Nucl. Acids Res. -- Nucleic Acids Research Advance Access

Nucleic Acids Research Advance Access

Nucleic Acids Research Advance Access articles are papers that have been copyedited and typeset but not yet paginated for inclusion in an issue of the journal. More information, including how to cite Advance Access papers, can be found on the Advance Access page.

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4 September 2008

Abstract Molecular Biology: Leila Shokri, Boriana Marintcheva, Mootaz Eldib, Andreas Hanke, Ioulia Rouzina, and Mark C. Williams
Kinetics and thermodynamics of salt-dependent T7 gene 2.5 protein binding to single- and double-stranded DNA
Nucleic Acids Research Advance Access published on September 4, 2008.
doi:10.1093/nar/gkn551
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Abstract Molecular Biology: Carmen Losasso, Erica Cretaio, Paola Fiorani, Ilda D’Annessa, Giovanni Chillemi, and Piero Benedetti
A single mutation in the 729 residue modulates human DNA topoisomerase IB DNA binding and drug resistance
Nucleic Acids Research Advance Access published on September 4, 2008.
doi:10.1093/nar/gkn557
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Genomic Integrity, repair and replication: Nasim Sabouri, Jörgen Viberg, Dinesh Kumar Goyal, Erik Johansson, and Andrei Chabes
Evidence for lesion bypass by yeast replicative DNA polymerases during DNA damage
Nucleic Acids Research Advance Access published on September 4, 2008.
doi:10.1093/nar/gkn555
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Abstract Survey and Summary: Andrea Kinner, Wenqi Wu, Christian Staudt, and George Iliakis
${gamma}$ -H2AX in recognition and signaling of DNA double-strand breaks in the context of chromatin
Nucleic Acids Research Advance Access published on September 4, 2008.
doi:10.1093/nar/gkn550
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2 September 2008

Abstract Molecular Biology: Giovanni Chillemi, Ilda D’Annessa, Paola Fiorani, Carmen Losasso, Piero Benedetti, and Alessandro Desideri
Thr729 in human topoisomerase I modulates anti-cancer drug resistance by altering protein domain communications as suggested by molecular dynamics simulations
Nucleic Acids Research Advance Access published on September 2, 2008.
doi:10.1093/nar/gkn558
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Abstract Methods Online: Xiaochun Fan, Nathan Lamarre-Vincent, Qian Wang, and Kevin Struhl
Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments
Nucleic Acids Research Advance Access published on September 2, 2008.
doi:10.1093/nar/gkn535
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Genome integrity, repair and replication: Hélène Labit, Irène Perewoska, Thomas Germe, Olivier Hyrien, and Kathrin Marheineke
DNA replication timing is deterministic at the level of chromosomal domains but stochastic at the level of replicons in Xenopus egg extracts
Nucleic Acids Research Advance Access published on September 2, 2008.
doi:10.1093/nar/gkn533
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Abstract RNA: Stacy Miller, Laura E. Jones, Karen Giovannitti, Dan Piper, and Martin J. Serra
Thermodynamic analysis of 5' and 3' single- and 3' double-nucleotide overhangs neighboring wobble terminal base pairs
Nucleic Acids Research Advance Access published on September 2, 2008.
doi:10.1093/nar/gkn525
[Abstract] [Full Text] [Print PDF] [Screen PDF]

30 August 2008

Abstract Nucleic Acid Enzymes: Gyri Teien Haugland, Nozomi Sakakibara, Angel L. Pey, Claire R. Rollor, Nils-Kåre Birkeland, and Zvi Kelman
Thermoplasma acidophilum Cdc6 protein stimulates MCM helicase activity by regulating its ATPase activity
Nucleic Acids Research Advance Access published on August 30, 2008.
doi:10.1093/nar/gkn548
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Computational Biology: Mounir Errami, Zhaohui Sun, Tara C. Long, Angela C. George, and Harold R. Garner
Déjà vu: a database of highly similar citations in the scientific literature
Nucleic Acids Research Advance Access published on August 30, 2008.
doi:10.1093/nar/gkn546
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Chemistry and Synthetic Biology: Yasuko Osakada, Kiyohiko Kawai, Mamoru Fujitsuka, and Tetsuro Majima
Kinetics of charge transfer in DNA containing a mismatch
Nucleic Acids Research Advance Access published on August 30, 2008.
doi:10.1093/nar/gkn505
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Structural Biology: Niti Kumar and Souvik Maiti
A thermodynamic overview of naturally occurring intramolecular DNA quadruplexes
Nucleic Acids Research Advance Access published on August 30, 2008.
doi:10.1093/nar/gkn543
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Molecular Biology: Maren Mierau, Guido A. Drexler, André Kutzera, Kerstin Braunschmidt, Joachim Ellwart, Friederike Eckardt-Schupp, Eberhard Fritz, Jürgen Bachl, and Berit Jungnickel
Non-conservative homologous recombination in human B lymphocytes is promoted by activation-induced cytidine deaminase and transcription
Nucleic Acids Research Advance Access published on August 30, 2008.
doi:10.1093/nar/gkn542
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Abstract Molecular biology: Ju Youn Lee, Zhe Ji, and Bin Tian
Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3'-end of genes
Nucleic Acids Research Advance Access published on August 30, 2008.
doi:10.1093/nar/gkn540
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Gene regulation, Chromatin and Epigenetics: Michelle M. Thiaville, Elizabeth E. Dudenhausen, Keytam S. Awad, Altin Gjymishka, Can Zhong, and Michael S. Kilberg
Activated transcription via mammalian amino acid response elements does not require enhanced recruitment of the Mediator complex
Nucleic Acids Research Advance Access published on August 30, 2008.
doi:10.1093/nar/gkn538
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

