Nucleic Acids Research

Chemistry and Synthetic Biology

Get checked abstract Hisao Saneyoshi, Stefania Mazzini, Anna Aviñó, Guillem Portella, Carlos González, Modesto Orozco, Víctor E. Marquez, and Ramon Eritja

Conformationally rigid nucleoside probes help understand the role of sugar pucker and nucleobase orientation in the thrombin-binding aptamer
Nucleic Acids Research Advance Access published on July 20, 2009
Nucl. Acids Res. 2009 37: 5589-5601; doi:10.1093/nar/gkp598 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Shintaro Ogata, Mayumi Takahashi, Noriaki Minakawa, and Akira Matsuda

Unnatural imidazopyridopyrimidine:naphthyridine base pairs: selective incorporation and extension reaction by Deep Vent (exo^– ) DNA polymerase
Nucleic Acids Research Advance Access published on July 23, 2009
Nucl. Acids Res. 2009 37: 5602-5609; doi:10.1093/nar/gkp611 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Computational Biology

Get checked abstract Ricardo A. Verdugo, Christian F. Deschepper, Gloria Muñoz, Daniel Pomp, and Gary A. Churchill

Importance of randomization in microarray experimental designs with Illumina platforms
Nucleic Acids Research Advance Access published on July 17, 2009
Nucl. Acids Res. 2009 37: 5610-5618; doi:10.1093/nar/gkp573 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Yao-Qing Shen, B. Franz Lang, and Gertraud Burger

Diversity and dispersal of a ubiquitous protein family: acyl-CoA dehydrogenases
Nucleic Acids Research Advance Access published on July 22, 2009
Nucl. Acids Res. 2009 37: 5619-5631; doi:10.1093/nar/gkp566 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Wenwei Xiong, Tonghua Li, Kai Chen, and Kailin Tang

Local combinational variables: an approach used in DNA-binding helix-turn-helix motif prediction with sequence information
Nucleic Acids Research Advance Access published on August 3, 2009
Nucl. Acids Res. 2009 37: 5632-5640; doi:10.1093/nar/gkp628 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Gene Regulation, Chromatin and Epigenetics

Get checked abstract Vladimir B. Teif and Karsten Rippe

Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities
Nucleic Acids Research Advance Access published on July 22, 2009
Nucl. Acids Res. 2009 37: 5641-5655; doi:10.1093/nar/gkp610 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jeong Do Kim, Keunsoo Kang, and Joomyeong Kim

YY1's role in DNA methylation of Peg3 and Xist
Nucleic Acids Research Advance Access published on July 23, 2009
Nucl. Acids Res. 2009 37: 5656-5664; doi:10.1093/nar/gkp613 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Dmitri Papatsenko, Yury Goltsev, and Michael Levine

Organization of developmental enhancers in the Drosophila embryo
Nucleic Acids Research Advance Access published on August 3, 2009
Nucl. Acids Res. 2009 37: 5665-5677; doi:10.1093/nar/gkp619 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genome Integrity, Repair and Replication

Get checked abstract Hiroshi Nishida, Naoto Tatewaki, Yuki Nakajima, Taku Magara, Kam Ming Ko, Yasuo Hamamori, and Tetsuya Konishi

Inhibition of ATR protein kinase activity by schisandrin B in DNA damage response
Nucleic Acids Research Advance Access published on July 22, 2009
Nucl. Acids Res. 2009 37: 5678-5689; doi:10.1093/nar/gkp593 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Pierre Boesch, Noha Ibrahim, François Paulus, Anne Cosset, Vladislav Tarasenko, and André Dietrich

Plant mitochondria possess a short-patch base excision DNA repair pathway
Nucleic Acids Research Advance Access published on July 22, 2009
Nucl. Acids Res. 2009 37: 5690-5700; doi:10.1093/nar/gkp606 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract M. Di Re, H. Sembongi, J. He, A. Reyes, T. Yasukawa, P. Martinsson, L. J. Bailey, S. Goffart, J. D. Boyd-Kirkup, T. S. Wong, A. R. Fersht, J. N. Spelbrink, and I. J. Holt

