Nucleic Acids Research

Survey and Summary

Get checked abstract John Atkinson and Peter McGlynn

Replication fork reversal and the maintenance of genome stability
Nucleic Acids Research Advance Access published on April 30, 2009
Nucl. Acids Res. 2009 37: 3475-3492; doi:10.1093/nar/gkp244 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Chemistry and Synthetic Biology

Get checked abstract Chunlai Chen, Wenjuan Wang, Jing Ge, and Xin Sheng Zhao

Kinetics and thermodynamics of DNA hybridization on gold nanoparticles
Nucleic Acids Research Advance Access published on April 20, 2009
Nucl. Acids Res. 2009 37: 3756-3765; doi:10.1093/nar/gkp230 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Supplementary Data]  

Computational Biology

Get checked abstract Yong Wang, Ruslan I. Sadreyev, and Nick V. Grishin

PROCAIN: protein profile comparison with assisting information
Nucleic Acids Research Advance Access published on April 7, 2009
Nucl. Acids Res. 2009 37: 3522-3530; doi:10.1093/nar/gkp212 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract S. de Nooijer, J. Wellink, B. Mulder, and T. Bisseling

Non-specific interactions are sufficient to explain the position of heterochromatic chromocenters and nucleoli in interphase nuclei
Nucleic Acids Research Advance Access published on April 9, 2009
Nucl. Acids Res. 2009 37: 3558-3568; doi:10.1093/nar/gkp219 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Rileen Sinha, Swetlana Nikolajewa, Karol Szafranski, Michael Hiller, Niels Jahn, Klaus Huse, Matthias Platzer, and Rolf Backofen

Accurate prediction of NAGNAG alternative splicing
Nucleic Acids Research Advance Access published on April 9, 2009
Nucl. Acids Res. 2009 37: 3569-3579; doi:10.1093/nar/gkp220 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jeremy Curuksu, Martin Zacharias, Richard Lavery, and Krystyna Zakrzewska

Local and global effects of strong DNA bending induced during molecular dynamics simulations
Nucleic Acids Research Advance Access published on April 20, 2009
Nucl. Acids Res. 2009 37: 3766-3773; doi:10.1093/nar/gkp234 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Gene Regulation, Chromatin and Epigenetics

Get checked abstract Yingbiao Ji and Alexei V. Tulin

Poly(ADP-ribosyl)ation of heterogeneous nuclear ribonucleoproteins modulates splicing
Nucleic Acids Research Advance Access published on April 3, 2009
Nucl. Acids Res. 2009 37: 3501-3513; doi:10.1093/nar/gkp218 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Sarath Chandra Janga, Heladia Salgado, and Agustino Martínez-Antonio

Transcriptional regulation shapes the organization of genes on bacterial chromosomes
Nucleic Acids Research Advance Access published on April 16, 2009
Nucl. Acids Res. 2009 37: 3680-3688; doi:10.1093/nar/gkp231 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract John S. Reece-Hoyes, Bart Deplancke, M. Inmaculada Barrasa, Julia Hatzold, Ryan B. Smit, H. Efsun Arda, Patricia A. Pope, Jeb Gaudet, Barbara Conradt, and Albertha J. M. Walhout

The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors
Nucleic Acids Research Advance Access published on April 16, 2009
Nucl. Acids Res. 2009 37: 3689-3698; doi:10.1093/nar/gkp232 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jing Zhou, Bo O. Zhou, Brian A. Lenzmeier, and Jin-Qiu Zhou

Histone deacetylase Rpd3 antagonizes Sir2-dependent silent chromatin propagation
Nucleic Acids Research Advance Access published on April 16, 2009
Nucl. Acids Res. 2009 37: 3699-3713; doi:10.1093/nar/gkp233 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Boris Hedtke and Bernhard Grimm

Silencing of a plant gene by transcriptional interference
Nucleic Acids Research Advance Access published on April 17, 2009
Nucl. Acids Res. 2009 37: 3739-3746; doi:10.1093/nar/gkp241 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Genome Integrity, Repair and Replication

Get checked abstract Ken Ishikawa, Naofumi Handa, and Ichizo Kobayashi

Cleavage of a model DNA replication fork by a Type I restriction endonuclease
Nucleic Acids Research Advance Access published on April 7, 2009
Nucl. Acids Res. 2009 37: 3531-3544; doi:10.1093/nar/gkp214 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology

Get checked abstract María Rodríguez-Mateos, David Abia, Juan J. García-Gómez, Antonio Morreale, Jesús de la Cruz, Cruz Santos, Miguel Remacha, and Juan P. G. Ballesta

The amino terminal domain from Mrt4 protein can functionally replace the RNA binding domain of the ribosomal P0 protein
Nucleic Acids Research Advance Access published on April 3, 2009
Nucl. Acids Res. 2009 37: 3514-3521; doi:10.1093/nar/gkp209 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Sonia Trigueros, Tung Tran, Nohemy Sorto, Jason Newmark, Sean D. Colloms, David J. Sherratt, and Marcelo E. Tolmasky

mwr Xer site-specific recombination is hypersensitive to DNA supercoiling
Nucleic Acids Research Advance Access published on April 9, 2009
Nucl. Acids Res. 2009 37: 3580-3587; doi:10.1093/nar/gkp208 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jian Zhang, Enhu Li, and Gary J. Olsen

