Nucleic Acids Research

Survey and Summary

Get checked abstract Snehal Bhikhu Patel and Michel Bellini

The assembly of a spliceosomal small nuclear ribonucleoprotein particle
Nucleic Acids Research Advance Access published on October 14, 2008
Nucl. Acids Res. 2008 36: 6482-6493; doi:10.1093/nar/gkn658 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Computational Biology

Get checked abstract Stefan E. Seemann, Jan Gorodkin, and Rolf Backofen

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments
Nucleic Acids Research Advance Access published on October 4, 2008
Nucl. Acids Res. 2008 36: 6355-6362; doi:10.1093/nar/gkn544 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Shuzhao Li, Alex Pozhitkov, and Marius Brouwer

A competitive hybridization model predicts probe signal intensity on high density DNA microarrays
Nucleic Acids Research Advance Access published on October 18, 2008
Nucl. Acids Res. 2008 36: 6585-6591; doi:10.1093/nar/gkn740 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Gene regulation, Chromatin and Epigenetics

Get checked abstract Su Mi Choi, Hyun-Ju Cho, Heesang Cho, Kang Ho Kim, Jae Bum Kim, and Hyunsung Park

Stra13/DEC1 and DEC2 inhibit sterol regulatory element binding protein-1c in a hypoxia-inducible factor-dependent mechanism
Nucleic Acids Research Advance Access published on October 5, 2008
Nucl. Acids Res. 2008 36: 6372-6385; doi:10.1093/nar/gkn620 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Philipp Jahnke, Weizhen Xu, Manuela Wülling, Melanie Albrecht, Heinz Gabriel, Gabriele Gillessen-Kaesbach, and Frank J. Kaiser

The Cohesin loading factor NIPBL recruits histone deacetylases to mediate local chromatin modifications
Nucleic Acids Research Advance Access published on October 14, 2008
Nucl. Acids Res. 2008 36: 6450-6458; doi:10.1093/nar/gkn688 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Xueping Yu, Jimmy Lin, Donald J. Zack, Joshua T. Mendell, and Jiang Qian

Analysis of regulatory network topology reveals functionally distinct classes of microRNAs
Nucleic Acids Research Advance Access published on October 15, 2008
Nucl. Acids Res. 2008 36: 6494-6503; doi:10.1093/nar/gkn712 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Thomas Langmann, Christine C. L. Lai, Karin Weigelt, Beatrice M. Tam, Regina Warneke-Wittstock, Orson L. Moritz, and Bernhard H. F. Weber

CRX controls retinal expression of the X-linked juvenile retinoschisis (RS1) gene
Nucleic Acids Research Advance Access published on October 16, 2008
Nucl. Acids Res. 2008 36: 6523-6534; doi:10.1093/nar/gkn737 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Raffaella Gatta and Roberto Mantovani

NF-Y substitutes H2A-H2B on active cell-cycle promoters: recruitment of CoREST-KDM1 and fine-tuning of H3 methylations
Nucleic Acids Research Advance Access published on October 21, 2008
Nucl. Acids Res. 2008 36: 6592-6607; doi:10.1093/nar/gkn699 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genome integrity, repair and replication

Get checked abstract Wei He, Yun Zhao, Chunbo Zhang, Lili An, Zhishang Hu, Yuheng Liu, Lu Han, Lijun Bi, Zhensheng Xie, Peng Xue, Fuquan Yang, and Haiying Hang

Rad9 plays an important role in DNA mismatch repair through physical interaction with MLH1
Nucleic Acids Research Advance Access published on October 8, 2008
Nucl. Acids Res. 2008 36: 6406-6417; doi:10.1093/nar/gkn686 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Punjab S. Malik and Lorraine S. Symington

Rad51 gain-of-function mutants that exhibit high affinity DNA binding cause DNA damage sensitivity in the absence of Srs2
Nucleic Acids Research Advance Access published on October 15, 2008
Nucl. Acids Res. 2008 36: 6504-6510; doi:10.1093/nar/gkn720 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Genomics

Get checked abstract Jun-ichi Takeda, Yutaka Suzuki, Ryuichi Sakate, Yoshiharu Sato, Masahide Seki, Takuma Irie, Nono Takeuchi, Takuya Ueda, Mitsuteru Nakao, Sumio Sugano, Takashi Gojobori, and Tadashi Imanishi

Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs
Nucleic Acids Research Advance Access published on October 5, 2008
Nucl. Acids Res. 2008 36: 6386-6395; doi:10.1093/nar/gkn677 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Liqiang Xi, Andrew Feber, Vanita Gupta, Maoxin Wu, Andrew D. Bergemann, Rodney J. Landreneau, Virginia R. Litle, Arjun Pennathur, James D. Luketich, and Tony E. Godfrey

Whole genome exon arrays identify differential expression of alternatively spliced, cancer-related genes in lung cancer
Nucleic Acids Research Advance Access published on October 16, 2008
Nucl. Acids Res. 2008 36: 6535-6547; doi:10.1093/nar/gkn697 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology

