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Previous Next 		Contents: Volume 35, Number 9, May 2007    [Index by Author] 
      Down Chemistry
      Down Computational Biology
      Down Genomics
      Down Molecular Biology
      Down Nucleic Acid Enzymes
      Down RNA
      Down Structural Biology
      Down Methods Online
      Down Corrigendum
 

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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:Back

Cheng-Chung Chang, Chih-Wei Chien, Yi-Hsueh Lin, Chi-Chih Kang, and Ta-Chau Chang
Investigation of spectral conversion of d(TTAGGG)4 and d(TTAGGG)13 upon potassium titration by a G-quadruplex recognizer BMVC molecule
Nucleic Acids Research Advance Access published on April 11, 2007
Nucl. Acids Res. 2007 35: 2846-2860; doi:10.1093/nar/gkm155 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Computational Biology:Back

Karin Lagesen, Peter Hallin, Einar Andreas Rødland, Hans-Henrik Stærfeldt, Torbjørn Rognes, and David W. Ussery
RNAmmer: consistent and rapid annotation of ribosomal RNA genes
Nucleic Acids Research Advance Access published on April 22, 2007
Nucl. Acids Res. 2007 35: 3100-3108; doi:10.1093/nar/gkm160 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Genomics:Back

Prasanna R. Bhat, Adam Lukaszewski, Xinping Cui, Jin Xu, Jan T. Svensson, Steve Wanamaker, J. Giles Waines, and Timothy J. Close
Mapping translocation breakpoints using a wheat microarray
Nucleic Acids Research Advance Access published on April 16, 2007
Nucl. Acids Res. 2007 35: 2936-2943; doi:10.1093/nar/gkm148 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Buyong Ma, Yongping Pan, Jie Zheng, Arnold J. Levine, and Ruth Nussinov
Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets
Nucleic Acids Research Advance Access published on April 16, 2007
Nucl. Acids Res. 2007 35: 2986-3001; doi:10.1093/nar/gkm192 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Robert W. Carter
Mitochondrial diversity within modern human populations
Nucleic Acids Research Advance Access published on April 16, 2007
Nucl. Acids Res. 2007 35: 3039-3045; doi:10.1093/nar/gkm207 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Molecular Biology:Back

Kristofer Munson, Jarrod Clark, Katarzyna Lamparska-Kupsik, and Steven S. Smith
Recovery of bisulfite-converted genomic sequences in the methylation-sensitive QPCR
Nucleic Acids Research Advance Access published on April 16, 2007
Nucl. Acids Res. 2007 35: 2893-2903; doi:10.1093/nar/gkm055 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kazunari Hashiguchi, Yoshihiro Matsumoto, and Akira Yasui
Recruitment of DNA repair synthesis machinery to sites of DNA damage/repair in living human cells
Nucleic Acids Research Advance Access published on April 16, 2007
Nucl. Acids Res. 2007 35: 2913-2923; doi:10.1093/nar/gkm115 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jingdan Liang, Zhijun Wang, Xinyi He, Jialiang Li, Xiufen Zhou, and Zixin Deng
DNA modification by sulfur: analysis of the sequence recognition specificity surrounding the modification sites
Nucleic Acids Research Advance Access published on April 16, 2007
Nucl. Acids Res. 2007 35: 2944-2954; doi:10.1093/nar/gkm176 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Masanobu Kinomoto, Takayuki Kanno, Mari Shimura, Yukihito Ishizaka, Asato Kojima, Takeshi Kurata, Tetsutaro Sata, and Kenzo Tokunaga
All APOBEC3 family proteins differentially inhibit LINE-1 retrotransposition
Nucleic Acids Research Advance Access published on April 16, 2007
Nucl. Acids Res. 2007 35: 2955-2964; doi:10.1093/nar/gkm181 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Marija Mihailovich, Rolf Thermann, Fabio Grohovaz, Matthias W. Hentze, and Daniele Zacchetti
Complex translational regulation of BACE1 involves upstream AUGs and stimulatory elements within the 5' untranslated region
Nucleic Acids Research Advance Access published on April 16, 2007
Nucl. Acids Res. 2007 35: 2975-2985; doi:10.1093/nar/gkm191 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jennifer P. Morton, Theodoros Kantidakis, and Robert J. White
RNA polymerase III transcription is repressed in response to the tumour suppressor ARF
Nucleic Acids Research Advance Access published on April 16, 2007
Nucl. Acids Res. 2007 35: 3046-3052; doi:10.1093/nar/gkm208 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Huadong Pei, Jingfang Liu, Jie Li, Aobo Guo, Jian Zhou, and Hua Xiang
Mechanism for the TtDnaA–Tt-oriC cooperative interaction at high temperature and duplex opening at an unusual AT-rich region in Thermoanaerobacter tengcongensis
Nucleic Acids Research Advance Access published on April 22, 2007
Nucl. Acids Res. 2007 35: 3087-3099; doi:10.1093/nar/gkm137 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Hideaki Ogiwara, Ayako Ui, Satoshi Kawashima, Kazuto Kugou, Fumitoshi Onoda, Hitoshi Iwahashi, Masahiko Harata, Kunihiro Ohta, Takemi Enomoto, and Masayuki Seki
Actin-related protein Arp4 functions in kinetochore assembly
Nucleic Acids Research Advance Access published on April 22, 2007
Nucl. Acids Res. 2007 35: 3109-3117; doi:10.1093/nar/gkm161 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Nucleic Acid Enzymes:Back

