
Nucl. Acids Res. 2008 36: e88; doi:10.1093/nar/gkn386 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Frank H. T. Nelissen, Adriaan J. van Gammeren, Marco Tessari, Frederic C. Girard, Hans A. Heus, and Sybren S. Wijmenga
Multiple segmental and selective isotope labeling of large RNA for NMR structural studies
Nucleic Acids Research Advance Access published on June 26, 2008
Nucl. Acids Res. 2008 36: e89; doi:10.1093/nar/gkn397 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

André Vidal Pinheiro, Pedro Baptista, and João Carlos Lima
Light activation of transcription: photocaging of nucleotides for control over RNA polymerization
Nucleic Acids Research Advance Access published on June 27, 2008
Nucl. Acids Res. 2008 36: e90; doi:10.1093/nar/gkn415 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Eric B. Shain and John M. Clemens
A new method for robust quantitative and qualitative analysis of real-time PCR
Nucleic Acids Research Advance Access published on July 4, 2008
Nucl. Acids Res. 2008 36: e91; doi:10.1093/nar/gkn408 [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.