Nucleic Acids Research

Survey and Summary

Get checked abstract Nayef Jarrous and Robert Reiner

Human RNase P: a tRNA-processing enzyme and transcription factor
Nucleic Acids Research Advance Access published on May 5, 2007
Nucl. Acids Res. 2007 35: 3519-3524; doi:10.1093/nar/gkm071 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Chemistry

Get checked abstract Ben J. Evison, Oula C. Mansour, Ernesto Menta, Don R. Phillips, and Suzanne M. Cutts

Pixantrone can be activated by formaldehyde to generate a potent DNA adduct forming agent
Nucleic Acids Research Advance Access published on May 5, 2007
Nucl. Acids Res. 2007 35: 3581-3589; doi:10.1093/nar/gkm285 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jennifer A. Dougan, Camilla Karlsson, W. Ewen Smith, and Duncan Graham

Enhanced oligonucleotide–nanoparticle conjugate stability using thioctic acid modified oligonucleotides
Nucleic Acids Research Advance Access published on May 8, 2007
Nucl. Acids Res. 2007 35: 3668-3675; doi:10.1093/nar/gkm237 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Computational Biology

Get checked abstract Padchanee Sangthong, John Hughes, and John E. G. McCarthy

Distributed control for recruitment, scanning and subunit joining steps of translation initiation
Nucleic Acids Research Advance Access published on May 5, 2007
Nucl. Acids Res. 2007 35: 3573-3580; doi:10.1093/nar/gkm283 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Debashis Sahoo, David L. Dill, Rob Tibshirani, and Sylvia K. Plevritis

Extracting binary signals from microarray time-course data
Nucleic Acids Research Advance Access published on May 21, 2007
Nucl. Acids Res. 2007 35: 3705-3712; doi:10.1093/nar/gkm284 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Yana Bromberg and Burkhard Rost

SNAP: predict effect of non-synonymous polymorphisms on function
Nucleic Acids Research Advance Access published on May 25, 2007
Nucl. Acids Res. 2007 35: 3823-3835; doi:10.1093/nar/gkm238 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Genomics

Get checked abstract Anchal Vishnoi, Rahul Roy, and Alok Bhattacharya

Comparative analysis of bacterial genomes: identification of divergent regions in mycobacterial strains using an anchor-based approach
Nucleic Acids Research Advance Access published on May 8, 2007
Nucl. Acids Res. 2007 35: 3654-3667; doi:10.1093/nar/gkm209 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Shurjo K. Sen, Charles T. Huang, Kyudong Han, and Mark A. Batzer

Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome
Nucleic Acids Research Advance Access published on May 21, 2007
Nucl. Acids Res. 2007 35: 3741-3751; doi:10.1093/nar/gkm317 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Molecular Biology

Get checked abstract Anatoly I. Dragan, Victoria V. Hargreaves, Elena N. Makeyeva, and Peter L. Privalov

Mechanisms of activation of interferon regulator factor 3: the role of C-terminal domain phosphorylation in IRF-3 dimerization and DNA binding
Nucleic Acids Research Advance Access published on May 5, 2007
Nucl. Acids Res. 2007 35: 3525-3534; doi:10.1093/nar/gkm142 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract D. S. F. Biard

Untangling the relationships between DNA repair pathways by silencing more than 20 DNA repair genes in human stable clones
Nucleic Acids Research Advance Access published on May 5, 2007
Nucl. Acids Res. 2007 35: 3535-3550; doi:10.1093/nar/gkm195 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jean-Pascal Capp, François Boudsocq, Anne-Gaelle Besnard, Bernard S. Lopez, Christophe Cazaux, Jean-Sébastien Hoffmann, and Yvan Canitrot

Involvement of DNA polymerase µ in the repair of a specific subset of DNA double-strand breaks in mammalian cells
Nucleic Acids Research Advance Access published on May 5, 2007
Nucl. Acids Res. 2007 35: 3551-3560; doi:10.1093/nar/gkm243 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Gregor D. Gilfillan, Cornelia König, Ina K. Dahlsveen, Nicky Prakoura, Tobias Straub, Rosemarie Lamm, Torsten Fauth, and Peter B. Becker

Cumulative contributions of weak DNA determinants to targeting the Drosophila dosage compensation complex
Nucleic Acids Research Advance Access published on May 5, 2007
Nucl. Acids Res. 2007 35: 3561-3572; doi:10.1093/nar/gkm282 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Carolin Jalal, Heike Uhlmann-Schiffler, and Hans Stahl