28 August 2008

Abstract RNA: Pratik Home, Saikat Mukherjee, and Samit Adhya
A mosaic of RNA binding and protein interaction motifs in a bifunctional mitochondrial tRNA import factor from Leishmania tropica
Nucleic Acids Research Advance Access published on August 28, 2008.
doi:10.1093/nar/gkn536
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Molecular Biology: Aaron Wynveen, Dominic J. Lee, Alexei A. Kornyshev, and Sergey Leikin
Helical coherence of DNA in crystals and solution
Nucleic Acids Research Advance Access published on August 28, 2008.
doi:10.1093/nar/gkn514
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

27 August 2008

Abstract Methods Online: Juliane Neupert, Daniel Karcher, and Ralph Bock
Design of simple synthetic RNA thermometers for temperature-controlled gene expression in Escherichia coli
Nucleic Acids Research Advance Access published on August 27, 2008.
doi:10.1093/nar/gkn545
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Methods Online: Yang-Wei Lin, Hsin-Tsung Ho, Chih-Ching Huang, and Huan-Tsung Chang
Fluorescence detection of single nucleotide polymorphisms using a universal molecular beacon
Nucleic Acids Research Advance Access published on August 27, 2008.
doi:10.1093/nar/gkn537
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract RNA: Nikolay G. Kolev, Emilia I. Hartland, and Paul W. Huber
A manganese-dependent ribozyme in the 3'-untranslated region of Xenopus Vg1 mRNA
Nucleic Acids Research Advance Access originally published on August 27, 2008. This version published August 28, 2008.
doi:10.1093/nar/gkn530
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Methods Online: Richard Cronn, Aaron Liston, Matthew Parks, David S. Gernandt, Rongkun Shen, and Todd Mockler
Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology
Nucleic Acids Research Advance Access published on August 27, 2008.
doi:10.1093/nar/gkn502
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

22 August 2008

Abstract Nucleic Acid Enzymes: Xiao Su Pan, Miriam Dias, Manlio Palumbo, and L. Mark Fisher
Clerocidin selectively modifies the gyrase-DNA gate to induce irreversible and reversible DNA damage
Nucleic Acids Research Advance Access published on August 22, 2008.
doi:10.1093/nar/gkn539
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Methods Online: John G. K. Williams, David L. Steffens, Jon P. Anderson, Teresa M. Urlacher, Donald T. Lamb, Daniel L. Grone, and Jolene C. Egelhoff
An artificial processivity clamp made with streptavidin facilitates oriented attachment of polymerase–DNA complexes to surfaces
Nucleic Acids Research Advance Access published on August 22, 2008.
doi:10.1093/nar/gkn531
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods Online: Zongzhi Liu, Todd Z. DeSantis, Gary L. Andersen, and Rob Knight
Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers
Nucleic Acids Research Advance Access published on August 22, 2008.
doi:10.1093/nar/gkn491
[Abstract] [Full Text] [Print PDF] [Screen PDF]

21 August 2008

Abstract Nucleic Acid Enzymes: Christof Maucksch, Manish Kumar Aneja, Elisabeth Hennen, Alexander Bohla, Florian Hoffmann, Markus Elfinger, Joseph Rosenecker, and Carsten Rudolph
Cell type differences in activity of the Streptomyces bacteriophage ${phi}$ C31 integrase
Nucleic Acids Research Advance Access published on August 21, 2008.
doi:10.1093/nar/gkn532
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract RNA: Ashley A. Frazer-Abel and Paul J. Hagerman
Core flexibility of a truncated metazoan mitochondrial tRNA
Nucleic Acids Research Advance Access published on August 21, 2008.
doi:10.1093/nar/gkn529
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Genome Integrity, Repair and Replication: Erwin van den Born, Marina V. Omelchenko, Anders Bekkelund, Vibeke Leihne, Eugene V. Koonin, Valerian V. Dolja, and Pål Ø. Falnes
Viral AlkB proteins repair RNA damage by oxidative demethylation
Nucleic Acids Research Advance Access published on August 21, 2008.
doi:10.1093/nar/gkn519
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Structural biology: Andrew N. Lane, J. Brad Chaires, Robert D. Gray, and John O. Trent
Stability and kinetics of G-quadruplex structures
Nucleic Acids Research Advance Access published on August 21, 2008.
doi:10.1093/nar/gkn517
[Abstract] [Full Text] [Print PDF] [Screen PDF]

