Nucleic Acids Research

Survey and Summary

Get checked abstract Chunsun Zhang and Da Xing

Miniaturized PCR chips for nucleic acid amplification and analysis: latest advances and future trends
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4223-4237; doi:10.1093/nar/gkm389 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Computational Biology

Get checked abstract Xinbin Dai, Ji He, and Xuechun Zhao

A new systematic computational approach to predicting target genes of transcription factors
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4433-4440; doi:10.1093/nar/gkm454 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Genomics

Get checked abstract Emanuele Buratti, Martin Chivers, Jana Královicová, Maurizio Romano, Marco Baralle, Adrian R. Krainer, and Igor Vorechovsky

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4250-4263; doi:10.1093/nar/gkm402 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Kai Zhao, Mingzhu Liu, and Richard R. Burgess

Adaptation in bacterial flagellar and motility systems: from regulon members to ‘foraging’-like behavior in E. coli
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4441-4452; doi:10.1093/nar/gkm456 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Zhenbao Yu, Zhen Li, Normand Jolicoeur, Linhua Zhang, Yves Fortin, Edwin Wang, Meiqun Wu, and Shi-Hsiang Shen

Aberrant allele frequencies of the SNPs located in microRNA target sites are potentially associated with human cancers
Nucleic Acids Research Advance Access published on June 21, 2007
Nucl. Acids Res. 2007 35: 4535-4541; doi:10.1093/nar/gkm480 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Molecular Biology

Get checked abstract Lothar Schermelleh, Andrea Haemmer, Fabio Spada, Nicole Rösing, Daniela Meilinger, Ulrich Rothbauer, M. Cristina Cardoso, and Heinrich Leonhardt

Dynamics of Dnmt1 interaction with the replication machinery and its role in postreplicative maintenance of DNA methylation
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4301-4312; doi:10.1093/nar/gkm432 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Shima Nakanishi, Rajendra Prasad, Samuel H. Wilson, and Michael Smerdon

Different structural states in oligonucleosomes are required for early versus late steps of base excision repair
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4313-4321; doi:10.1093/nar/gkm436 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Sumati Sundaram, Li Kim Lee, and Charles M. Roth

Interplay of polyethyleneimine molecular weight and oligonucleotide backbone chemistry in the dynamics of antisense activity
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4396-4408; doi:10.1093/nar/gkm450 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Hana Faiger, Marina Ivanchenko, and Tali E. Haran

Nearest-neighbor non-additivity versus long-range non-additivity in TATA-box structure and its implications for TBP-binding mechanism
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4409-4419; doi:10.1093/nar/gkm451 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jie Yang, Tuuli Välineva, Jingxin Hong, Tianxu Bu, Zhi Yao, Ole N. Jensen, Mikko J. Frilander, and Olli Silvennoinen

Transcriptional co-activator protein p100 interacts with snRNP proteins and facilitates the assembly of the spliceosome
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4485-4494; doi:10.1093/nar/gkm470 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Saïd Abes, John J. Turner, Gabriela D. Ivanova, David Owen, Donna Williams, Andrey Arzumanov, Philippe Clair, Michael J. Gait, and Bernard Lebleu

Efficient splicing correction by PNA conjugation to an R₆-Penetratin delivery peptide
Nucleic Acids Research Advance Access published on June 21, 2007
Nucl. Acids Res. 2007 35: 4495-4502; doi:10.1093/nar/gkm418 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Carrie L. N. Ross, Ranoo R. Patel, Tamra C. Mendelson, and Vassie C. Ware

Functional conservation between structurally diverse ribosomal proteins from Drosophila melanogaster and Saccharomyces cerevisiae: fly L23a can substitute for yeast L25 in ribosome assembly and function
Nucleic Acids Research Advance Access published on June 21, 2007
Nucl. Acids Res. 2007 35: 4503-4514; doi:10.1093/nar/gkm428 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Jane Lee, Jason Beliakoff, and Zijie Sun

The novel PIAS-like protein hZimp10 is a transcriptional co-activator of the p53 tumor suppressor
Nucleic Acids Research Advance Access published on June 21, 2007
Nucl. Acids Res. 2007 35: 4523-4534; doi:10.1093/nar/gkm476 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Amber Goodchild, Andrew King, Mary Margaret Gozar, Toby Passioura, Carly Tucker, and Laurent Rivory

Cytotoxic G-rich oligodeoxynucleotides: putative protein targets and required sequence motif
Nucleic Acids Research Advance Access published on June 22, 2007
Nucl. Acids Res. 2007 35: 4562-4572; doi:10.1093/nar/gkm465 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Nucleic Acid Enzymes

Get checked abstract Zunyi Yang, A. Michael Sismour, Pinpin Sheng, Nyssa L. Puskar, and Steven A. Benner

Enzymatic incorporation of a third nucleobase pair
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4238-4249; doi:10.1093/nar/gkm395 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Balasubrahmanyam Addepalli and Arthur G. Hunt

A novel endonuclease activity associated with the Arabidopsis ortholog of the 30-kDa subunit of cleavage and polyadenylation specificity factor
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4453-4463; doi:10.1093/nar/gkm457 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Smitha Antony, Christophe Marchand, Andrew G. Stephen, Laurent Thibaut, Keli K. Agama, Robert J. Fisher, and Yves Pommier