Redundant role of DEAD box proteins p68 (Ddx5) and p72/p82 (Ddx17) in ribosome biogenesis and cell proliferation
Nucleic Acids Research Advance Access published on May 7, 2007
Nucl. Acids Res. 2007 35: 3590-3601; doi:10.1093/nar/gkm058 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Hyeong Cheol Park, Man Lyang Kim, Sang Min Lee, Jeong Dong Bahk, Dae-Jin Yun, Chae Oh Lim, Jong Chan Hong, Sang Yeol Lee, Moo Je Cho, and Woo Sik Chung

Pathogen-induced binding of the soybean zinc finger homeodomain proteins GmZF-HD1 and GmZF-HD2 to two repeats of ATTA homeodomain binding site in the calmodulin isoform 4 (GmCaM4) promoter
Nucleic Acids Research Advance Access published on May 7, 2007
Nucl. Acids Res. 2007 35: 3612-3623; doi:10.1093/nar/gkm273 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract John M. Hinz, Peter B. Nham, Salustra S. Urbin, Irene M. Jones, and Larry H. Thompson

Disparate contributions of the Fanconi anemia pathway and homologous recombination in preventing spontaneous mutagenesis
Nucleic Acids Research Advance Access published on May 21, 2007
Nucl. Acids Res. 2007 35: 3733-3740; doi:10.1093/nar/gkm315 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Heide Muckenfuss, Julia K. Kaiser, Erika Krebil, Marion Battenberg, Christina Schwer, Klaus Cichutek, Carsten Münk, and Egbert Flory

Sp1 and Sp3 regulate basal transcription of the human APOBEC3G gene
Nucleic Acids Research Advance Access published on May 21, 2007
Nucl. Acids Res. 2007 35: 3784-3796; doi:10.1093/nar/gkm340 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Tetsuya Takahashi, Masayoshi Tada, Shuichi Igarashi, Akihide Koyama, Hidetoshi Date, Akio Yokoseki, Atsushi Shiga, Yutaka Yoshida, Shoji Tsuji, Masatoyo Nishizawa, and Osamu Onodera

Aprataxin, causative gene product for EAOH/AOA1, repairs DNA single-strand breaks with damaged 3'-phosphate and 3'-phosphoglycolate ends
Nucleic Acids Research Advance Access published on May 22, 2007
Nucl. Acids Res. 2007 35: 3797-3809; doi:10.1093/nar/gkm158 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract René M. Linka, Andrew C.G. Porter, Arsen Volkov, Christian Mielke, Fritz Boege, and Morten O. Christensen

C-Terminal regions of topoisomerase II and IIß determine isoform-specific functioning of the enzymes in vivo
Nucleic Acids Research Advance Access published on May 25, 2007
Nucl. Acids Res. 2007 35: 3810-3822; doi:10.1093/nar/gkm102 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Nucleic Acid Enzymes

Get checked abstract Hui Zhu and Stewart Shuman

Characterization of Agrobacterium tumefaciens DNA ligases C and D
Nucleic Acids Research Advance Access published on May 8, 2007
Nucl. Acids Res. 2007 35: 3631-3645; doi:10.1093/nar/gkm145 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Chunang Gu and Yinsheng Wang

In vitro replication and thermodynamic studies of methylation and oxidation modifications of 6-thioguanine
Nucleic Acids Research Advance Access published on May 21, 2007
Nucl. Acids Res. 2007 35: 3693-3704; doi:10.1093/nar/gkm247 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Felix Mueller-Planitz and Daniel Herschlag

DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity
Nucleic Acids Research Advance Access published on May 21, 2007
Nucl. Acids Res. 2007 35: 3764-3773; doi:10.1093/nar/gkm335 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Ji Hoon Kim and Ronald G. Larson

Single-molecule analysis of 1D diffusion and transcription elongation of T7 RNA polymerase along individual stretched DNA molecules
Nucleic Acids Research Advance Access published on May 25, 2007
Nucl. Acids Res. 2007 35: 3848-3858; doi:10.1093/nar/gkm332 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Ulrike Hardeland, Christophe Kunz, Frauke Focke, Marta Szadkowski, and Primo Schär

Cell cycle regulation as a mechanism for functional separation of the apparently redundant uracil DNA glycosylases TDG and UNG2
Nucleic Acids Research Advance Access published on May 25, 2007
Nucl. Acids Res. 2007 35: 3859-3867; doi:10.1093/nar/gkm337 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