Slobodan Jergic, Kiyoshi Ozawa, Neal K. Williams, Xun-Cheng Su, Daniel D. Scott, Samir M. Hamdan, Jeffrey A. Crowther, Gottfried Otting, and Nicholas E. Dixon
The unstructured C-terminus of the {tau} subunit of Escherichia coli DNA polymerase III holoenzyme is the site of interaction with the {alpha} subunit
Nucleic Acids Research Advance Access published on March 13, 2007
Nucl. Acids Res. 2007 35: 2813-2824; doi:10.1093/nar/gkm079 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Ram Gopal Nitharwal, Subhankar Paul, Ashraf Dar, Nirupam Roy Choudhury, Rajesh K Soni, Dhaneswar Prusty, Sukrat Sinha, Tara Kashav, Gauranga Mukhopadhyay, Tapan Kumar Chaudhuri, Samudrala Gourinath, and Suman Kumar Dhar
The domain structure of Helicobacter pylori DnaB helicase: the N-terminal domain can be dispensable for helicase activity whereas the extreme C-terminal region is essential for its function
Nucleic Acids Research Advance Access published on April 11, 2007
Nucl. Acids Res. 2007 35: 2861-2874; doi:10.1093/nar/gkm167 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

George C. Lin, Joachim Jaeger, and Joann B. Sweasy
Loop II of DNA polymerase beta is important for polymerization activity and fidelity
Nucleic Acids Research Advance Access published on April 16, 2007
Nucl. Acids Res. 2007 35: 2924-2935; doi:10.1093/nar/gkm126 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Marcel Hohl, Isabelle Dunand-Sauthier, Lidija Staresincic, Pascale Jaquier-Gubler, Fabrizio Thorel, Mauro Modesti, Stuart G. Clarkson, and Orlando D. Schärer
Domain swapping between FEN-1 and XPG defines regions in XPG that mediate nucleotide excision repair activity and substrate specificity
Nucleic Acids Research Advance Access published on April 22, 2007
Nucl. Acids Res. 2007 35: 3053-3063; doi:10.1093/nar/gkm092 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Zachary F. Pursell, Isabelle Isoz, Else-Britt Lundström, Erik Johansson, and Thomas A. Kunkel
Regulation of B family DNA polymerase fidelity by a conserved active site residue: characterization of M644W, M644L and M644F mutants of yeast DNA polymerase {varepsilon}
Nucleic Acids Research Advance Access published on April 22, 2007
Nucl. Acids Res. 2007 35: 3076-3086; doi:10.1093/nar/gkm132 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Zunyi Yang, A. Michael Sismour, and Steven A. Benner
Nucleoside alpha-thiotriphosphates, polymerases and the exonuclease III analysis of oligonucleotides containing phosphorothioate linkages
Nucleic Acids Research Advance Access published on April 22, 2007
Nucl. Acids Res. 2007 35: 3118-3127; doi:10.1093/nar/gkm168 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

