Nucleic Acids Research

Survey and Summary

Get checked abstract Igor D. Vilfan, Wiecher Kamping, Michiel van den Hout, Andrea Candelli, Susanne Hage, and Nynke H. Dekker

An RNA toolbox for single-molecule force spectroscopy studies
Nucleic Acids Research Advance Access published on September 28, 2007
Nucl. Acids Res. 2007 35: 6625-6639; doi:10.1093/nar/gkm585 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Chemistry

Get checked abstract Weidong Wu, Brian P. Stupi, Vladislav A. Litosh, Dena Mansouri, Demetra Farley, Sidney Morris, Sherry Metzker, and Michael L. Metzker

Termination of DNA synthesis by N⁶-alkylated, not 3'-O-alkylated, photocleavable 2'-deoxyadenosine triphosphates
Nucleic Acids Research Advance Access published on September 18, 2007
Nucl. Acids Res. 2007 35: 6339-6349; doi:10.1093/nar/gkm689 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Computational Biology

Get checked abstract Alexander E. Vinogradov and Olga V. Anatskaya

Organismal complexity, cell differentiation and gene expression: human over mouse
Nucleic Acids Research Advance Access published on September 18, 2007
Nucl. Acids Res. 2007 35: 6350-6356; doi:10.1093/nar/gkm723 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Genomics

Get checked abstract Torsten Werner, Alexander Hammer, Mandy Wahlbuhl, Michael R. Bösl, and Michael Wegner

Multiple conserved regulatory elements with overlapping functions determine Sox10 expression in mouse embryogenesis
Nucleic Acids Research Advance Access published on September 26, 2007
Nucl. Acids Res. 2007 35: 6526-6538; doi:10.1093/nar/gkm727 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jian-Min Sun, Hou Yu Chen, Paula S. Espino, and James R. Davie

Phosphorylated serine 28 of histone H3 is associated with destabilized nucleosomes in transcribed chromatin
Nucleic Acids Research Advance Access published on October 2, 2007
Nucl. Acids Res. 2007 35: 6640-6647; doi:10.1093/nar/gkm737 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Molecular Biology

Get checked abstract Hirohide Saito, Shunnichi Kashida, Tan Inoue, and Kiyotaka Shiba

The role of peptide motifs in the evolution of a protein network
Nucleic Acids Research Advance Access published on September 18, 2007
Nucl. Acids Res. 2007 35: 6357-6366; doi:10.1093/nar/gkm692 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Dilrukshi K. Ekanayake, Michael J. Cipriano, and Robert Sabatini

Telomeric co-localization of the modified base J and contingency genes in the protozoan parasite Trypanosoma cruzi
Nucleic Acids Research Advance Access published on September 18, 2007
Nucl. Acids Res. 2007 35: 6367-6377; doi:10.1093/nar/gkm693 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Benjamin J. Boese and Ronald R. Breaker

In vitro selection and characterization of cellulose-binding DNA aptamers
Nucleic Acids Research Advance Access published on September 18, 2007
Nucl. Acids Res. 2007 35: 6378-6388; doi:10.1093/nar/gkm708 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Anne K. Hyvärinen, Jaakko L. O. Pohjoismäki, Aurelio Reyes, Sjoerd Wanrooij, Takehiro Yasukawa, Pekka J. Karhunen, Johannes N. Spelbrink, Ian J. Holt, and Howard T. Jacobs

The mitochondrial transcription termination factor mTERF modulates replication pausing in human mitochondrial DNA
Nucleic Acids Research Advance Access published on September 20, 2007
Nucl. Acids Res. 2007 35: 6458-6474; doi:10.1093/nar/gkm676 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Michelle L. Heacock, Rachel A. Idol, Joanna D. Friesner, Anne B. Britt, and Dorothy E. Shippen