20 August 2008

Abstract Methods Online: Eoin P. Quinlivan and Jesse F. Gregory III
DNA methylation determination by liquid chromatography–tandem mass spectrometry using novel biosynthetic [U-¹⁵N]deoxycytidine and [U-¹⁵N]methyldeoxycytidine internal standards
Nucleic Acids Research Advance Access published on August 20, 2008.
doi:10.1093/nar/gkn534
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Nucleic Acid Enzymes: Michael A. Carpenter and Ashok S. Bhagwat
DNA base flipping by both members of the PspGI restriction–modification system
Nucleic Acids Research Advance Access published on August 20, 2008.
doi:10.1093/nar/gkn528
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Molecular Biology: Naoyuki Sarai, Wataru Kagawa, Norie Fujikawa, Kengo Saito, Juri Hikiba, Kozo Tanaka, Kiyoshi Miyagawa, Hitoshi Kurumizaka, and Shigeyuki Yokoyama
Biochemical analysis of the N-terminal domain of human RAD54B
Nucleic Acids Research Advance Access published on August 20, 2008.
doi:10.1093/nar/gkn516
[Abstract] [Full Text] [Print PDF] [Screen PDF]

18 August 2008

Abstract Methods Online: Dany Morisset, David Dobnik, Sandrine Hamels, Jana Zel, and Kristina Gruden
NAIMA: target amplification strategy allowing quantitative on-chip detection of GMOs
Nucleic Acids Research Advance Access published on August 18, 2008.
doi:10.1093/nar/gkn524
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Methods Online: Jian Qin, Robert C. Jones, and Ramesh Ramakrishnan
Studying copy number variations using a nanofluidic platform
Nucleic Acids Research Advance Access published on August 18, 2008.
doi:10.1093/nar/gkn518
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods Online: Simon J. Furney, Borja Calvo, Pedro Larrañaga, Jose A. Lozano, and Nuria Lopez-Bigas
Prioritization of candidate cancer genes—an aid to oncogenomic studies
Nucleic Acids Research Advance Access published on August 18, 2008.
doi:10.1093/nar/gkn482
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods Online: Julio Gómez-Rodríguez, Valance Washington, Jun Cheng, Amalia Dutra, Evgenia Pak, Pentao Liu, Daniel W. McVicar, and Pamela L. Schwartzberg
Advantages of q-PCR as a method of screening for gene targeting in mammalian cells using conventional and whole BAC-based constructs
Nucleic Acids Research Advance Access published on August 18, 2008.
doi:10.1093/nar/gkn523
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

14 August 2008

Abstract Gene regulation, Chromatin and Epigenetics: C. Claus Stolt, Petra Lommes, Simone Hillgärtner, and Michael Wegner
The transcription factor Sox5 modulates Sox10 function during melanocyte development
Nucleic Acids Research Advance Access published on August 14, 2008.
doi:10.1093/nar/gkn527
[Abstract] [Full Text] [Print PDF] [Screen PDF]

13 August 2008

Abstract Methods Online: Jun Fu, Silke C. Wenzel, Olena Perlova, Junping Wang, Frank Gross, Zhiru Tang, Yulong Yin, A. Francis Stewart, Rolf Müller, and Youming Zhang
Efficient transfer of two large secondary metabolite pathway gene clusters into heterologous hosts by transposition
Nucleic Acids Research Advance Access published on August 13, 2008.
doi:10.1093/nar/gkn499
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract RNA: Qin Liu, Hanjiang Fu, Fang Sun, Haoming Zhang, Yi Tie, Jie Zhu, Ruiyun Xing, Zhixian Sun, and Xiaofei Zheng
miR-16 family induces cell cycle arrest by regulating multiple cell cycle genes
Nucleic Acids Research Advance Access published on August 13, 2008.
doi:10.1093/nar/gkn522
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Computational Biology: Jiajian Liu, Xing Xu, and Gary D. Stormo
The cis-regulatory map of Shewanella genomes
Nucleic Acids Research Advance Access published on August 13, 2008.
doi:10.1093/nar/gkn515
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Structural Biology: Pete W. Dunten, Elizabeth J. Little, Mark T. Gregory, Veena M. Manohar, Michael Dalton, David Hough, Jurate Bitinaite, and Nancy C. Horton
The structure of SgrAI bound to DNA; recognition of an 8 base pair target
Nucleic Acids Research Advance Access published on August 13, 2008.
doi:10.1093/nar/gkn510
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

