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Contents: Volume 37, Number 12, July 2009   [Index by Author] 

Down Chemistry and Synthetic Biology
Down Computational Biology
Down Gene Regulation, Chromatin and Epigenetics
Down Genome Integrity, Repair and Replication
Down Molecular Biology
Down Nucleic Acids Enzymes
Down RNA
Down Structural Biology
Down Methods Online
Down Front-Matter/Back-Matter


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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.

Chemistry and Synthetic Biology Back

Jean-Louis Leroy
The formation pathway of i-motif tetramers
Nucleic Acids Research Advance Access published on May 11, 2009
Nucl. Acids Res. 2009 37: 4127-4134; doi:10.1093/nar/gkp340 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Computational Biology Back

Arif Ozgun Harmanci, Gaurav Sharma, and David H. Mathews
Stochastic sampling of the RNA structural alignment space
Nucleic Acids Research Advance Access published on May 8, 2009
Nucl. Acids Res. 2009 37: 4063-4075; doi:10.1093/nar/gkp276 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

N. Alpay Temiz and Carlos J. Camacho
Experimentally based contact energies decode interactions responsible for protein–DNA affinity and the role of molecular waters at the binding interface
Nucleic Acids Research Advance Access published on May 8, 2009
Nucl. Acids Res. 2009 37: 4076-4088; doi:10.1093/nar/gkp289 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Gene Regulation, Chromatin and Epigenetics Back

Mayumi Oda, Jacob L. Glass, Reid F. Thompson, Yongkai Mo, Emmanuel N. Olivier, Maria E. Figueroa, Rebecca R. Selzer, Todd A. Richmond, Xinmin Zhang, Luke Dannenberg, Roland D. Green, Ari Melnick, Eli Hatchwell, Eric E. Bouhassira, Amit Verma, Masako Suzuki, and John M. Greally
High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers
Nucleic Acids Research Advance Access published on April 22, 2009
Nucl. Acids Res. 2009 37: 3829-3839; doi:10.1093/nar/gkp260 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Fenyong Sun, Qiongyu Chen, Songhai Yang, Qiuhui Pan, Ji Ma, Yang Wan, Chih-Hao Chang, and An Hong
Remodeling of chromatin structure within the promoter is important for bmp-2-induced fgfr3 expression
Nucleic Acids Research Advance Access published on April 28, 2009
Nucl. Acids Res. 2009 37: 3897-3911; doi:10.1093/nar/gkp261 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

R. Magnus N. Friis, Bob P. Wu, Stacey N. Reinke, Darren J. Hockman, Brian D. Sykes, and Michael C. Schultz
A glycolytic burst drives glucose induction of global histone acetylation by picNuA4 and SAGA
Nucleic Acids Research Advance Access published on April 30, 2009
Nucl. Acids Res. 2009 37: 3969-3980; doi:10.1093/nar/gkp270 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Harri Makkonen, Miia Kauhanen, Ville Paakinaho, Tiina Jääskeläinen, and Jorma J. Palvimo
Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers
Nucleic Acids Research Advance Access published on May 11, 2009
Nucl. Acids Res. 2009 37: 4135-4148; doi:10.1093/nar/gkp352 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genome Integrity, Repair and Replication Back