Protein-coding gene promoters in Methanocaldococcus (Methanococcus) jannaschii
Nucleic Acids Research Advance Access published on April 9, 2009
Nucl. Acids Res. 2009 37: 3588-3601; doi:10.1093/nar/gkp213 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Shun-Fu Tseng, Zih-Jie Shen, Hung-Ji Tsai, Yi-Hsuan Lin, and Shu-Chun Teng

Rapid Cdc13 turnover and telomere length homeostasis are controlled by Cdk1-mediated phosphorylation of Cdc13
Nucleic Acids Research Advance Access published on April 9, 2009
Nucl. Acids Res. 2009 37: 3602-3611; doi:10.1093/nar/gkp235 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Supplementary Data]  

Get checked abstract Pallavi Lonkar, Ki-Hyun Kim, Jean Y. Kuan, Joanna Y. Chin, Faye A. Rogers, Melissa P. Knauert, Ryszard Kole, Peter E. Nielsen, and Peter M. Glazer

Targeted correction of a thalassemia-associated β-globin mutation induced by pseudo-complementary peptide nucleic acids
Nucleic Acids Research Advance Access published on April 13, 2009
Nucl. Acids Res. 2009 37: 3635-3644; doi:10.1093/nar/gkp217 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Alexandra Kataropoulou, Chiara Bovolenta, Amalia Belfiore, Sonia Trabatti, Anna Garbelli, Simona Porcellini, Rossella Lupo, and Giovanni Maga

Mutational analysis of the HIV-1 auxiliary protein Vif identifies independent domains important for the physical and functional interaction with HIV-1 reverse transcriptase
Nucleic Acids Research Advance Access published on April 15, 2009
Nucl. Acids Res. 2009 37: 3660-3669; doi:10.1093/nar/gkp226 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Ju Huck Lee, Hyun Suk Jung, and Arthur Günzl

Transcriptionally active TFIIH of the early-diverged eukaryote Trypanosoma brucei harbors two novel core subunits but not a cyclin-activating kinase complex
Nucleic Acids Research Advance Access published on April 22, 2009
Nucl. Acids Res. 2009 37: 3811-3820; doi:10.1093/nar/gkp236 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acids Enzymes

Get checked abstract Joshua I. Friedman, Ananya Majumdar, and James T. Stivers

Nontarget DNA binding shapes the dynamic landscape for enzymatic recognition of DNA damage
Nucleic Acids Research Advance Access published on April 1, 2009
Nucl. Acids Res. 2009 37: 3493-3500; doi:10.1093/nar/gkp161 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Moheshwarnath Issur, Simon Despins, Isabelle Bougie, and Martin Bisaillon

Nucleotide analogs and molecular modeling studies reveal key interactions involved in substrate recognition by the yeast RNA triphosphatase
Nucleic Acids Research Advance Access published on April 16, 2009
Nucl. Acids Res. 2009 37: 3714-3722; doi:10.1093/nar/gkp227 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Matthias Altmeyer, Simon Messner, Paul O. Hassa, Monika Fey, and Michael O. Hottiger

Molecular mechanism of poly(ADP-ribosyl)ation by PARP1 and identification of lysine residues as ADP-ribose acceptor sites
Nucleic Acids Research Advance Access published on April 16, 2009
Nucl. Acids Res. 2009 37: 3723-3738; doi:10.1093/nar/gkp229 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jana E. Stone, Grace E. Kissling, Scott A. Lujan, Igor B. Rogozin, Carrie M. Stith, Peter M. J. Burgers, and Thomas A. Kunkel

Low-fidelity DNA synthesis by the L979F mutator derivative of Saccharomyces cerevisiae DNA polymerase
Nucleic Acids Research Advance Access published on April 20, 2009
Nucl. Acids Res. 2009 37: 3774-3787; doi:10.1093/nar/gkp238 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA

Get checked abstract Kenny Schlosser, Jeffrey C. F. Lam, and Yingfu Li

A genotype-to-phenotype map of in vitro selected RNA-cleaving DNAzymes: implications for accessing the target phenotype
Nucleic Acids Research Advance Access published on April 8, 2009
Nucl. Acids Res. 2009 37: 3545-3557; doi:10.1093/nar/gkp222 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Wijdan Al-Ahmadi, Maha Al-Ghamdi, Latifa Al-Haj, Maher Al-Saif, and Khalid S. A. Khabar

Alternative polyadenylation variants of the RNA binding protein, HuR: abundance, role of AU-rich elements and auto-Regulation
Nucleic Acids Research Advance Access published on April 9, 2009
Nucl. Acids Res. 2009 37: 3612-3624; doi:10.1093/nar/gkp223 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Supplementary Data]  