The accessory subunit of mitochondrial DNA polymerase determines the DNA content of mitochondrial nucleoids in human cultured cells
Nucleic Acids Research Advance Access published on July 22, 2009
Nucl. Acids Res. 2009 37: 5701-5713; doi:10.1093/nar/gkp614 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Emmanouil Rampakakis and Maria Zannis-Hadjopoulos

Transient dsDNA breaks during pre-replication complex assembly
Nucleic Acids Research Advance Access published on July 28, 2009
Nucl. Acids Res. 2009 37: 5714-5724; doi:10.1093/nar/gkp617 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Gijsbert P. van Nierop, Antoine A. F. de Vries, Maarten Holkers, Krijn R. Vrijsen, and Manuel A. F. V. Gonçalves

Stimulation of homology-directed gene targeting at an endogenous human locus by a nicking endonuclease
Nucleic Acids Research Advance Access published on August 3, 2009
Nucl. Acids Res. 2009 37: 5725-5736; doi:10.1093/nar/gkp643 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Sheera Adar, Lior Izhar, Ayal Hendel, Nicholas Geacintov, and Zvi Livneh

Repair of gaps opposite lesions by homologous recombination in mammalian cells
Nucleic Acids Research Advance Access published on August 4, 2009
Nucl. Acids Res. 2009 37: 5737-5748; doi:10.1093/nar/gkp632 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Genomics

Get checked abstract Sigve Nakken, Torbjørn Rognes, and Eivind Hovig

The disruptive positions in human G-quadruplex motifs are less polymorphic and more conserved than their neutral counterparts
Nucleic Acids Research Advance Access published on July 17, 2009
Nucl. Acids Res. 2009 37: 5749-5756; doi:10.1093/nar/gkp590 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Brigid M. Davis and Matthew K. Waldor

High-throughput sequencing reveals suppressors of Vibrio cholerae rpoE mutations: one fewer porin is enough
Nucleic Acids Research Advance Access published on July 20, 2009
Nucl. Acids Res. 2009 37: 5757-5767; doi:10.1093/nar/gkp568 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Yoshinao Azuma, Akira Hosoyama, Minenosuke Matsutani, Naoko Furuya, Hiroshi Horikawa, Takeshi Harada, Hideki Hirakawa, Satoru Kuhara, Kazunobu Matsushita, Nobuyuki Fujita, and Mutsunori Shirai

Whole-genome analyses reveal genetic instability of Acetobacter pasteurianus
Nucleic Acids Research Advance Access published on July 28, 2009
Nucl. Acids Res. 2009 37: 5768-5783; doi:10.1093/nar/gkp612 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology

Get checked abstract Jesper Worm, Jan Stenvang, Andreas Petri, Klaus Stensgaard Frederiksen, Susanna Obad, Joacim Elmén, Maj Hedtjärn, Ellen Marie Straarup, Jens Bo Hansen, and Sakari Kauppinen

Silencing of microRNA-155 in mice during acute inflammatory response leads to derepression of c/ebp Beta and down-regulation of G-CSF
Nucleic Acids Research Advance Access published on July 13, 2009
Nucl. Acids Res. 2009 37: 5784-5792; doi:10.1093/nar/gkp577 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes

Get checked abstract Michelle Mitchell, Song Xue, Rachel Erdman, Lennart Randau, Dieter Söll, and Hong Li

Crystal structure and assembly of the functional Nanoarchaeum equitans tRNA splicing endonuclease
Nucleic Acids Research Advance Access published on July 3, 2009
Nucl. Acids Res. 2009 37: 5793-5802; doi:10.1093/nar/gkp537 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Joanna Andrecka, Barbara Treutlein, Maria Angeles Izquierdo Arcusa, Adam Muschielok, Robert Lewis, Alan C. M. Cheung, Patrick Cramer, and Jens Michaelis

Nano positioning system reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex
Nucleic Acids Research Advance Access published on July 20, 2009
Nucl. Acids Res. 2009 37: 5803-5809; doi:10.1093/nar/gkp601 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Laura E. Corina, Weihua Qiu, Ami Desai, and David L. Herrin

