Nucleic Acids Research

Survey and Summary:

Rebecca A. Haeusler and David R. Engelke

Spatial organization of transcription by RNA polymerase III
Nucleic Acids Research Advance Access published on September 13, 2006
Nucl. Acids Res. 2006 34: 4826-4836; doi:10.1093/nar/gkl656 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sigrid D. Auweter, Florian C. Oberstrass, and Frédéric H.-T. Allain

Sequence-specific binding of single-stranded RNA: is there a code for recognition?
Nucleic Acids Research Advance Access published on September 18, 2006
Nucl. Acids Res. 2006 34: 4943-4959; doi:10.1093/nar/gkl620 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Chemistry:

Nicole A. Leal, Makoto Sukeda, and Steven A. Benner

Dynamic assembly of primers on nucleic acid templates
Nucleic Acids Research Advance Access published on September 8, 2006
Nucl. Acids Res. 2006 34: 4702-4710; doi:10.1093/nar/gkl625 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Computational Biology:

KiYoung Lee, Dae-Won Kim, DoKyun Na, Kwang H. Lee, and Doheon Lee

PLPD: reliable protein localization prediction from imbalanced and overlapped datasets
Nucleic Acids Research Advance Access published on September 11, 2006
Nucl. Acids Res. 2006 34: 4655-4666; doi:10.1093/nar/gkl638 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Xueping Yu, Jimmy Lin, Donald J. Zack, and Jiang Qian

Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues
Nucleic Acids Research Advance Access published on September 18, 2006
Nucl. Acids Res. 2006 34: 4925-4936; doi:10.1093/nar/gkl595 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Szabolcs Semsey, Anna M. C. Andersson, Sandeep Krishna, Mogens Høgh Jensen, Eric Massé, and Kim Sneppen

Genetic regulation of fluxes: iron homeostasis of Escherichia coli
Nucleic Acids Research Advance Access published on September 18, 2006
Nucl. Acids Res. 2006 34: 4960-4967; doi:10.1093/nar/gkl627 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Genomics:

Cathryn Rehmeyer, Weixi Li, Motoaki Kusaba, Yun-Sik Kim, Doug Brown, Chuck Staben, Ralph Dean, and Mark Farman

Organization of chromosome ends in the rice blast fungus, Magnaporthe oryzae
Nucleic Acids Research Advance Access published on September 8, 2006
Nucl. Acids Res. 2006 34: 4685-4701; doi:10.1093/nar/gkl588 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Hasmik Yepiskoposyan, Dieter Egli, Tim Fergestad, Anand Selvaraj, Carina Treiber, Gerd Multhaup, Oleg Georgiev, and Walter Schaffner

Transcriptome response to heavy metal stress in Drosophila reveals a new zinc transporter that confers resistance to zinc
Nucleic Acids Research Advance Access published on September 14, 2006
Nucl. Acids Res. 2006 34: 4866-4877; doi:10.1093/nar/gkl606 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Molecular Biology:

Rodolphe Suspène, Christophe Rusniok, Jean-Pierre Vartanian, and Simon Wain-Hobson

Twin gradients in APOBEC3 edited HIV-1 DNA reflect the dynamics of lentiviral replication
Nucleic Acids Research Advance Access published on September 8, 2006
Nucl. Acids Res. 2006 34: 4677-4684; doi:10.1093/nar/gkl555 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Chih-Yin Lin, Sonia Navarro, Sita Reddy, and Lucio Comai

CK2-mediated stimulation of Pol I transcription by stabilization of UBF–SL1 interaction
Nucleic Acids Research Advance Access published on September 13, 2006
Nucl. Acids Res. 2006 34: 4752-4766; doi:10.1093/nar/gkl581 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Erika D. von Gromoff, Michael Schroda, Ulrike Oster, and Christoph F. Beck

Identification of a plastid response element that acts as an enhancer within the Chlamydomonas HSP70A promoter
Nucleic Acids Research Advance Access published on September 13, 2006
Nucl. Acids Res. 2006 34: 4767-4779; doi:10.1093/nar/gkl602 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Wen Zhang, Emily Walker, Owen J. Tamplin, Janet Rossant, William L. Stanford, and Timothy R. Hughes

