Skip Navigation

Receive this page by email each issue: [Sign up for eTOCs]

Cover Image
[Cover Caption] 
Other Issues:
Previous Next 		Contents: Volume 37, Number 8, May 2009   [Index by Author] 

Down Survey and Summary
Down Computational Biology
Down Gene Regulation, Chromatin and Epigenetics
Down Genome Integrity, Repair and Replication
Down Genomics
Down Molecular Biology
Down Nucleic Acid Enzymes
Down RNA
Down Structural Biology
Down Methods Online
Down Front-Matter/Back-Matter


[Search ALL Issues]

Table of Contents (Print 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.

Survey and Summary Back

N. D. Mendes, A. T. Freitas, and M.-F. Sagot
Current tools for the identification of miRNA genes and their targets
Nucleic Acids Research Advance Access published on March 18, 2009
Nucl. Acids Res. 2009 37: 2419-2433; doi:10.1093/nar/gkp145 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Computational Biology Back

Srinivas Ramachandran, Brenda R. Temple, Stephen G. Chaney, and Nikolay V. Dokholyan
Structural basis for the sequence-dependent effects of platinum–DNA adducts
Nucleic Acids Research Advance Access published on March 2, 2009
Nucl. Acids Res. 2009 37: 2434-2448; doi:10.1093/nar/gkp029 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Jorge Duitama, Dipu Mohan Kumar, Edward Hemphill, Mazhar Khan, Ion I. Mandoiu, and Craig E. Nelson
PrimerHunter: a primer design tool for PCR-based virus subtype identification
Nucleic Acids Research Advance Access published on March 5, 2009
Nucl. Acids Res. 2009 37: 2483-2492; doi:10.1093/nar/gkp073 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Tasha A. Desai, Dmitry A. Rodionov, Mikhail S. Gelfand, Eric J. Alm, and Christopher V. Rao
Engineering transcription factors with novel DNA-binding specificity using comparative genomics
Nucleic Acids Research Advance Access published on March 5, 2009
Nucl. Acids Res. 2009 37: 2493-2503; doi:10.1093/nar/gkp079 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Kyu-il Cho, Dongsup Kim, and Doheon Lee
A feature-based approach to modeling protein–protein interaction hot spots
Nucleic Acids Research Advance Access published on March 9, 2009
Nucl. Acids Res. 2009 37: 2672-2687; doi:10.1093/nar/gkp132 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Gene Regulation, Chromatin and Epigenetics Back

M. Rodríguez-Paredes, M. Ceballos-Chávez, M. Esteller, M. García-Domínguez, and J. C. Reyes
The chromatin remodeling factor CHD8 interacts with elongating RNA polymerase II and controls expression of the cyclin E2 gene
Nucleic Acids Research Advance Access published on March 2, 2009
Nucl. Acids Res. 2009 37: 2449-2460; doi:10.1093/nar/gkp101 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Joanna Somers and Tom Owen-Hughes
Mutations to the histone H3 {alpha}N region selectively alter the outcome of ATP-dependent nucleosome-remodelling reactions
Nucleic Acids Research Advance Access published on March 5, 2009
Nucl. Acids Res. 2009 37: 2504-2513; doi:10.1093/nar/gkp114 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Elisa Leimgruber, Queralt Seguín-Estévez, Isabelle Dunand-Sauthier, Natalia Rybtsova, Christoph D. Schmid, Giovanna Ambrosini, Philipp Bucher, and Walter Reith
Nucleosome eviction from MHC class II promoters controls positioning of the transcription start site
Nucleic Acids Research Advance Access published on March 5, 2009
Nucl. Acids Res. 2009 37: 2514-2528; doi:10.1093/nar/gkp116 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Yisheng Yang, Benny Hung-Junn Chang, Susan L. Samson, Ming V. Li, and Lawrence Chan
The Krüppel-like zinc finger protein Glis3 directly and indirectly activates insulin gene transcription
Nucleic Acids Research Advance Access published on March 5, 2009
Nucl. Acids Res. 2009 37: 2529-2538; doi:10.1093/nar/gkp122 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Karla Pérez-Toledo, Ana Paola Rojas-Meza, Liliana Mancio-Silva, Nora Adriana Hernández-Cuevas, Dulce Maria Delgadillo, Miguel Vargas, Santiago Martínez-Calvillo, Artur Scherf, and Rosaura Hernandez-Rivas
Plasmodium falciparum heterochromatin protein 1 binds to tri-methylated histone 3 lysine 9 and is linked to mutually exclusive expression of var genes
Nucleic Acids Research Advance Access published on March 6, 2009
Nucl. Acids Res. 2009 37: 2596-2606; doi:10.1093/nar/gkp115 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Taraswi Banerjee, Somsubhra Nath, and Susanta Roychoudhury
DNA damage induced p53 downregulates Cdc20 by direct binding to its promoter causing chromatin remodeling
Nucleic Acids Research Advance Access published on March 9, 2009
Nucl. Acids Res. 2009 37: 2688-2698; doi:10.1093/nar/gkp110 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Rainer Melzer and Günter Theißen
Reconstitution of ‘floral quartets’ in vitro involving class B and class E floral homeotic proteins
Nucleic Acids Research Advance Access published on March 10, 2009
Nucl. Acids Res. 2009 37: 2723-2736; doi:10.1093/nar/gkp129 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genome Integrity, Repair and Replication Back