Telomere dynamics and fusion of critically shortened telomeres in plants lacking DNA ligase IV
Nucleic Acids Research Advance Access published on September 25, 2007
Nucl. Acids Res. 2007 35: 6490-6500; doi:10.1093/nar/gkm472 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Qing Bai, Jessica A. Garver, Neil A. Hukriede, and Edward A. Burton

Generation of a transgenic zebrafish model of Tauopathy using a novel promoter element derived from the zebrafish eno2 gene
Nucleic Acids Research Advance Access published on September 25, 2007
Nucl. Acids Res. 2007 35: 6501-6516; doi:10.1093/nar/gkm608 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Felipe Cortés-Ledesma, Cristina Tous, and Andrés Aguilera

Different genetic requirements for repair of replication-born double-strand breaks by sister-chromatid recombination and break-induced replication
Nucleic Acids Research Advance Access published on September 28, 2007
Nucl. Acids Res. 2007 35: 6560-6570; doi:10.1093/nar/gkm488 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Lydia Messaoudi, Yun-Gui Yang, Aiko Kinomura, Diana A. Stavreva, Gonghong Yan, Marie-Line Bortolin-Cavaillé, Hiroshi Arakawa, Jean-Marie Buerstedde, Pierre Hainaut, Jérome Cavaillé, Minoru Takata, and Eric Van Dyck

Subcellular distribution of human RDM1 protein isoforms and their nucleolar accumulation in response to heat shock and proteotoxic stress
Nucleic Acids Research Advance Access published on September 28, 2007
Nucl. Acids Res. 2007 35: 6571-6587; doi:10.1093/nar/gkm753 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Eva Sjøttem, Cecilie Rekdal, Gunbjørg Svineng, Sylvia Sagen Johnsen, Helle Klenow, Rebecca Dale Uglehus, and Terje Johansen

The ePHD protein SPBP interacts with TopBP1 and together they co-operate to stimulate Ets1-mediated transcription
Nucleic Acids Research Advance Access published on October 2, 2007
Nucl. Acids Res. 2007 35: 6648-6662; doi:10.1093/nar/gkm739 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Aman Husbands, Elizabeth M. Bell, Bin Shuai, Harley M.S. Smith, and Patricia S. Springer

LATERAL ORGAN BOUNDARIES defines a new family of DNA-binding transcription factors and can interact with specific bHLH proteins
Nucleic Acids Research Advance Access published on October 2, 2007
Nucl. Acids Res. 2007 35: 6663-6671; doi:10.1093/nar/gkm775 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes

Get checked abstract Marie-angela I. Economopoulou, Emmanouel G. Fragoulis, and Diamantis C. Sideris

Molecular cloning and characterization of the human RNase , an ortholog of Cc RNase
Nucleic Acids Research Advance Access published on September 18, 2007
Nucl. Acids Res. 2007 35: 6389-6398; doi:10.1093/nar/gkm718 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Gaëlle Demarre, Clara Frumerie, Deshmukh N. Gopaul, and Didier Mazel

Identification of key structural determinants of the IntI1 integron integrase that influence attC x attI1 recombination efficiency
Nucleic Acids Research Advance Access published on September 20, 2007
Nucl. Acids Res. 2007 35: 6475-6489; doi:10.1093/nar/gkm709 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Agnieszka Kwiatek and Andrzej Piekarowicz

The restriction endonuclease R.NmeDI from Neisseria meningitidis that recognizes a palindromic sequence and cuts the DNA on both sides of the recognition sequence
Nucleic Acids Research Advance Access published on September 26, 2007
Nucl. Acids Res. 2007 35: 6539-6546; doi:10.1093/nar/gkm702 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Olga Chilkova, Peter Stenlund, Isabelle Isoz, Carrie M. Stith, Pawel Grabowski, Else-Britt Lundström, Peter M. Burgers, and Erik Johansson

