Nucleic Acids Research

Chemistry and Synthetic Biology

Get checked abstract Jianshuang Wang and Yinsheng Wang

Chemical synthesis of oligodeoxyribonucleotides containing N3- and O⁴-carboxymethylthymidine and their formation in DNA
Nucleic Acids Research Advance Access published on November 28, 2008
Nucl. Acids Res. 2009 37: 336-345; doi:10.1093/nar/gkn946 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Özgül Persil Çetinkol and Nicholas V. Hud

Molecular recognition of poly(A) by small ligands: an alternative method of analysis reveals nanomolar, cooperative and shape-selective binding
Nucleic Acids Research Advance Access published on December 10, 2008
Nucl. Acids Res. 2009 37: 611-621; doi:10.1093/nar/gkn977 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Computational Biology

Get checked abstract Rajkumar Bondugula, Michael S. Lee, and Anders Wallqvist

FIEFDom: a transparent domain boundary recognition system using a fuzzy mean operator
Nucleic Acids Research Advance Access published on December 4, 2008
Nucl. Acids Res. 2009 37: 452-462; doi:10.1093/nar/gkn944 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Yue Lu and Sing-Hoi Sze

Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues
Nucleic Acids Research Advance Access published on December 4, 2008
Nucl. Acids Res. 2009 37: 463-472; doi:10.1093/nar/gkn945 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Ching-Ti Liu, Shinsheng Yuan, and Ker-Chau Li

Patterns of co-expression for protein complexes by size in Saccharomyces cerevisiae
Nucleic Acids Research Advance Access published on December 4, 2008
Nucl. Acids Res. 2009 37: 526-532; doi:10.1093/nar/gkn972 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Alessandro Coppe, Francesco Ferrari, Andrea Bisognin, Gian Antonio Danieli, Sergio Ferrari, Silvio Bicciato, and Stefania Bortoluzzi

Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation
Nucleic Acids Research Advance Access published on December 5, 2008
Nucl. Acids Res. 2009 37: 533-549; doi:10.1093/nar/gkn948 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Chuanhua Xing, Donald L. Bitzer, Winser E. Alexander, Mladen A. Vouk, and Anne-Marie Stomp

Identification of protein-coding sequences using the hybridization of 18S rRNA and mRNA during translation
Nucleic Acids Research Advance Access published on December 10, 2008
Nucl. Acids Res. 2009 37: 591-601; doi:10.1093/nar/gkn917 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Csaba Ortutay and Mauno Vihinen

Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies
Nucleic Acids Research Advance Access published on December 10, 2008
Nucl. Acids Res. 2009 37: 622-628; doi:10.1093/nar/gkn982 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Gene regulation, Chromatin and Epigenetics

Get checked abstract Koh-ichi Utani and Noriaki Shimizu

How transcription proceeds in a large artificial heterochromatin in human cells
Nucleic Acids Research Advance Access published on November 29, 2008
Nucl. Acids Res. 2009 37: 393-404; doi:10.1093/nar/gkn970 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Laura M. Green, Kate J. Wagner, Hayley A. Campbell, Kelly Addison, and Stefan G. E. Roberts

Dynamic interaction between WT1 and BASP1 in transcriptional regulation during differentiation
Nucleic Acids Research Advance Access published on December 2, 2008
Nucl. Acids Res. 2009 37: 431-440; doi:10.1093/nar/gkn955 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jong Kyong Kim, Pierre-Olivier Estève, Steven E. Jacobsen, and Sriharsa Pradhan

UHRF1 binds G9a and participates in p21 transcriptional regulation in mammalian cells
Nucleic Acids Research Advance Access published on December 4, 2008
Nucl. Acids Res. 2009 37: 493-505; doi:10.1093/nar/gkn961 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Mitsuo Wakasugi, Hiromi Kasashima, Yuko Fukase, Mayumi Imura, Rika Imai, Saki Yamada, James E. Cleaver, and Tsukasa Matsunaga