Inna Shokolenko, Natalia Venediktova, Alexandra Bochkareva, Glenn L. Wilson, and Mikhail F. Alexeyev
Oxidative stress induces degradation of mitochondrial DNA
Nucleic Acids Research Advance Access published on March 5, 2009
Nucl. Acids Res. 2009 37: 2539-2548; doi:10.1093/nar/gkp100 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Patricia Auffret van der Kemp, Marcelo de Padula, Guenaelle Burguiere-Slezak, Helle D. Ulrich, and Serge Boiteux
PCNA monoubiquitylation and DNA polymerase {eta} ubiquitin-binding domain are required to prevent 8-oxoguanine-induced mutagenesis in Saccharomyces cerevisiae
Nucleic Acids Research Advance Access published on March 5, 2009
Nucl. Acids Res. 2009 37: 2549-2559; doi:10.1093/nar/gkp105 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Cynthia A. Haseltine and Stephen C. Kowalczykowski
An archaeal Rad54 protein remodels DNA and stimulates DNA strand exchange by RadA
Nucleic Acids Research Advance Access published on March 12, 2009
Nucl. Acids Res. 2009 37: 2757-2770; doi:10.1093/nar/gkp068 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Genomics Back

Bareket Dassa, Nir London, Barry L. Stoddard, Ora Schueler-Furman, and Shmuel Pietrokovski
Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family
Nucleic Acids Research Advance Access published on March 5, 2009
Nucl. Acids Res. 2009 37: 2560-2573; doi:10.1093/nar/gkp095 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Barbara P. Mello, Eduardo F. Abrantes, César H. Torres, Ariane Machado-Lima, Rogério da Silva Fonseca, Dirce M. Carraro, Ricardo R. Brentani, Luiz F. L. Reis, and Helena Brentani
No-match ORESTES explored as tumor markers
Nucleic Acids Research Advance Access published on March 6, 2009
Nucl. Acids Res. 2009 37: 2607-2617; doi:10.1093/nar/gkp074 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Supplementary Data]  

Heng Li, Jie Xiao, Jinming Li, Le Lu, Shu Feng, and Peter Dröge
Human genomic Z-DNA segments probed by the Z{alpha} domain of ADAR1
Nucleic Acids Research Advance Access published on March 10, 2009
Nucl. Acids Res. 2009 37: 2737-2746; doi:10.1093/nar/gkp124 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology Back