Lior Ungar, Nir Yosef, Yael Sela, Roded Sharan, Eytan Ruppin, and Martin Kupiec
A genome-wide screen for essential yeast genes that affect telomere length maintenance
Nucleic Acids Research Advance Access published on April 22, 2009
Nucl. Acids Res. 2009 37: 3840-3849; doi:10.1093/nar/gkp259 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Aroumougame Asaithamby and David J. Chen
Cellular responses to DNA double-strand breaks after low-dose {gamma}-irradiation
Nucleic Acids Research Advance Access published on April 28, 2009
Nucl. Acids Res. 2009 37: 3912-3923; doi:10.1093/nar/gkp237 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Mari Katsura, Takanori Tsuruga, Osamu Date, Takashi Yoshihara, Mari Ishida, Yoshitaka Tomoda, Miyuki Okajima, Motoki Takaku, Hitoshi Kurumizaka, Aiko Kinomura, Hiromu K. Mishima, and Kiyoshi Miyagawa
The ATR-Chk1 pathway plays a role in the generation of centrosome aberrations induced by Rad51C dysfunction
Nucleic Acids Research Advance Access published on April 29, 2009
Nucl. Acids Res. 2009 37: 3959-3968; doi:10.1093/nar/gkp262 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Marijn T. J. van Loenhout, Thijn van der Heijden, Roland Kanaar, Claire Wyman, and Cees Dekker
Dynamics of RecA filaments on single-stranded DNA
Nucleic Acids Research Advance Access published on May 8, 2009
Nucl. Acids Res. 2009 37: 4089-4099; doi:10.1093/nar/gkp326 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Paula P. Cardenas, Begoña Carrasco, Humberto Sanchez, Gintaras Deikus, David H Bechhofer, and Juan C Alonso
Bacillus subtilis polynucleotide phosphorylase 3'-to-5' DNase activity is involved in DNA repair
Nucleic Acids Research Advance Access published on May 11, 2009
Nucl. Acids Res. 2009 37: 4157-4169; doi:10.1093/nar/gkp314 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology Back

Stefan Kippenberger, Jutta Müller, Maike Schultz, Annette Dorn, Andreas Bock, Hüseyin Aygün, Diamant Thaçi, Matthias Hofmann, Roland Kaufmann, and August Bernd
Oligonucleotides suppress PKB/Akt and act as superinductors of apoptosis in human keratinocytes
Nucleic Acids Research Advance Access published on April 22, 2009
Nucl. Acids Res. 2009 37: 3850-3864; doi:10.1093/nar/gkp252 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Yi-Xin Huo, Yuan-Tao Zhang, Yan Xiao, Xiaodong Zhang, Martin Buck, Annie Kolb, and Yi-Ping Wang
IHF-binding sites inhibit DNA loop formation and transcription initiation
Nucleic Acids Research Advance Access published on April 24, 2009
Nucl. Acids Res. 2009 37: 3878-3886; doi:10.1093/nar/gkp258 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Peter Sandin, Gudrun Stengel, Thomas Ljungdahl, Karl Börjesson, Bertil Macao, and L. Marcus Wilhelmsson
Highly efficient incorporation of the fluorescent nucleotide analogs tC and tCO by Klenow fragment
Nucleic Acids Research Advance Access published on April 28, 2009
Nucl. Acids Res. 2009 37: 3924-3933; doi:10.1093/nar/gkp266 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Weidong Han, Zhiqiang Wu, Yali Zhao, Yuanguang Meng, Yiling Si, Jie Yang, Xiaobing Fu, and Li Yu
FHL2 interacts with and acts as a functional repressor of Id2 in human neuroblastoma cells
Nucleic Acids Research Advance Access published on May 5, 2009
Nucl. Acids Res. 2009 37: 3996-4009; doi:10.1093/nar/gkp332 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yuan-Bin Xie, Balachandar Nedumaran, and Hueng-Sik Choi
Molecular characterization of SMILE as a novel corepressor of nuclear receptors
Nucleic Acids Research Advance Access published on May 8, 2009
Nucl. Acids Res. 2009 37: 4100-4115; doi:10.1093/nar/gkp333 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acids Enzymes Back