Get checked abstract Rachida Abes, Hong M. Moulton, Philippe Clair, Sung-Tae Yang, Said Abes, Kamran Melikov, Paul Prevot, Derek S. Youngblood, Patrick L. Iversen, Leonid V. Chernomordik, and Bernard Lebleu

Delivery of steric block morpholino oligomers by (R-X-R)₄ peptides: structure–activity studies
Nucleic Acids Research Advance Access published on September 16, 2008
Nucl. Acids Res. 2008 36: 6343-6354; doi:10.1093/nar/gkn541 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Yide Jiang and Martha M. Howe

Regional mutagenesis of the gene encoding the phage Mu late gene activator C identifies two separate regions important for DNA binding
Nucleic Acids Research Advance Access published on October 5, 2008
Nucl. Acids Res. 2008 36: 6396-6405; doi:10.1093/nar/gkn639 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Gabriela D. Ivanova, Andrey Arzumanov, Rachida Abes, Haifang Yin, Matthew J. A. Wood, Bernard Lebleu, and Michael J. Gait

Improved cell-penetrating peptide–PNA conjugates for splicing redirection in HeLa cells and exon skipping in mdx mouse muscle
Nucleic Acids Research Advance Access published on October 8, 2008
Nucl. Acids Res. 2008 36: 6418-6428; doi:10.1093/nar/gkn671 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Alexandra Dimitri, John A. Burns, Suse Broyde, and David A. Scicchitano

Transcription elongation past O⁶-methylguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase
Nucleic Acids Research Advance Access published on October 14, 2008
Nucl. Acids Res. 2008 36: 6459-6471; doi:10.1093/nar/gkn657 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Graziana Gatto, Annalisa Rossi, Daniela Rossi, Sven Kroening, Stefano Bonatti, and Massimo Mallardo

Epstein–Barr virus latent membrane protein 1 trans-activates miR-155 transcription through the NF-B pathway
Nucleic Acids Research Advance Access published on October 21, 2008
Nucl. Acids Res. 2008 36: 6608-6619; doi:10.1093/nar/gkn666 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes

Get checked abstract Chandravanu Dash, Brian J. Scarth, Christopher Badorrek, Matthias Götte, and Stuart F. J. Le Grice

Examining the ribonuclease H primer grip of HIV-1 reverse transcriptase by charge neutralization of RNA/DNA hybrids
Nucleic Acids Research Advance Access published on October 4, 2008
Nucl. Acids Res. 2008 36: 6363-6371; doi:10.1093/nar/gkn678 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Richard D. Morgan, Tanya K. Bhatia, Lindsay Lovasco, and Theodore B. Davis

MmeI: a minimal Type II restriction-modification system that only modifies one DNA strand for host protection
Nucleic Acids Research Advance Access published on October 17, 2008
Nucl. Acids Res. 2008 36: 6558-6570; doi:10.1093/nar/gkn711 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA

Get checked abstract Franck Vazquez, Todd Blevins, Jérôme Ailhas, Thomas Boller, and Frederick Meins, Jr

Evolution of Arabidopsis MIR genes generates novel microRNA classes
Nucleic Acids Research Advance Access published on October 8, 2008
Nucl. Acids Res. 2008 36: 6429-6438; doi:10.1093/nar/gkn670 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Thomas Ohrt, Jörg Mütze, Wolfgang Staroske, Lasse Weinmann, Julia Höck, Karin Crell, Gunter Meister, and Petra Schwille

Fluorescence correlation spectroscopy and fluorescence cross-correlation spectroscopy reveal the cytoplasmic origination of loaded nuclear RISC in vivo in human cells
Nucleic Acids Research Advance Access published on October 8, 2008
Nucl. Acids Res. 2008 36: 6439-6449; doi:10.1093/nar/gkn693 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Mikkel Christensen-Dalsgaard and Kenn Gerdes

Translation affects YoeB and MazF messenger RNA interferase activities by different mechanisms
Nucleic Acids Research Advance Access published on October 14, 2008
Nucl. Acids Res. 2008 36: 6472-6481; doi:10.1093/nar/gkn667 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Harris S. Soifer, Masayuki Sano, Kumi Sakurai, Pritsana Chomchan, Pål Sætrom, Mark A. Sherman, Michael A. Collingwood, Mark A. Behlke, and John J. Rossi

A role for the Dicer helicase domain in the processing of thermodynamically unstable hairpin RNAs
Nucleic Acids Research Advance Access published on October 15, 2008
Nucl. Acids Res. 2008 36: 6511-6522; doi:10.1093/nar/gkn687 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Hrvoje Lusic, Estella M. Gustilo, Franck A.P. Vendeix, Rob Kaiser, Michael O. Delaney, William D. Graham, Virginia A. Moye, William A. Cantara, Paul F. Agris, and Alexander Deiters