Shuwen Wang, Yuanjun Zhao, Chunguang Hu, and Jiyue Zhu
Differential repression of human and mouse TERT genes during cell differentiation
Nucleic Acids Research Advance Access published on March 6, 2009
Nucl. Acids Res. 2009 37: 2618-2629; doi:10.1093/nar/gkp125 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Yu-Tao Yang, Yan-Li Yu, Guo-Dong Yang, Jie-Dao Zhang, and Cheng-Chao Zheng
Tissue-specific expression of the PNZIP promoter is mediated by combinatorial interaction of different cis-elements and a novel transcriptional factor
Nucleic Acids Research Advance Access published on March 6, 2009
Nucl. Acids Res. 2009 37: 2630-2644; doi:10.1093/nar/gkp126 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Xiyuan Bai, Derek Silvius, Edward D. Chan, Denise Escalier, and Shaun Xin Xu
Identification and characterization of a novel testis-specific gene CKT2, which encodes a substrate for protein kinase CK2
Nucleic Acids Research Advance Access published on March 9, 2009
Nucl. Acids Res. 2009 37: 2699-2711; doi:10.1093/nar/gkp094 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Noa Ofer, Pnina Weisman-Shomer, Jeny Shklover, and Michael Fry
The quadruplex r(CGG)n destabilizing cationic porphyrin TMPyP4 cooperates with hnRNPs to increase the translation efficiency of fragile X premutation mRNA
Nucleic Acids Research Advance Access published on March 9, 2009
Nucl. Acids Res. 2009 37: 2712-2722; doi:10.1093/nar/gkp130 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Amy M. Tsou, Tao Cai, Zhi Liu, Jun Zhu, and Rahul V. Kulkarni
Regulatory targets of quorum sensing in Vibrio cholerae: evidence for two distinct HapR-binding motifs
Nucleic Acids Research Advance Access published on March 10, 2009
Nucl. Acids Res. 2009 37: 2747-2756; doi:10.1093/nar/gkp121 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes Back

Lu Zheng, Radhakrishnan Kanagaraj, Boris Mihaljevic, Sybille Schwendener, Alessandro A. Sartori, Bertran Gerrits, Igor Shevelev, and Pavel Janscak
MRE11 complex links RECQ5 helicase to sites of DNA damage
Nucleic Acids Research Advance Access published on March 6, 2009
Nucl. Acids Res. 2009 37: 2645-2657; doi:10.1093/nar/gkp147 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA Back

H. Alexander Ebhardt, Herbert H. Tsang, Denny C. Dai, Yifeng Liu, Babak Bostan, and Richard P. Fahlman
Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications
Nucleic Acids Research Advance Access published on March 2, 2009
Nucl. Acids Res. 2009 37: 2461-2470; doi:10.1093/nar/gkp093 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Norimasa Kashiwagi, Hiroyuki Furuta, and Yoshiya Ikawa
Primitive templated catalysis of a peptide ligation by self-folding RNAs
Nucleic Acids Research Advance Access published on March 5, 2009
Nucl. Acids Res. 2009 37: 2574-2583; doi:10.1093/nar/gkp111 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nalinie S. Wickramasinghe, Tissa T. Manavalan, Susan M. Dougherty, Krista A. Riggs, Yong Li, and Carolyn M. Klinge
Estradiol downregulates miR-21 expression and increases miR-21 target gene expression in MCF-7 breast cancer cells
Nucleic Acids Research Advance Access published on March 5, 2009
Nucl. Acids Res. 2009 37: 2584-2595; doi:10.1093/nar/gkp117 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Isabel López de Silanes, Myriam Gorospe, Hiroaki Taniguchi, Kotb Abdelmohsen, Subramanya Srikantan, Miguel Alaminos, María Berdasco, Rocío G. Urdinguio, Mario F. Fraga, Filipe V. Jacinto, and Manel Esteller
The RNA-binding protein HuR regulates DNA methylation through stabilization of DNMT3b mRNA
Nucleic Acids Research Advance Access published on March 6, 2009
Nucl. Acids Res. 2009 37: 2658-2671; doi:10.1093/nar/gkp123 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology Back

Jin-li Zhang, Yan Fu, Lin Zheng, Wei Li, Hao Li, Qian Sun, Ying Xiao, and Feng Geng
Natural isoflavones regulate the quadruplex–duplex competition in human telomeric DNA
Nucleic Acids Research Advance Access published on March 3, 2009
Nucl. Acids Res. 2009 37: 2471-2482; doi:10.1093/nar/gkp055 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Methods Online Back