Biochemical and mutagenic analysis of I-CreII reveals distinct but important roles for both the H-N-H and GIY-YIG motifs
Nucleic Acids Research Advance Access published on August 3, 2009
Nucl. Acids Res. 2009 37: 5810-5821; doi:10.1093/nar/gkp624 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA

Get checked abstract Stefan Maas and Willemijn M. Gommans

Identification of a selective nuclear import signal in adenosine deaminases acting on RNA
Nucleic Acids Research Advance Access published on July 17, 2009
Nucl. Acids Res. 2009 37: 5822-5829; doi:10.1093/nar/gkp599 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Ahmed M. Wahid, Veronica K. Coventry, and Graeme L. Conn

The PKR-binding domain of adenovirus VA RNA_I exists as a mixture of two functionally non-equivalent structures
Nucleic Acids Research Advance Access published on July 27, 2009
Nucl. Acids Res. 2009 37: 5830-5837; doi:10.1093/nar/gkp595 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Mikhail Schepetilnikov, Gregory Schott, Konstantina Katsarou, Odon Thiébeauld, Mario Keller, and Lyubov A. Ryabova

Molecular dissection of the prototype foamy virus (PFV) RNA 5'-UTR identifies essential elements of a ribosomal shunt
Nucleic Acids Research Advance Access published on July 28, 2009
Nucl. Acids Res. 2009 37: 5838-5847; doi:10.1093/nar/gkp609 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Margherita Doria, Francesca Neri, Angela Gallo, Maria Giulia Farace, and Alessandro Michienzi

Editing of HIV-1 RNA by the double-stranded RNA deaminase ADAR1 stimulates viral infection
Nucleic Acids Research Advance Access published on August 3, 2009
Nucl. Acids Res. 2009 37: 5848-5858; doi:10.1093/nar/gkp604 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Oliver Rackham, Stefan M. K. Davies, Anne-Marie J. Shearwood, Kristina L. Hamilton, James Whelan, and Aleksandra Filipovska

Pentatricopeptide repeat domain protein 1 lowers the levels of mitochondrial leucine tRNAs in cells
Nucleic Acids Research Advance Access published on August 3, 2009
Nucl. Acids Res. 2009 37: 5859-5867; doi:10.1093/nar/gkp627 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Lynda Latrèche, Olivier Jean-Jean, Donna M. Driscoll, and Laurent Chavatte

Novel structural determinants in human SECIS elements modulate the translational recoding of UGA as selenocysteine
Nucleic Acids Research Advance Access published on August 3, 2009
Nucl. Acids Res. 2009 37: 5868-5880; doi:10.1093/nar/gkp635 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Keith A. Spriggs, Laura C. Cobbold, Simon H. Ridley, Mark Coldwell, Andrew Bottley, Martin Bushell, Anne E. Willis, and Kenneth Siddle

The human insulin receptor mRNA contains a functional internal ribosome entry segment
Nucleic Acids Research Advance Access published on August 4, 2009
Nucl. Acids Res. 2009 37: 5881-5893; doi:10.1093/nar/gkp623 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Dustin J. Paul, Steven J. Seedhouse, and Matthew D. Disney

Two-dimensional combinatorial screening and the RNA Privileged Space Predictor program efficiently identify aminoglycoside–RNA hairpin loop interactions
Nucleic Acids Research Advance Access published on September 2, 2009
Nucl. Acids Res. 2009 37: 5894-5907; doi:10.1093/nar/gkp594 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology

Get checked abstract Guangsen Fu, Jinjun Wu, Wei Liu, Deyu Zhu, Yonglin Hu, Jiaoyu Deng, Xian-En Zhang, Lijun Bi, and Da-Cheng Wang

Crystal structure of DNA gyrase B' domain sheds lights on the mechanism for T-segment navigation
Nucleic Acids Research Advance Access published on July 13, 2009
Nucl. Acids Res. 2009 37: 5908-5916; doi:10.1093/nar/gkp586 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract R. Lavery, M. Moakher, J. H. Maddocks, D. Petkeviciute, and K. Zakrzewska