Luke J. Peakman and Mark D. Szczelkun
S-Adenosyl homocysteine and DNA ends stimulate promiscuous nuclease activities in the Type III restriction endonuclease EcoPI
Nucleic Acids Research Advance Access published on April 28, 2009
Nucl. Acids Res. 2009 37: 3934-3945; doi:10.1093/nar/gkp267 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Tavish Barnes, Wan-Cheol Kim, Anil K. Mantha, Sang-Eun Kim, Tadahide Izumi, Sankar Mitra, and Chow H. Lee
Identification of Apurinic/apyrimidinic endonuclease 1 (APE1) as the endoribonuclease that cleaves c-myc mRNA
Nucleic Acids Research Advance Access published on April 28, 2009
Nucl. Acids Res. 2009 37: 3946-3958; doi:10.1093/nar/gkp275 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Konstantin Akopiants, Rui-Zhe Zhou, Susovan Mohapatra, Kristoffer Valerie, Susan P. Lees-Miller, Kyung-Jong Lee, David J. Chen, Patrick Revy, Jean-Pierre de Villartay, and Lawrence F. Povirk
Requirement for XLF/Cernunnos in alignment-based gap filling by DNA polymerases {lambda} and µ for nonhomologous end joining in human whole-cell extracts
Nucleic Acids Research Advance Access published on May 6, 2009
Nucl. Acids Res. 2009 37: 4055-4062; doi:10.1093/nar/gkp283 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA Back

Suzette A. Pabit, Xiangyun Qiu, Jessica S. Lamb, Li Li, Steve P. Meisburger, and Lois Pollack
Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA
Nucleic Acids Research Advance Access published on April 24, 2009
Nucl. Acids Res. 2009 37: 3887-3896; doi:10.1093/nar/gkp257 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nilesh Vaidya and Niles Lehman
One RNA plays three roles to provide catalytic activity to a group I intron lacking an endogenous internal guide sequence
Nucleic Acids Research Advance Access published on April 30, 2009
Nucl. Acids Res. 2009 37: 3981-3989; doi:10.1093/nar/gkp271 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Leonardo Alves-Junior, Sandra Niemeier, Arne Hauenschild, Marc Rehmsmeier, and Thomas Merkle
Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana
Nucleic Acids Research Advance Access published on May 5, 2009
Nucl. Acids Res. 2009 37: 4010-4021; doi:10.1093/nar/gkp272 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Zhen Huang, Weimin Pei, Yan Han, Sabarinath Jayaseelan, Alexander Shekhtman, Hua Shi, and Li Niu
One RNA aptamer sequence, two structures: a collaborating pair that inhibits AMPA receptors
Nucleic Acids Research Advance Access published on May 5, 2009
Nucl. Acids Res. 2009 37: 4022-4032; doi:10.1093/nar/gkp284 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Shinichiro Shoji, Nimo M. Abdi, Ralf Bundschuh, and Kurt Fredrick
Contribution of ribosomal residues to P-site tRNA binding
Nucleic Acids Research Advance Access published on May 5, 2009
Nucl. Acids Res. 2009 37: 4033-4042; doi:10.1093/nar/gkp296 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Andrea D’Ambrogio, Emanuele Buratti, Cristiana Stuani, Corrado Guarnaccia, Maurizio Romano, Youhna M. Ayala, and Francisco E. Baralle
Functional mapping of the interaction between TDP-43 and hnRNP A2 in vivo
Nucleic Acids Research Advance Access published on May 8, 2009
Nucl. Acids Res. 2009 37: 4116-4126; doi:10.1093/nar/gkp342 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Structural Biology Back

Thomas Monecke, Achim Dickmanns, and Ralf Ficner
Structural basis for m7G-cap hypermethylation of small nuclear, small nucleolar and telomerase RNA by the dimethyltransferase TGS1
Nucleic Acids Research Advance Access published on April 22, 2009
Nucl. Acids Res. 2009 37: 3865-3877; doi:10.1093/nar/gkp249 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Pavol Cekan, Elvar Örn Jonsson, and Snorri Th. Sigurdsson
Folding of the cocaine aptamer studied by EPR and fluorescence spectroscopies using the bifunctional spectroscopic probe Ç
Nucleic Acids Research Advance Access published on April 30, 2009
Nucl. Acids Res. 2009 37: 3990-3995; doi:10.1093/nar/gkp277 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Loussiné Zargarian, Igor Kanevsky, Ali Bazzi, Jonathan Boynard, Françoise Chaminade, Philippe Fossé, and Olivier Mauffret
Structural and dynamic characterization of the upper part of the HIV-1 cTAR DNA hairpin
Nucleic Acids Research Advance Access published on May 5, 2009
Nucl. Acids Res. 2009 37: 4043-4054; doi:10.1093/nar/gkp297 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Agnieszka Kiliszek, Ryszard Kierzek, Wlodzimierz J. Krzyzosiak, and Wojciech Rypniewski
Structural insights into CUG repeats containing the ‘stretched U–U wobble’: implications for myotonic dystrophy
Nucleic Acids Research Advance Access published on May 11, 2009
Nucl. Acids Res. 2009 37: 4149-4156; doi:10.1093/nar/gkp350 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