12 August 2008

Abstract Gene Regulation, Chromatin and Epigenetics: Catherine Teyssier, Stéphanie Bianco, Olivia Lanvin, and Jean-Marc Vanacker
The orphan receptor ERR ${alpha}$ interferes with steroid signaling
Nucleic Acids Research Advance Access published on August 12, 2008.
doi:10.1093/nar/gkn520
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Genome integrity, repair and replication: Anja Restle, Martin Färber, Cindy Baumann, Michael Böhringer, Karl Heinz Scheidtmann, Carsten Müller-Tidow, and Lisa Wiesmüller
Dissecting the role of p53 phosphorylation in homologous recombination provides new clues for gain-of-function mutants
Nucleic Acids Research Advance Access published on August 12, 2008.
doi:10.1093/nar/gkn503
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods Online: Nigel M. Williams, Hywel Williams, Elisa Majounie, Nadine Norton, Beate Glaser, Huw R. Morris, Michael J. Owen, and Michael C. O’Donovan
Analysis of copy number variation using quantitative interspecies competitive PCR
Nucleic Acids Research Advance Access published on August 12, 2008.
doi:10.1093/nar/gkn495
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

9 August 2008

Abstract Molecular Biology: Na Liu, Lifeng Wang, Xia Li, Qi Yang, Xinping Liu, Jing Zhang, Jian Zhang, Yousheng Wu, Shaoping Ji, Yingqi Zhang, Angang Yang, Hua Han, and Libo Yao
N-Myc downstream-regulated gene 2 is involved in p53-mediated apoptosis
Nucleic Acids Research Advance Access published on August 9, 2008.
doi:10.1093/nar/gkn504
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

8 August 2008

Abstract Nucleic Acid Enzymes: Kevin V. Kepple, Namita Patel, Peter Salamon, and Anca M. Segall
Interactions between branched DNAs and peptide inhibitors of DNA repair
Nucleic Acids Research Advance Access published on August 8, 2008.
doi:10.1093/nar/gkn512
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Molecular Biology: Tariq Perwez, Danyal Hami, Valerie F. Maples, Zhao Min, Bi-Cheng Wang, and Sidney R. Kushner
Intragenic suppressors of temperature-sensitive rne mutations lead to the dissociation of RNase E activity on mRNA and tRNA substrates in Escherichia coli
Nucleic Acids Research Advance Access published on August 8, 2008.
doi:10.1093/nar/gkn476
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Molecular Biology: Munehiko Asayama and Sousuke Imamura
Stringent promoter recognition and autoregulation by the group 3 ${sigma}$ -factor SigF in the cyanobacterium Synechocystis sp. strain PCC 6803
Nucleic Acids Research Advance Access published on August 8, 2008.
doi:10.1093/nar/gkn453
[Abstract] [Full Text] [Print PDF] [Screen PDF]

6 August 2008

Abstract Gene regulation, Chromatin and Epigenetics: Sailen Barik
An intronic microRNA silences genes that are functionally antagonistic to its host gene
Nucleic Acids Research Advance Access published on August 6, 2008.
doi:10.1093/nar/gkn513
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract RNA: María Flor García-Mayoral, Irene Díaz-Moreno, David Hollingworth, and Andres Ramos
The sequence selectivity of KSRP explains its flexibility in the recognition of the RNA targets
Nucleic Acids Research Advance Access published on August 6, 2008.
doi:10.1093/nar/gkn509
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract RNA: P. Patrick Dotson II, Ashley K. Johnson, and Stephen M. Testa
Tetrahymena thermophila and Candida albicans Group I intron-derived ribozymes can catalyze the trans-excision-splicing reaction
Nucleic Acids Research Advance Access published on August 6, 2008.
doi:10.1093/nar/gkn507
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Molecular Biology: Junko Kimura, Su Tien Nguyen, Hanshao Liu, Naoe Taira, Yoshio Miki, and Kiyotsugu Yoshida
A functional genome-wide RNAi screen identifies TAF1 as a regulator for apoptosis in response to genotoxic stress
Nucleic Acids Research Advance Access published on August 6, 2008.
doi:10.1093/nar/gkn506
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Molecular Biology: Cristina Cañas, Begoña Carrasco, Silvia Ayora, and Juan C. Alonso
The RecU Holliday junction resolvase acts at early stages of homologous recombination
Nucleic Acids Research Advance Access originally published on August 6, 2008. This version published August 9, 2008.
doi:10.1093/nar/gkn500