The eukaryotic leading and lagging strand DNA polymerases are loaded onto primer-ends via separate mechanisms but have comparable processivity in the presence of PCNA
Nucleic Acids Research Advance Access published on September 28, 2007
Nucl. Acids Res. 2007 35: 6588-6597; doi:10.1093/nar/gkm741 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Yoke W. Kow, Barry Imhoff, Bernard Weiss, David C. I. Hung, Antreas A. Hindoyan, Randall M. Story, and Steven D. Goodman

Escherichia coli HU protein has a role in the repair of abasic sites in DNA
Nucleic Acids Research Advance Access published on October 4, 2007
Nucl. Acids Res. 2007 35: 6672-6680; doi:10.1093/nar/gkm567 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Hiroyuki Ohshima, Nobutaka Hirano, and Hideo Takahashi

A hexanucleotide sequence (dC₁–dC₆ tract) restricts the dC-specific cleavage of single-stranded DNA by endonuclease IV of bacteriophage T4
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2007 35: 6681-6689; doi:10.1093/nar/gkm721 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

RNA

Get checked abstract Jana Královicová and Igor Vorechovsky

Global control of aberrant splice-site activation by auxiliary splicing sequences: evidence for a gradient in exon and intron definition
Nucleic Acids Research Advance Access published on September 18, 2007
Nucl. Acids Res. 2007 35: 6399-6413; doi:10.1093/nar/gkm680 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Alexey A. Malygin, Natalia M. Parakhnevitch, Anton V. Ivanov, Ian C. Eperon, and Galina G. Karpova

Human ribosomal protein S13 regulates expression of its own gene at the splicing step by a feedback mechanism
Nucleic Acids Research Advance Access published on September 18, 2007
Nucl. Acids Res. 2007 35: 6414-6423; doi:10.1093/nar/gkm701 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Tanya V. Aspinall, James M.B. Gordon, Hayley J. Bennett, Panagiotis Karahalios, John-Paul Bukowski, Scott C. Walker, David R. Engelke, and Johanna M. Avis

Interactions between subunits of Saccharomyces cerevisiae RNase MRP support a conserved eukaryotic RNase P/MRP architecture
Nucleic Acids Research Advance Access published on September 19, 2007
Nucl. Acids Res. 2007 35: 6439-6450; doi:10.1093/nar/gkm553 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Olga M. Alekhina, Konstantin S. Vassilenko, and Alexander S. Spirin

Translation of non-capped mRNAs in a eukaryotic cell-free system: acceleration of initiation rate in the course of polysome formation
Nucleic Acids Research Advance Access published on September 26, 2007
Nucl. Acids Res. 2007 35: 6547-6559; doi:10.1093/nar/gkm725 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Timothy A. Vickers, Walt F. Lima, Josh G. Nichols, and Stanley T. Crooke

Reduced levels of Ago2 expression result in increased siRNA competition in mammalian cells
Nucleic Acids Research Advance Access published on September 28, 2007
Nucl. Acids Res. 2007 35: 6598-6610; doi:10.1093/nar/gkm663 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology

Get checked abstract Feng Li, Pradeep S. Pallan, Martin A. Maier, Kallanthottathil G. Rajeev, Steven L. Mathieu, Christoph Kreutz, Yupeng Fan, Jayodita Sanghvi, Ronald Micura, Eriks Rozners, Muthiah Manoharan, and Martin Egli

Crystal structure, stability and in vitro RNAi activity of oligoribonucleotides containing the ribo-difluorotoluyl nucleotide: insights into substrate requirements by the human RISC Ago2 enzyme
Nucleic Acids Research Advance Access published on September 18, 2007
Nucl. Acids Res. 2007 35: 6424-6438; doi:10.1093/nar/gkm664 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Cyril M. Sanders, Oleg V. Kovalevskiy, Dmytro Sizov, Andrey A. Lebedev, Michail N. Isupov, and Alfred A. Antson