RNA:Back

Faqing Yuan, Laura Griffin, LauraJane Phelps, Volker Buschmann, Kenneth Weston, and Nancy L. Greenbaum
Use of a novel Förster resonance energy transfer method to identify locations of site-bound metal ions in the U2–U6 snRNA complex
Nucleic Acids Research Advance Access published on April 11, 2007
Nucl. Acids Res. 2007 35: 2833-2845; doi:10.1093/nar/gkm134 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jan Krützfeldt, Satoru Kuwajima, Ravi Braich, Kallanthottathil G. Rajeev, John Pena, Thomas Tuschl, Muthiah Manoharan, and Markus Stoffel
Specificity, duplex degradation and subcellular localization of antagomirs
Nucleic Acids Research Advance Access published on April 16, 2007
Nucl. Acids Res. 2007 35: 2885-2892; doi:10.1093/nar/gkm024 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Joon-Hwa Lee and Arthur Pardi
Thermodynamics and kinetics for base-pair opening in the P1 duplex of the Tetrahymena group I ribozyme
Nucleic Acids Research Advance Access published on April 16, 2007
Nucl. Acids Res. 2007 35: 2965-2974; doi:10.1093/nar/gkm184 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Takbum Ohn, Yueh-Chin Chiang, Darren J. Lee, Gang Yao, Chongxu Zhang, and Clyde L. Denis
CAF1 plays an important role in mRNA deadenylation separate from its contact to CCR4
Nucleic Acids Research Advance Access published on April 16, 2007
Nucl. Acids Res. 2007 35: 3002-3015; doi:10.1093/nar/gkm196 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

F. Allemand, J. Haentjens, C. Chiaruttini, C. Royer, and M. Springer
Escherichia coli ribosomal protein L20 binds as a single monomer to its own mRNA bearing two potential binding sites
Nucleic Acids Research Advance Access published on April 16, 2007
Nucl. Acids Res. 2007 35: 3016-3031; doi:10.1093/nar/gkm197 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nelly Piton, Yuguang Mu, Gerhard Stock, Thomas F. Prisner, Olav Schiemann, and Joachim W. Engels
Base-specific spin-labeling of RNA for structure determination
Nucleic Acids Research Advance Access published on April 22, 2007
Nucl. Acids Res. 2007 35: 3128-3143; doi:10.1093/nar/gkm169 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Alexander P. Gultyaev and Andreas Roussis
Identification of conserved secondary structures and expansion segments in enod40 RNAs reveals new enod40 homologues in plants
Nucleic Acids Research Advance Access published on April 22, 2007
Nucl. Acids Res. 2007 35: 3144-3152; doi:10.1093/nar/gkm173 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Structural Biology:Back

Xun-Cheng Su, Slobodan Jergic, Max A. Keniry, Nicholas E. Dixon, and Gottfried Otting
Solution structure of Domains IVa and V of the {tau} subunit of Escherichia coli DNA polymerase III and interaction with the {alpha} subunit
Nucleic Acids Research Advance Access published on April 22, 2007
Nucl. Acids Res. 2007 35: 2825-2832; doi:10.1093/nar/gkm080 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Chunlai Chen, Wenjuan Wang, Zhang Wang, Fang Wei, and Xin Sheng Zhao
Influence of secondary structure on kinetics and reaction mechanism of DNA hybridization
Nucleic Acids Research Advance Access published on April 11, 2007
Nucl. Acids Res. 2007 35: 2875-2884; doi:10.1093/nar/gkm177 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