Synthesis and investigation of the 5-formylcytidine modified, anticodon stem and loop of the human mitochondrial tRNA^Met
Nucleic Acids Research Advance Access published on October 16, 2008
Nucl. Acids Res. 2008 36: 6548-6557; doi:10.1093/nar/gkn703 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Feng Xiao, Hui Zhang, and Peixuan Guo

Novel mechanism of hexamer ring assembly in protein/RNA interactions revealed by single molecule imaging
Nucleic Acids Research Advance Access published on October 21, 2008
Nucl. Acids Res. 2008 36: 6620-6632; doi:10.1093/nar/gkn669 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology

Get checked abstract Lei Jia, Nicholas E. Geacintov, and Suse Broyde

The N-clasp of human DNA polymerase promotes blockage or error-free bypass of adenine- or guanine-benzo[a]pyrenyl lesions
Nucleic Acids Research Advance Access published on October 17, 2008
Nucl. Acids Res. 2008 36: 6571-6584; doi:10.1093/nar/gkn719 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Minna M. Poranen, Paula S. Salgado, Minni R. L. Koivunen, Sam Wright, Dennis H. Bamford, David I. Stuart, and Jonathan M. Grimes

Structural explanation for the role of Mn²⁺ in the activity of 6 RNA-dependent RNA polymerase
Nucleic Acids Research Advance Access published on October 21, 2008
Nucl. Acids Res. 2008 36: 6633-6644; doi:10.1093/nar/gkn632 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Methods Online

Get checked abstract Qing Lu, Esperanza Nunez, Chunrun Lin, Kimberly Christensen, Tracy Downs, Dennis A. Carson, Jessica Wang-Rodriguez, and Yu-Tsueng Liu

A sensitive array-based assay for identifying multiple TMPRSS2:ERG fusion gene variants
Nucleic Acids Research Advance Access published on September 15, 2008
Nucl. Acids Res. 2008 36: e130; doi:10.1093/nar/gkn585 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Alexandre V. Lebedev, Natasha Paul, Joyclyn Yee, Victor A. Timoshchuk, Jonathan Shum, Kei Miyagi, Jack Kellum, Richard I. Hogrefe, and Gerald Zon

Hot Start PCR with heat-activatable primers: a novel approach for improved PCR performance
Nucleic Acids Research Advance Access published on September 16, 2008
Nucl. Acids Res. 2008 36: e131; doi:10.1093/nar/gkn575 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Lena Poulsen, Martin Jensen Søe, Detlef Snakenborg, Lisbeth Birk Møller, and Martin Dufva

Multi-stringency wash of partially hybridized 60-mer probes reveals that the stringency along the probe decreases with distance from the microarray surface
Nucleic Acids Research Advance Access published on September 19, 2008
Nucl. Acids Res. 2008 36: e132; doi:10.1093/nar/gkn600 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Frank Schnütgen, Jens Hansen, Silke De-Zolt, Carsten Horn, Marcus Lutz, Thomas Floss, Wolfgang Wurst, Patricia Ruiz Noppinger, and Harald von Melchner

Enhanced gene trapping in mouse embryonic stem cells
Nucleic Acids Research Advance Access published on September 23, 2008
Nucl. Acids Res. 2008 36: e133; doi:10.1093/nar/gkn603 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Eugenio Sangiorgi, Zhang Shuhua, and Mario R. Capecchi

In vivo evaluation of PhiC31 recombinase activity using a self-excision cassette
Nucleic Acids Research Advance Access published on October 1, 2008
Nucl. Acids Res. 2008 36: e134; doi:10.1093/nar/gkn627 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Bo Cheng and David H. Price

Analysis of factor interactions with RNA polymerase II elongation complexes using a new electrophoretic mobility shift assay
Nucleic Acids Research Advance Access published on October 1, 2008
Nucl. Acids Res. 2008 36: e135; doi:10.1093/nar/gkn630 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract KiYoung Lee, Han-Yu Chuang, Andreas Beyer, Min-Kyung Sung, Won-Ki Huh, Bonghee Lee, and Trey Ideker

Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species
Nucleic Acids Research Advance Access published on October 4, 2008
Nucl. Acids Res. 2008 36: e136; doi:10.1093/nar/gkn619 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Yun Li, Pei Hao, Siyuan Zheng, Kang Tu, Haiwei Fan, Ruixin Zhu, Guohui Ding, Changzheng Dong, Chuan Wang, Xuan Li, H.-J. Thiesen, Y. Eugene Chen, Hualiang Jiang, Lei Liu, and Yixue Li

Gene expression module-based chemical function similarity search
Nucleic Acids Research Advance Access published on October 8, 2008
Nucl. Acids Res. 2008 36: e137; doi:10.1093/nar/gkn610 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Front-Matter/Back-Matter

Nucleic Acids Research: VOLUME 36 ISSUE 20 2008
Nucl. Acids Res. 2008 36: i; doi:10.1093/nar/gkn950 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acids Research
Nucl. Acids Res. 2008 36: ii; doi:10.1093/nar/gkn949 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Subscriptions
Nucl. Acids Res. 2008 36: iii; doi:10.1093/nar/gkn951 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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