Zfp206 regulates ES cell gene expression and differentiation
Nucleic Acids Research Advance Access published on September 13, 2006
Nucl. Acids Res. 2006 34: 4780-4790; doi:10.1093/nar/gkl631 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Daniela Schmitter, Jody Filkowski, Alain Sewer, Ramesh S. Pillai, Edward J. Oakeley, Mihaela Zavolan, Petr Svoboda, and Witold Filipowicz

Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells
Nucleic Acids Research Advance Access published on September 13, 2006
Nucl. Acids Res. 2006 34: 4801-4815; doi:10.1093/nar/gkl646 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Alexandra Kessler, Guennadi Sezonov, J. Iñaki Guijarro, Nicole Desnoues, Thierry Rose, Muriel Delepierre, Stephen D. Bell, and David Prangishvili

A novel archaeal regulatory protein, Sta1, activates transcription from viral promoters
Nucleic Acids Research Advance Access published on September 14, 2006
Nucl. Acids Res. 2006 34: 4837-4845; doi:10.1093/nar/gkl502 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Norikazu Yabuta, Hiroaki Onda, Masafumi Watanabe, Naohisa Yoshioka, Ippei Nagamori, Tomoyuki Funatsu, Shingo Toji, Katsuyuki Tamai, and Hiroshi Nojima

Isolation and characterization of the TIGA genes, whose transcripts are induced by growth arrest
Nucleic Acids Research Advance Access published on September 14, 2006
Nucl. Acids Res. 2006 34: 4878-4892; doi:10.1093/nar/gkl651 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Christine Friedeberg, Garry Scarlett, John McGeeghan, Anita Abu-daya, Matthew Guille, and Geoff Kneale

Identification of a structural and functional domain in xNAP1 involved in protein–protein interactions
Nucleic Acids Research Advance Access published on September 18, 2006
Nucl. Acids Res. 2006 34: 4893-4899; doi:10.1093/nar/gkl434 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yang-Gyun Kim, Hyun-Ju Park, Kyeong Kyu Kim, Ky Lowenhaupt, and Alexander Rich

A peptide with alternating lysines can act as a highly specific Z-DNA binding domain
Nucleic Acids Research Advance Access published on September 18, 2006
Nucl. Acids Res. 2006 34: 4937-4942; doi:10.1093/nar/gkl607 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

A. Helena Mangs, Helen J.L. Speirs, Christine Goy, David J. Adams, M. Andrea Markus, and Brian J. Morris

XE7: A novel splicing factor that interacts with ASF/SF2 and ZNF265
Nucleic Acids Research Advance Access published on September 18, 2006
Nucl. Acids Res. 2006 34: 4976-4986; doi:10.1093/nar/gkl660 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sabrina Grenetier, Céline Bouchoux, and Valérie Goguel

CTD kinase I is required for the integrity of the rDNA tandem array
Nucleic Acids Research Advance Access published on September 19, 2006
Nucl. Acids Res. 2006 34: 4996-5006; doi:10.1093/nar/gkl493 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acid Enzymes:

Andrew B. Smith and Anthony Maxwell

A strand-passage conformation of DNA gyrase is required to allow the bacterial toxin, CcdB, to access its binding site
Nucleic Acids Research Advance Access published on September 8, 2006
Nucl. Acids Res. 2006 34: 4667-4676; doi:10.1093/nar/gkl636 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Xuejun Zhong, Parie Garg, Carrie M. Stith, Stephanie A. Nick McElhinny, Grace E. Kissling, Peter M. J. Burgers, and Thomas A. Kunkel

The fidelity of DNA synthesis by yeast DNA polymerase zeta alone and with accessory proteins
Nucleic Acids Research Advance Access published on September 13, 2006
Nucl. Acids Res. 2006 34: 4731-4742; doi:10.1093/nar/gkl465 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nobutaka Hirano, Hiroyuki Ohshima, and Hideo Takahashi