B. Dorvel, G. Sigalov, Q. Zhao, J. Comer, V. Dimitrov, U. Mirsaidov, A. Aksimentiev, and G. Timp
Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore
Nucleic Acids Research Advance Access published on May 11, 2009
Nucl. Acids Res. 2009 37: 4170-4179; doi:10.1093/nar/gkp317 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Methods Online Back

Engin Gürlevik, Norman Woller, Peter Schache, Nisar P. Malek, Thomas C. Wirth, Lars Zender, Michael P. Manns, Stefan Kubicka, and Florian Kühnel
p53-dependent antiviral RNA-interference facilitates tumor-selective viral replication
Nucleic Acids Research Advance Access published on May 14, 2009
Nucl. Acids Res. 2009 37: e84; doi:10.1093/nar/gkp374 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Adam Ameur, Alvaro Rada-Iglesias, Jan Komorowski, and Claes Wadelius
Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP
Nucleic Acids Research Advance Access published on May 18, 2009
Nucl. Acids Res. 2009 37: e85; doi:10.1093/nar/gkp381 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Supplementary Data]  

Francesca Malentacchi, Giulia Forni, Serena Vinci, and Claudio Orlando
Quantitative evaluation of DNA methylation by optimization of a differential-high resolution melt analysis protocol
Nucleic Acids Research Advance Access published on May 19, 2009
Nucl. Acids Res. 2009 37: e86; doi:10.1093/nar/gkp383 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yaroslav Chushak and Morley O. Stone
In silico selection of RNA aptamers
Nucleic Acids Research Advance Access published on May 21, 2009
Nucl. Acids Res. 2009 37: e87; doi:10.1093/nar/gkp408 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Nir Yosef, Martin Kupiec, Eytan Ruppin, and Roded Sharan
A complex-centric view of protein network evolution
Nucleic Acids Research Advance Access published on May 22, 2009
Nucl. Acids Res. 2009 37: e88; doi:10.1093/nar/gkp414 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Sitharthan Kamalakaran, Jude Kendall, Xiaoyue Zhao, Chunlao Tang, Sohail Khan, Kandasamy Ravi, Theresa Auletta, Michael Riggs, Yun Wang, Åslaug Helland, Bjørn Naume, Nevenka Dimitrova, Anne-Lise Børresen-Dale, Jim Hicks, and Robert Lucito
Methylation detection oligonucleotide microarray analysis: a high-resolution method for detection of CpG island methylation
Nucleic Acids Research Advance Access published on May 27, 2009
Nucl. Acids Res. 2009 37: e89; doi:10.1093/nar/gkp413 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Lan Lin, Song Liu, Heather Brockway, Junhee Seok, Peng Jiang, Wing Hung Wong, and Yi Xing
Using high-density exon arrays to profile gene expression in closely related species
Nucleic Acids Research Advance Access published on May 27, 2009
Nucl. Acids Res. 2009 37: e90; doi:10.1093/nar/gkp420 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Front-Matter/Back-Matter Back

Nucleic Acids Research: VOLUME 37 ISSUE 12 2009
Nucl. Acids Res. 2009 37: i; doi:10.1093/nar/gkp621 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acids Research
Nucl. Acids Res. 2009 37: ii; doi:10.1093/nar/gkp620 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Subscriptions
Nucl. Acids Res. 2009 37: iii; doi:10.1093/nar/gkp622 [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.