Papillomavirus E1 helicase assembly maintains an asymmetric state in the absence of DNA and nucleotide cofactors
Nucleic Acids Research Advance Access published on September 19, 2007
Nucl. Acids Res. 2007 35: 6451-6457; doi:10.1093/nar/gkm705 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Anh Tuân Phan, Vitaly Kuryavyi, Kim Ngoc Luu, and Dinshaw J. Patel

Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K⁺ solution
Nucleic Acids Research Advance Access published on September 25, 2007
Nucl. Acids Res. 2007 35: 6517-6525; doi:10.1093/nar/gkm706 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Pradeep S. Pallan, Paolo Lubini, Martin Bolli, and Martin Egli

Backbone-base inclination as a fundamental determinant of nucleic acid self- and cross-pairing
Nucleic Acids Research Advance Access published on September 28, 2007
Nucl. Acids Res. 2007 35: 6611-6624; doi:10.1093/nar/gkm612 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Methods Online

Get checked abstract Masahito Hayashi and Yoshie Harada

Direct observation of the reversible unwinding of a single DNA molecule caused by the intercalation of ethidium bromide
Nucleic Acids Research Advance Access published on September 28, 2007
Nucl. Acids Res. 2007 35: e125; doi:10.1093/nar/gkm529 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Yanwen Xu, Gang Xu, Bindong Liu, and Guoqiang Gu

Cre reconstitution allows for DNA recombination selectively in dual-marker-expressing cells in transgenic mice
Nucleic Acids Research Advance Access published on September 24, 2007
Nucl. Acids Res. 2007 35: e126; doi:10.1093/nar/gkm559 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Haukur Gudnason, Martin Dufva, D.D. Bang, and Anders Wolff

Comparison of multiple DNA dyes for real-time PCR: effects of dye concentration and sequence composition on DNA amplification and melting temperature
Nucleic Acids Research Advance Access published on September 26, 2007
Nucl. Acids Res. 2007 35: e127; doi:10.1093/nar/gkm671 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Fabiana Perocchi, Zhenyu Xu, Sandra Clauder-Münster, and Lars M. Steinmetz

Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D
Nucleic Acids Research Advance Access published on September 26, 2007
Nucl. Acids Res. 2007 35: e128; doi:10.1093/nar/gkm683 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Yizhi Song, Thomas Hahn, Ian P. Thompson, Timothy J. Mason, Gail M. Preston, Guanghe Li, Larysa Paniwnyk, and Wei E. Huang

Ultrasound-mediated DNA transfer for bacteria
Nucleic Acids Research Advance Access published on September 22, 2007
Nucl. Acids Res. 2007 35: e129; doi:10.1093/nar/gkm710 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Poornima Parameswaran, Roxana Jalili, Li Tao, Shadi Shokralla, Baback Gharizadeh, Mostafa Ronaghi, and Andrew Z. Fire

A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2007 35: e130; doi:10.1093/nar/gkm760 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Giulia Amicarelli, Erlet Shehi, G. Mike Makrigiorgos, and Daniel Adlerstein

FLAG assay as a novel method for real-time signal generation during PCR: application to detection and genotyping of KRAS codon 12 mutations
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2007 35: e131; doi:10.1093/nar/gkm809 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Hedda A. Meijer, Martin Bushell, Kirsti Hill, Timothy W. Gant, Anne E. Willis, Peter Jones, and Cornelia H. de Moor

A novel method for poly(A) fractionation reveals a large population of mRNAs with a short poly(A) tail in mammalian cells
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2007 35: e132; doi:10.1093/nar/gkm830 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Benedict J. Kemp, Julia Hatzold, Laura A. Sternick, Joshua Cornman-Homonoff, Jessica M. Whitaker, Pamela J. Tieu, and Eric J. Lambie

In vivo construction of recombinant molecules within the Caenorhabditis elegans germ line using short regions of terminal homology
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2007 35: e133; doi:10.1093/nar/gkm857 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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