José Gallego and David Loakes
Solution structure and dynamics of DNA duplexes containing the universal base analogues 5-nitroindole and 5-nitroindole 3-carboxamide
Nucleic Acids Research Advance Access published on April 16, 2007
Nucl. Acids Res. 2007 35: 2904-2912; doi:10.1093/nar/gkm074 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Giovanni Chillemi, Alessandro Bruselles, Paola Fiorani, Susana Bueno, and Alessandro Desideri
The open state of human topoisomerase I as probed by molecular dynamics simulation
Nucleic Acids Research Advance Access published on April 16, 2007
Nucl. Acids Res. 2007 35: 3032-3038; doi:10.1093/nar/gkm199 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Julien Gros, Frédéric Rosu, Samir Amrane, Anne De Cian, Valérie Gabelica, Laurent Lacroix, and Jean-Louis Mergny
Guanines are a quartet's best friend: impact of base substitutions on the kinetics and stability of tetramolecular quadruplexes
Nucleic Acids Research Advance Access published on April 22, 2007
Nucl. Acids Res. 2007 35: 3064-3075; doi:10.1093/nar/gkm111 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Anette Thyssen Jonstrup, Kasper R. Andersen, Lan B. Van, and Ditlev E. Brodersen
The 1.4-Å crystal structure of the S. pombe Pop2p deadenylase subunit unveils the configuration of an active enzyme
Nucleic Acids Research Advance Access published on April 22, 2007
Nucl. Acids Res. 2007 35: 3153-3164; doi:10.1093/nar/gkm178 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:Back

Zahra Hassani, Jean-Christophe François, Gladys Alfama, Ghislaine Morvan Dubois, Mathilde Paris, Carine Giovannangeli, and Barbara A. Demeneix
A hybrid CMV-H1 construct improves efficiency of PEI-delivered shRNA in the mouse brain
Nucleic Acids Research Advance Access published on April 10, 2007
Nucl. Acids Res. 2007 35: e65; doi:10.1093/nar/gkm152 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ivan Brukner, Razan El-Ramahi, Izabella Gorska-Flipot, Maja Krajinovic, and Damian Labuda
An in vitro selection scheme for oligonucleotide probes to discriminate between closely related DNA sequences
Nucleic Acids Research Advance Access published on April 10, 2007
Nucl. Acids Res. 2007 35: e66; doi:10.1093/nar/gkm156 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jørn R. Henriksen, Cecilie Løkke, Martin Hammerø, Dirk Geerts, Rogier Versteeg, Trond Flægstad, and Christer Einvik
Comparison of RNAi efficiency mediated by tetracycline-responsive H1 and U6 promoter variants in mammalian cell lines
Nucleic Acids Research Advance Access published on April 10, 2007
Nucl. Acids Res. 2007 35: e67; doi:10.1093/nar/gkm193 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yuan Yao, Quan Wang, Yu-hua Hao, and Zheng Tan
An exonuclease I hydrolysis assay for evaluating G-quadruplex stabilization by small molecules
Nucleic Acids Research Advance Access published on April 10, 2007
Nucl. Acids Res. 2007 35: e68; doi:10.1093/nar/gkm194 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Taesung Park, Youngchul Kim, Stefan Bekiranov, and Jae K. Lee
Error-pooling-based statistical methods for identifying novel temporal replication profiles of human chromosomes observed by DNA tiling arrays
Nucleic Acids Research Advance Access published on April 11, 2007
Nucl. Acids Res. 2007 35: e69; doi:10.1093/nar/gkm130 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Alex E. Pozhitkov, Robert D. Stedtfeld, Syed A. Hashsham, and Peter A. Noble
Revision of the nonequilibrium thermal dissociation and stringent washing approaches for identification of mixed nucleic acid targets by microarrays
Nucleic Acids Research Advance Access published on April 11, 2007
Nucl. Acids Res. 2007 35: e70; doi:10.1093/nar/gkm154 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Paul Chuchana, Dorian Marchand, Mélanie Nugoli, Carmen Rodriguez, Nicolas Molinari, and Jose A. Garcia-Sanz
An adaptation of the LMS method to determine expression variations in profiling data
Nucleic Acids Research Advance Access published on April 25, 2007
Nucl. Acids Res. 2007 35: e71; doi:10.1093/nar/gkm093 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Corrigendum:Back

Bernard A. Konfortov, Alan T. Bankier, and Paul H. Dear
An efficient method for multi-locus molecular haplotyping
Nucleic Acids Research Advance Access published on April 10, 2007
Nucl. Acids Res. 2007 35: 3165; doi:10.1093/nar/gkm185 [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.