Conformational analysis of nucleic acids revisited: Curves+
Nucleic Acids Research Advance Access published on July 22, 2009
Nucl. Acids Res. 2009 37: 5917-5929; doi:10.1093/nar/gkp608 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Yanyan Zhu, Yan Wang, and Guangju Chen

Differences in conformational dynamics of [Pt₃(HPTAB)]⁶⁺–DNA adducts with various cross-linking modes
Nucleic Acids Research Advance Access published on August 4, 2009
Nucl. Acids Res. 2009 37: 5930-5942; doi:10.1093/nar/gkp618 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online

Get checked abstract Shuwen Wang, Yuanjun Zhao, Melanie A. Leiby, and Jiyue Zhu

Studying human telomerase gene transcription by a chromatinized reporter generated by recombinase-mediated targeting of a bacterial artificial chromosome
Nucleic Acids Research Advance Access published on June 15, 2009
Nucl. Acids Res. 2009 37: e111; doi:10.1093/nar/gkp511 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Éva Hegedüs, Endre Kókai, Alexander Kotlyar, Viktor Dombrádi, and Gábor Szabó

Separation of 1–23-kb complementary DNA strands by urea–agarose gel electrophoresis
Nucleic Acids Research Advance Access published on June 23, 2009
Nucl. Acids Res. 2009 37: e112; doi:10.1093/nar/gkp539 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Geetu Tuteja, Peter White, Jonathan Schug, and Klaus H. Kaestner

Extracting transcription factor targets from ChIP-Seq data
Nucleic Acids Research Advance Access published on June 24, 2009
Nucl. Acids Res. 2009 37: e113; doi:10.1093/nar/gkp536 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Frank H. T. Nelissen, Frederic C. Girard, Marco Tessari, Hans A. Heus, and Sybren S. Wijmenga

Preparation of selective and segmentally labeled single-stranded DNA for NMR by self-primed PCR and asymmetrical endonuclease double digestion
Nucleic Acids Research Advance Access published on June 24, 2009
Nucl. Acids Res. 2009 37: e114; doi:10.1093/nar/gkp540 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Caroline C. Friedel, Lars Dölken, Zsolt Ruzsics, Ulrich H. Koszinowski, and Ralf Zimmer

Conserved principles of mammalian transcriptional regulation revealed by RNA half-life
Nucleic Acids Research Advance Access published on June 26, 2009
Nucl. Acids Res. 2009 37: e115; doi:10.1093/nar/gkp542 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Ana M. Blanco, Laura Rausell, Begoña Aguado, Manuel Perez-Alonso, and Rubén Artero

A FRET-based assay for characterization of alternative splicing events using peptide nucleic acid fluorescence in situ hybridization
Nucleic Acids Research Advance Access published on June 26, 2009
Nucl. Acids Res. 2009 37: e116; doi:10.1093/nar/gkp551 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Lin Wan, Kelian Sun, Qi Ding, Yuehua Cui, Ming Li, Yalu Wen, Robert C. Elston, Minping Qian, and Wenjiang J Fu

Hybridization modeling of oligonucleotide SNP arrays for accurate DNA copy number estimation
Nucleic Acids Research Advance Access published on July 7, 2009
Nucl. Acids Res. 2009 37: e117; doi:10.1093/nar/gkp559 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Dean A. Rowe-Magnus

Integrase-directed recovery of functional genes from genomic libraries
Nucleic Acids Research Advance Access published on July 13, 2009
Nucl. Acids Res. 2009 37: e118; doi:10.1093/nar/gkp561 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Front-Matter/Back-Matter

Nucleic Acids Research: VOLUME 37 ISSUE 17 2009
Nucl. Acids Res. 2009 37: i; doi:10.1093/nar/gkp923 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acids Research
Nucl. Acids Res. 2009 37: ii; doi:10.1093/nar/gkp921 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Subscriptions
Nucl. Acids Res. 2009 37: iii; doi:10.1093/nar/gkp925 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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