Nucleic Acids Research

Chemistry and Synthetic Biology

Get checked abstract 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

Get checked abstract 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]  

Get checked abstract 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

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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

Get checked abstract 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]  

Get checked abstract Aroumougame Asaithamby and David J. Chen

Cellular responses to DNA double-strand breaks after low-dose -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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract Peter Sandin, Gudrun Stengel, Thomas Ljungdahl, Karl Börjesson, Bertil Macao, and L. Marcus Wilhelmsson

Highly efficient incorporation of the fluorescent nucleotide analogs tC and tC^O 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]  

Get checked abstract 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]  

Get checked abstract 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

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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 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

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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

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]  

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