Marcel Walser, Rene Pellaux, Andreas Meyer, Matthias Bechtold, Herve Vanderschuren, Richard Reinhardt, Joseph Magyar, Sven Panke, and Martin Held
Novel method for high-throughput colony PCR screening in nanoliter-reactors
Nucleic Acids Research Advance Access published on March 12, 2009
Nucl. Acids Res. 2009 37: e57; doi:10.1093/nar/gkp160 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Douglas D. Young, Hrvoje Lusic, Mark O. Lively, and Alexander Deiters
Restriction enzyme-free mutagenesis via the light regulation of DNA polymerization
Nucleic Acids Research Advance Access published on March 17, 2009
Nucl. Acids Res. 2009 37: e58; doi:10.1093/nar/gkp150 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Renjun Pei, Jeffrey Rothman, Yuli Xie, and Milan N. Stojanovic
Light-up properties of complexes between thiazole orange-small molecule conjugates and aptamers
Nucleic Acids Research Advance Access published on March 17, 2009
Nucl. Acids Res. 2009 37: e59; doi:10.1093/nar/gkp154 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Vivek Jayaswal, Mark Lutherborrow, David D. F. Ma, and Yee Hwa Yang
Identification of microRNAs with regulatory potential using a matched microRNA-mRNA time-course data
Nucleic Acids Research Advance Access published on March 18, 2009
Nucl. Acids Res. 2009 37: e60; doi:10.1093/nar/gkp153 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yun-Shien Lee, Chun-Houh Chen, Chi-Neu Tsai, Chia-Lung Tsai, Angel Chao, and Tzu-Hao Wang
Microarray labeling extension values: laboratory signatures for Affymetrix GeneChips
Nucleic Acids Research Advance Access published on March 18, 2009
Nucl. Acids Res. 2009 37: e61; doi:10.1093/nar/gkp168 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Sahar Javaherian, Michael U. Musheev, Mirzo Kanoatov, Maxim V. Berezovski, and Sergey N. Krylov
Selection of aptamers for a protein target in cell lysate and their application to protein purification
Nucleic Acids Research Advance Access published on March 20, 2009
Nucl. Acids Res. 2009 37: e62; doi:10.1093/nar/gkp176 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Julia Sandberg, Patrik L. Ståhl, Afshin Ahmadian, Magnus K. Bjursell, and Joakim Lundeberg
Flow cytometry for enrichment and titration in massively parallel DNA sequencing
Nucleic Acids Research Advance Access published on March 20, 2009
Nucl. Acids Res. 2009 37: e63; doi:10.1093/nar/gkp188 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Noriko Tabata, Yuko Sakuma, Yumiko Honda, Nobuhide Doi, Hideaki Takashima, Etsuko Miyamoto-Sato, and Hiroshi Yanagawa
Rapid antibody selection by mRNA display on a microfluidic chip
Nucleic Acids Research Advance Access published on March 30, 2009
Nucl. Acids Res. 2009 37: e64; doi:10.1093/nar/gkp184 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Isabelle Gilbert, Sara Scantland, Isabelle Dufort, Olga Gordynska, Aurélie Labbe, Marc-André Sirard, and Claude Robert
Real-time monitoring of aRNA production during T7 amplification to prevent the loss of sample representation during microarray hybridization sample preparation
Nucleic Acids Research Advance Access published on March 30, 2009
Nucl. Acids Res. 2009 37: e65; doi:10.1093/nar/gkp193 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Front-Matter/Back-Matter Back

Nucleic Acids Research: VOLUME 37 ISSUE 8 2009
Nucl. Acids Res. 2009 37: i; doi:10.1093/nar/gkp396 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acids Research
Nucl. Acids Res. 2009 37: ii; doi:10.1093/nar/gkp395 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Subscriptions
Nucl. Acids Res. 2009 37: iii; doi:10.1093/nar/gkp401 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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.