RNA

Get checked abstract Philip J. Santangelo and Gang Bao

Dynamics of filamentous viral RNPs prior to egress
Nucleic Acids Research Advance Access published on May 7, 2007
Nucl. Acids Res. 2007 35: 3602-3611; doi:10.1093/nar/gkm246 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Niroshika Keppetipola, Jayakrishnan Nandakumar, and Stewart Shuman

Reprogramming the tRNA-splicing activity of a bacterial RNA repair enzyme
Nucleic Acids Research Advance Access published on May 8, 2007
Nucl. Acids Res. 2007 35: 3624-3630; doi:10.1093/nar/gkm110 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Joachim Forner, Bärbel Weber, Sabine Thuss, Steffen Wildum, and Stefan Binder

Mapping of mitochondrial mRNA termini in Arabidopsis thaliana: t-elements contribute to 5' and 3' end formation
Nucleic Acids Research Advance Access published on May 8, 2007
Nucl. Acids Res. 2007 35: 3676-3692; doi:10.1093/nar/gkm270 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Andrea Rentmeister, Günter Mayer, Nicole Kuhn, and Michael Famulok

Conformational changes in the expression domain of the Escherichia coli thiM riboswitch
Nucleic Acids Research Advance Access published on May 21, 2007
Nucl. Acids Res. 2007 35: 3713-3722; doi:10.1093/nar/gkm300 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Vera K. Schoft, Sandy Schopoff, and Michael F. Jantsch

Regulation of glutamate receptor B pre-mRNA splicing by RNA editing
Nucleic Acids Research Advance Access published on May 21, 2007
Nucl. Acids Res. 2007 35: 3723-3732; doi:10.1093/nar/gkm314 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Stefan L. Ameres, Dmitry Shcherbakov, Ekaterina Nikonova, Wolfgang Piendl, Renée Schroeder, and Katharina Semrad

RNA chaperone activity of L1 ribosomal proteins: phylogenetic conservation and splicing inhibition
Nucleic Acids Research Advance Access published on May 21, 2007
Nucl. Acids Res. 2007 35: 3752-3763; doi:10.1093/nar/gkm318 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Darui Xu, Theresa Landon, Nancy L. Greenbaum, and Marcia O. Fenley

The electrostatic characteristics of G·U wobble base pairs
Nucleic Acids Research Advance Access published on May 25, 2007
Nucl. Acids Res. 2007 35: 3836-3847; doi:10.1093/nar/gkm274 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Structural Biology

Get checked abstract Zhong-yuan Kan, Yi Lin, Feng Wang, Xin-ying Zhuang, Yong Zhao, Dai-wen Pang, Yu-hua Hao, and Zheng Tan

G-quadruplex formation in human telomeric (TTAGGG)₄ sequence with complementary strand in close vicinity under molecularly crowded condition
Nucleic Acids Research Advance Access published on May 8, 2007
Nucl. Acids Res. 2007 35: 3646-3653; doi:10.1093/nar/gkm203 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Eva Torreira, Guy Schoehn, Yolanda Fernández, Núria Jorba, Rob W.H. Ruigrok, Stephen Cusack, Juan Ortín, and Oscar Llorca

Three-dimensional model for the isolated recombinant influenza virus polymerase heterotrimer
Nucleic Acids Research Advance Access published on May 21, 2007
Nucl. Acids Res. 2007 35: 3774-3783; doi:10.1093/nar/gkm336 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online

Get checked abstract Vladimir B. Teif

General transfer matrix formalism to calculate DNA–protein–drug binding in gene regulation: application to O_R operator of phage
Nucleic Acids Research Advance Access published on May 25, 2007
Nucl. Acids Res. 2007 35: e80; doi:10.1093/nar/gkm268 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Xiangdong Meng, Stacey Thibodeau-Beganny, Tao Jiang, J. Keith Joung, and Scot A. Wolfe

Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based method
Nucleic Acids Research Advance Access published on May 30, 2007
Nucl. Acids Res. 2007 35: e81; doi:10.1093/nar/gkm385 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Jer-Horng Wu and Wen-Tso Liu

Quantitative multiplexing analysis of PCR-amplified ribosomal RNA genes by hierarchical oligonucleotide primer extension reaction
Nucleic Acids Research Advance Access published on June 6, 2007
Nucl. Acids Res. 2007 35: e82; doi:10.1093/nar/gkm413 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Yu Zheng and Richard J. Roberts

Selection of restriction endonucleases using artificial cells
Nucleic Acids Research Advance Access published on June 12, 2007
Nucl. Acids Res. 2007 35: e83; doi:10.1093/nar/gkm410 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

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