Novel high-throughput electrochemiluminescent assay for identification of human tyrosyl-DNA phosphodiesterase (Tdp1) inhibitors and characterization of furamidine (NSC 305831) as an inhibitor of Tdp1
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4474-4484; doi:10.1093/nar/gkm463 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Undine Mechold, Gang Fang, Saravuth Ngo, Vasily Ogryzko, and Antoine Danchin

YtqI from Bacillus subtilis has both oligoribonuclease and pAp-phosphatase activity
Nucleic Acids Research Advance Access published on June 22, 2007
Nucl. Acids Res. 2007 35: 4552-4561; doi:10.1093/nar/gkm462 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

RNA

Get checked abstract Ellen M. Westerhout and Ben Berkhout

A systematic analysis of the effect of target RNA structure on RNA interference
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4322-4330; doi:10.1093/nar/gkm437 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Nadja Heidrich, Isabella Moll, and Sabine Brantl

In vitro analysis of the interaction between the small RNA SR1 and its primary target ahrC mRNA
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4331-4346; doi:10.1093/nar/gkm439 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Stanley C. Sedore, Sarah A. Byers, Sebastian Biglione, Jason P. Price, Wendy J. Maury, and David H. Price

Manipulation of P-TEFb control machinery by HIV: recruitment of P-TEFb from the large form by Tat and binding of HEXIM1 to TAR
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4347-4358; doi:10.1093/nar/gkm443 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Emanuele Buratti, Cristiana Stuani, Greta De Prato, and Francisco E. Baralle

SR protein-mediated inhibition of CFTR exon 9 inclusion: molecular characterization of the intronic splicing silencer
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4359-4368; doi:10.1093/nar/gkm444 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Emanuele Buratti, Ashish Dhir, Marzena A. Lewandowska, and Francisco E. Baralle

RNA structure is a key regulatory element in pathological ATM and CFTR pseudoexon inclusion events
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4369-4383; doi:10.1093/nar/gkm447 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Shiyi Yao, Joshua B. Blaustein, and David H. Bechhofer

Processing of Bacillus subtilis small cytoplasmic RNA: evidence for an additional endonuclease cleavage site
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4464-4473; doi:10.1093/nar/gkm460 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Marcelo H. Viegas, Niels H. Gehring, Stephen Breit, Matthias W. Hentze, and Andreas E. Kulozik

The abundance of RNPS1, a protein component of the exon junction complex, can determine the variability in efficiency of the Nonsense Mediated Decay pathway
Nucleic Acids Research Advance Access published on June 22, 2007
Nucl. Acids Res. 2007 35: 4542-4551; doi:10.1093/nar/gkm461 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Structural Biology

Get checked abstract S. Sunita, Elzbieta Purta, Malgorzata Durawa, Karolina L. Tkaczuk, J. Swaathi, Janusz M. Bujnicki, and J. Sivaraman

Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4264-4274; doi:10.1093/nar/gkm411 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Pingna Xu, Lida Oum, Lorena S. Beese, Nicholas E. Geacintov, and Suse Broyde

Following an environmental carcinogen N²-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4275-4288; doi:10.1093/nar/gkm416 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Masaru Tsunoda, Yoshio Kusakabe, Nobutada Tanaka, Satoshi Ohno, Masashi Nakamura, Toshiya Senda, Tomohisa Moriguchi, Norio Asai, Mitsuo Sekine, Takashi Yokogawa, Kazuya Nishikawa, and Kazuo T. Nakamura

Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4289-4300; doi:10.1093/nar/gkm417 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Julien Boudet, Valérie Duval, Hélène Van Melckebeke, Martin Blackledge, Ana Amoroso, Bernard Joris, and Jean-Pierre Simorre

Conformational and thermodynamic changes of the repressor/DNA operator complex upon monomerization shed new light on regulation mechanisms of bacterial resistance against ß-lactam antibiotics
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4384-4395; doi:10.1093/nar/gkm448 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Robert Alazard, Lionel Mourey, Christine Ebel, Peter V. Konarev, Maxim V. Petoukhov, Dmitri I. Svergun, and Monique Erard

Fine-tuning of intrinsic N-Oct-3 POU domain allostery by regulatory DNA targets
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: 4420-4432; doi:10.1093/nar/gkm453 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Pierre Legrand, Noël Pinaud, Lionel Minvielle-Sébastia, and Sébastien Fribourg

The structure of the CstF-77 homodimer provides insights into CstF assembly
Nucleic Acids Research Advance Access published on June 21, 2007
Nucl. Acids Res. 2007 35: 4515-4522; doi:10.1093/nar/gkm458 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online

Get checked abstract Christian Hoffmann, Nana Minkah, Jeremy Leipzig, Gary Wang, Max Q. Arens, Pablo Tebas, and Frederic D. Bushman

DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: e91; doi:10.1093/nar/gkm435 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Supplementary Data] [Supplementary Data]  

Get checked abstract Nadia Hégarat, Gildas Mouta Cardoso, Filippo Rusconi, Jean-Christophe Franois, and Danièle Praseuth

Analytical biochemistry of DNA–protein assemblies from crude cell extracts
Nucleic Acids Research Advance Access published on July 7, 2007
Nucl. Acids Res. 2007 35: e92; doi:10.1093/nar/gkm490 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Fei Xiao, Piotr Widlak, and William T. Garrard

Engineered apoptotic nucleases for chromatin research
Nucleic Acids Research Advance Access published on July 10, 2007
Nucl. Acids Res. 2007 35: e93; doi:10.1093/nar/gkm486 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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