Physical and functional interaction between DDB and XPA in nucleotide excision repair
Nucleic Acids Research Advance Access published on December 4, 2008
Nucl. Acids Res. 2009 37: 516-525; doi:10.1093/nar/gkn964 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genome integrity, repair and replication

Get checked abstract Linda Savolainen and Thomas Helleday

Transcription-associated recombination is independent of XRCC2 and mechanistically separate from homology-directed DNA double-strand break repair
Nucleic Acids Research Advance Access published on November 29, 2008
Nucl. Acids Res. 2009 37: 405-412; doi:10.1093/nar/gkn971 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Enriqueta Riballo, Lisa Woodbine, Thomas Stiff, Sarah A. Walker, Aaron A. Goodarzi, and Penny A. Jeggo

XLF-Cernunnos promotes DNA ligase IV–XRCC4 re-adenylation following ligation
Nucleic Acids Research Advance Access published on December 4, 2008
Nucl. Acids Res. 2009 37: 482-492; doi:10.1093/nar/gkn957 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Arabela A. Grigorescu, Joseph H. A. Vissers, Dejan Ristic, Ying Z. Pigli, Thomas W. Lynch, Claire Wyman, and Phoebe A. Rice

Inter-subunit interactions that coordinate Rad51's activities
Nucleic Acids Research Advance Access published on December 9, 2008
Nucl. Acids Res. 2009 37: 557-567; doi:10.1093/nar/gkn973 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Xiao Meng, Yajing Zhou, Sufang Zhang, Ernest Y. C. Lee, David N. Frick, and Marietta Y. W. T. Lee

DNA damage alters DNA polymerase to a form that exhibits increased discrimination against modified template bases and mismatched primers
Nucleic Acids Research Advance Access published on December 11, 2008
Nucl. Acids Res. 2009 37: 647-657; doi:10.1093/nar/gkn1000 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Molecular Biology

Get checked abstract Crystal R. Whitfield, Simon J. Wardle, and David B. Haniford

The global bacterial regulator H-NS promotes transpososome formation and transposition in the Tn5 system
Nucleic Acids Research Advance Access published on November 28, 2008
Nucl. Acids Res. 2009 37: 309-321; doi:10.1093/nar/gkn935 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Max Koeppel, Simon J. van Heeringen, Leonie Smeenk, Anna C. Navis, Eva M. Janssen-Megens, and Marion Lohrum

The novel p53 target gene IRF2BP2 participates in cell survival during the p53 stress response
Nucleic Acids Research Advance Access published on November 28, 2008
Nucl. Acids Res. 2009 37: 322-335; doi:10.1093/nar/gkn940 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Valeriy Sorokin, Konstantin Severinov, and Mikhail S. Gelfand

Systematic prediction of control proteins and their DNA binding sites
Nucleic Acids Research Advance Access published on December 4, 2008
Nucl. Acids Res. 2009 37: 441-451; doi:10.1093/nar/gkn931 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jeffry D. Sander, Peter Zaback, J. Keith Joung, Daniel F. Voytas, and Drena Dobbs

An affinity-based scoring scheme for predicting DNA-binding activities of modularly assembled zinc-finger proteins
Nucleic Acids Research Advance Access published on December 4, 2008
Nucl. Acids Res. 2009 37: 506-515; doi:10.1093/nar/gkn962 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Paul M. K. Gordon, Ekkehard Schütz, Julia Beck, Howard B. Urnovitz, Catherine Graham, Renee Clark, Sandor Dudas, Stefanie Czub, Maria Sensen, Bertram Brenig, Martin H. Groschup, Robert B. Church, and Christoph W. Sensen

Disease-specific motifs can be identified in circulating nucleic acids from live elk and cattle infected with transmissible spongiform encephalopathies
Nucleic Acids Research Advance Access published on December 5, 2008
Nucl. Acids Res. 2009 37: 550-556; doi:10.1093/nar/gkn963 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Tuck Seng Wong, Sridharan Rajagopalan, Fiona M. Townsley, Stefan M. Freund, Miriana Petrovich, David Loakes, and Alan R. Fersht