Get checked abstract Li-hua Guo, Liying Sun, Sotaro Chiba, Hiroyuki Araki, and Nobuhiro Suzuki

Coupled termination/reinitiation for translation of the downstream open reading frame B of the prototypic hypovirus CHV1-EP713
Nucleic Acids Research Advance Access published on April 13, 2009
Nucl. Acids Res. 2009 37: 3645-3659; doi:10.1093/nar/gkp224 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Aaron T. Frank, Andrew C. Stelzer, Hashim M. Al-Hashimi, and Ioan Andricioaei

Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition
Nucleic Acids Research Advance Access published on April 15, 2009
Nucl. Acids Res. 2009 37: 3670-3679; doi:10.1093/nar/gkp156 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Anthony C. Forster

Low modularity of aminoacyl-tRNA substrates in polymerization by the ribosome
Nucleic Acids Research Advance Access published on April 17, 2009
Nucl. Acids Res. 2009 37: 3747-3755; doi:10.1093/nar/gkp240 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jake Baum, Anthony T. Papenfuss, Gunnar R. Mair, Chris J. Janse, Dina Vlachou, Andrew P. Waters, Alan F. Cowman, Brendan S. Crabb, and Tania F. de Koning-Ward

Molecular genetics and comparative genomics reveal RNAi is not functional in malaria parasites
Nucleic Acids Research Advance Access published on April 20, 2009
Nucl. Acids Res. 2009 37: 3788-3798; doi:10.1093/nar/gkp239 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Supplementary Data]  

Get checked abstract Soken Tsuchiya, Masahito Oku, Yukako Imanaka, Ryo Kunimoto, Yasushi Okuno, Kazuya Terasawa, Fumiaki Sato, Gozoh Tsujimoto, and Kazuharu Shimizu

MicroRNA-338-3p and microRNA-451 contribute to the formation of basolateral polarity in epithelial cells
Nucleic Acids Research Advance Access published on April 22, 2009
Nucl. Acids Res. 2009 37: 3821-3827; doi:10.1093/nar/gkp255 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology

Get checked abstract Ja Yil Lee and D. S. Kim

Dramatic effect of single-base mutation on the conformational dynamics of human telomeric G-quadruplex
Nucleic Acids Research Advance Access published on April 9, 2009
Nucl. Acids Res. 2009 37: 3625-3634; doi:10.1093/nar/gkp216 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Monika Sokolowska, Honorata Czapinska, and Matthias Bochtler

Crystal structure of the ββ-Me type II restriction endonuclease Hpy99I with target DNA
Nucleic Acids Research Advance Access published on April 20, 2009
Nucl. Acids Res. 2009 37: 3799-3810; doi:10.1093/nar/gkp228 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Methods Online

Get checked abstract Yujun Han, James M. Burnette, III, and Susan R. Wessler

TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences
Nucleic Acids Research Advance Access published on May 8, 2009
Nucl. Acids Res. 2009 37: e78; doi:10.1093/nar/gkp295 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Hui Sun Leong and David Kipling

Text-based over-representation analysis of microarray gene lists with annotation bias
Nucleic Acids Research Advance Access published on May 8, 2009
Nucl. Acids Res. 2009 37: e79; doi:10.1093/nar/gkp310 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Leming Zhou, Mihaela Pertea, Arthur L. Delcher, and Liliana Florea

Sim4cc: a cross-species spliced alignment program
Nucleic Acids Research Advance Access published on May 8, 2009
Nucl. Acids Res. 2009 37: e80; doi:10.1093/nar/gkp319 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Pedro Rodriguez-Collazo, Sanford H. Leuba, and Jordanka Zlatanova

Robust methods for purification of histones from cultured mammalian cells with the preservation of their native modifications
Nucleic Acids Research Advance Access published on May 13, 2009
Nucl. Acids Res. 2009 37: e81; doi:10.1093/nar/gkp273 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Federico Colecchia, Denise Kottwitz, Mandy Wagner, Cosima V. Pfenninger, Gerald Thiel, Ingo Tamm, Carsten Peterson, and Ulrike A. Nuber

Tissue-specific regulatory network extractor (TS-REX): a database and software resource for the tissue and cell type-specific investigation of transcription factor-gene networks
Nucleic Acids Research Advance Access published on May 13, 2009
Nucl. Acids Res. 2009 37: e82; doi:10.1093/nar/gkp311 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Srayanta Mukherjee and Yang Zhang

MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming
Nucleic Acids Research Advance Access published on May 14, 2009
Nucl. Acids Res. 2009 37: e83; doi:10.1093/nar/gkp318 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Front-Matter/Back-Matter

Nucleic Acids Research: VOLUME 37 ISSUE 11 2009
Nucl. Acids Res. 2009 37: i; doi:10.1093/nar/gkp567 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acids Research
Nucl. Acids Res. 2009 37: ii; doi:10.1093/nar/gkp564 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Subscriptions
Nucl. Acids Res. 2009 37: iii; doi:10.1093/nar/gkp565 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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