Physical and functional interactions between human mitochondrial single-stranded DNA-binding protein and tumour suppressor p53
Nucleic Acids Research Advance Access published on December 9, 2008
Nucl. Acids Res. 2009 37: 568-581; doi:10.1093/nar/gkn974 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Almudena Pacheco, Sonia López de Quinto, Jorge Ramajo, Noemí Fernández, and Encarnación Martínez-Salas

A novel role for Gemin5 in mRNA translation
Nucleic Acids Research Advance Access published on December 9, 2008
Nucl. Acids Res. 2009 37: 582-590; doi:10.1093/nar/gkn979 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes

Get checked abstract David C. Zappulla, Jennifer N. Roberts, Karen J. Goodrich, Thomas R. Cech, and Deborah S. Wuttke

Inhibition of yeast telomerase action by the telomeric ssDNA-binding protein, Cdc13p
Nucleic Acids Research Advance Access published on November 29, 2008
Nucl. Acids Res. 2009 37: 354-367; doi:10.1093/nar/gkn830 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Adrian G. Grozav, Kenichi Chikamori, Toshiyuki Kozuki, Dale R. Grabowski, Ronald M. Bukowski, Belinda Willard, Michael Kinter, Anni H. Andersen, Ram Ganapathi, and Mahrukh K. Ganapathi

Casein kinase I / phosphorylates topoisomerase II at serine-1106 and modulates DNA cleavage activity
Nucleic Acids Research Advance Access published on November 29, 2008
Nucl. Acids Res. 2009 37: 382-392; doi:10.1093/nar/gkn934 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Dagmar Klostermeier and Markus G. Rudolph

A novel dimerization motif in the C-terminal domain of the Thermus thermophilus DEAD box helicase Hera confers substantial flexibility
Nucleic Acids Research Advance Access published on December 2, 2008
Nucl. Acids Res. 2009 37: 421-430; doi:10.1093/nar/gkn947 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Bahram Arezi and Holly Hogrefe

Novel mutations in Moloney Murine Leukemia Virus reverse transcriptase increase thermostability through tighter binding to template-primer
Nucleic Acids Research Advance Access published on December 4, 2008
Nucl. Acids Res. 2009 37: 473-481; doi:10.1093/nar/gkn952 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Xuan Li and Wolf-Dietrich Heyer

RAD54 controls access to the invading 3'-OH end after RAD51-mediated DNA strand invasion in homologous recombination in Saccharomyces cerevisiae
Nucleic Acids Research Advance Access published on December 11, 2008
Nucl. Acids Res. 2009 37: 638-646; doi:10.1093/nar/gkn980 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA

Get checked abstract Montserrat Terrazas and Eric T. Kool

RNA major groove modifications improve siRNA stability and biological activity
Nucleic Acids Research Advance Access published on November 28, 2008
Nucl. Acids Res. 2009 37: 346-353; doi:10.1093/nar/gkn958 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract David Dufour, Marcos de la Peña, Selma Gago, Ricardo Flores, and José Gallego

Structure–function analysis of the ribozymes of chrysanthemum chlorotic mottle viroid: a loop–loop interaction motif conserved in most natural hammerheads
Nucleic Acids Research Advance Access published on November 29, 2008
Nucl. Acids Res. 2009 37: 368-381; doi:10.1093/nar/gkn918 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Kenny Schlosser and Yingfu Li

DNAzyme-mediated catalysis with only guanosine and cytidine nucleotides
Nucleic Acids Research Advance Access published on December 2, 2008
Nucl. Acids Res. 2009 37: 413-420; doi:10.1093/nar/gkn930 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology

Get checked abstract Priscilla Hiu-Mei Too, Meiji Kit-Wan Ma, Amanda Nga-Sze Mak, Yuen-Ting Wong, Christine Kit-Ching Tung, Guang Zhu, Shannon Wing-Ngor Au, Kam-Bo Wong, and Pang-Chui Shaw

The C-terminal fragment of the ribosomal P protein complexed to trichosanthin reveals the interaction between the ribosome-inactivating protein and the ribosome
Nucleic Acids Research Advance Access published on December 10, 2008
Nucl. Acids Res. 2009 37: 602-610; doi:10.1093/nar/gkn922 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Sung Chul Ha, Jongkeun Choi, Hye-Yeon Hwang, Alexander Rich, Yang-Gyun Kim, and Kyeong Kyu Kim

The structures of non-CG-repeat Z-DNAs co-crystallized with the Z-DNA-binding domain, hZ_ADAR1
Nucleic Acids Research Advance Access published on December 11, 2008
Nucl. Acids Res. 2009 37: 629-637; doi:10.1093/nar/gkn976 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Methods Online

Get checked abstract Yu Jin Jung, Yu Shin Park, Ki-Jun Yoon, Young-Yun Kong, Joon Won Park, and Hong Gil Nam

Molecule-level imaging of Pax6 mRNA distribution in mouse embryonic neocortex by molecular interaction force microscopy
Nucleic Acids Research Advance Access published on November 29, 2008
Nucl. Acids Res. 2009 37: e10; doi:10.1093/nar/gkn965 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Koki Moriyoshi

pBT, a novel vector for tetracycline-regulated yeast three-hybrid assay
Nucleic Acids Research Advance Access published on December 2, 2008
Nucl. Acids Res. 2009 37: e11; doi:10.1093/nar/gkn969 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Matthias Schaefer, Tim Pollex, Katharina Hanna, and Frank Lyko

RNA cytosine methylation analysis by bisulfite sequencing
Nucleic Acids Research Advance Access published on December 5, 2008
Nucl. Acids Res. 2009 37: e12; doi:10.1093/nar/gkn954 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Mizuki Takenaka and Axel Brennicke

Multiplex single-base extension typing to identify nuclear genes required for RNA editing in plant organelles
Nucleic Acids Research Advance Access published on December 5, 2008
Nucl. Acids Res. 2009 37: e13; doi:10.1093/nar/gkn975 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Michiko Kimoto, Rie Kawai, Tsuneo Mitsui, Shigeyuki Yokoyama, and Ichiro Hirao

An unnatural base pair system for efficient PCR amplification and functionalization of DNA molecules
Nucleic Acids Research Advance Access published on December 10, 2008
Nucl. Acids Res. 2009 37: e14; doi:10.1093/nar/gkn956 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Josefine Ederth, Chandra Sekhar Mandava, Santanu Dasgupta, and Suparna Sanyal

A single-step method for purification of active His-tagged ribosomes from a genetically engineered Escherichia coli
Nucleic Acids Research Advance Access published on December 11, 2008
Nucl. Acids Res. 2009 37: e15; doi:10.1093/nar/gkn992 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Zengyi Shao, Hua Zhao, and Huimin Zhao

DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways
Nucleic Acids Research Advance Access published on December 12, 2008
Nucl. Acids Res. 2009 37: e16; doi:10.1093/nar/gkn991 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract D. Sarkar, R. Parkin, S. Wyman, A. Bendoraite, C. Sather, J. Delrow, A. K. Godwin, C. Drescher, W. Huber, R. Gentleman, and M. Tewari

Quality Assessment and Data Analysis for microRNA Expression Arrays
Nucleic Acids Research Advance Access published on December 22, 2008
Nucl. Acids Res. 2009 37: e17; doi:10.1093/nar/gkn932 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Front-Matter/Back-Matter

Nucleic Acids Research: VOLUME 37 ISSUE 2 2009
Nucl. Acids Res. 2009 37: i; doi:10.1093/nar/gkp061 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acids Research
Nucl. Acids Res. 2009 37: ii; doi:10.1093/nar/gkp060 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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Nucl. Acids Res. 2009 37: iii; doi:10.1093/nar/gkp062 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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