Biochemical analysis of the substrate specificity and sequence preference of endonuclease IV from bacteriophage T4, a dC-specific endonuclease implicated in restriction of dC-substituted T4 DNA synthesis
Nucleic Acids Research Advance Access published on September 13, 2006
Nucl. Acids Res. 2006 34: 4743-4751; doi:10.1093/nar/gkl553 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Laura E. Rosen, Holly A. Morrison, Selma Masri, Michael J. Brown, Brendan Springstubb, Django Sussman, Barry L. Stoddard, and Lenny M. Seligman

Homing endonuclease I-CreI derivatives with novel DNA target specificities
Nucleic Acids Research Advance Access published on September 13, 2006
Nucl. Acids Res. 2006 34: 4791-4800; doi:10.1093/nar/gkl645 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tonatiuh Romero Salas, Irina Petruseva, Olga Lavrik, Anne Bourdoncle, Jean-Louis Mergny, Alain Favre, and Carole Saintomé

Human replication protein A unfolds telomeric G-quadruplexes
Nucleic Acids Research Advance Access published on September 14, 2006
Nucl. Acids Res. 2006 34: 4857-4865; doi:10.1093/nar/gkl564 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

RNA:

Satoshi Shibata, Mitsuho Sasaki, Takashi Miki, Akira Shimamoto, Yasuhiro Furuichi, Jun Katahira, and Yoshihiro Yoneda

Exportin-5 orthologues are functionally divergent among species
Nucleic Acids Research Advance Access published on September 8, 2006
Nucl. Acids Res. 2006 34: 4711-4721; doi:10.1093/nar/gkl663 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yong Wah Tan, Shouguo Fang, Hui Fan, Julien Lescar, and D.X. Liu

Amino acid residues critical for RNA-binding in the N-terminal domain of the nucleocapsid protein are essential determinants for the infectivity of coronavirus in cultured cells
Nucleic Acids Research Advance Access published on September 13, 2006
Nucl. Acids Res. 2006 34: 4816-4825; doi:10.1093/nar/gkl650 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sujiet Puthenveetil, Landon Whitby, Jin Ren, Kevin Kelnar, Joseph F. Krebs, and Peter A. Beal

Controlling activation of the RNA-dependent protein kinase by siRNAs using site-specific chemical modification
Nucleic Acids Research Advance Access published on September 18, 2006
Nucl. Acids Res. 2006 34: 4900-4911; doi:10.1093/nar/gkl464 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Zhi John Lu, Douglas H. Turner, and David H. Mathews

A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation
Nucleic Acids Research Advance Access published on September 18, 2006
Nucl. Acids Res. 2006 34: 4912-4924; doi:10.1093/nar/gkl472 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Kristian H. Link, Lixia Guo, and Ronald R. Breaker

Examination of the structural and functional versatility of glmS ribozymes by using in vitro selection
Nucleic Acids Research Advance Access published on September 18, 2006
Nucl. Acids Res. 2006 34: 4968-4975; doi:10.1093/nar/gkl643 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Sophie Jaeger, Franck Martin, Joëlle Rudinger-Thirion, Richard Giegé, and Gilbert Eriani

Binding of human SLBP on the 3'-UTR of histone precursor H4-12 mRNA induces structural rearrangements that enable U7 snRNA anchoring
Nucleic Acids Research Advance Access published on September 18, 2006
Nucl. Acids Res. 2006 34: 4987-4995; doi:10.1093/nar/gkl666 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Structural Biology:

Qi Cai, Ana Karin Kusnetzow, Wayne L. Hubbell, Ian S. Haworth, Gian Paola C. Gacho, Ned Van Eps, Kálmán Hideg, Eric J. Chambers, and Peter Z. Qin

Site-directed spin labeling measurements of nanometer distances in nucleic acids using a sequence-independent nitroxide probe
Nucleic Acids Research Advance Access published on September 10, 2006
Nucl. Acids Res. 2006 34: 4722-4730; doi:10.1093/nar/gkl546 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Robert J. McDonald, Jason D. Kahn, and L. James Maher, III

DNA bending by bHLH charge variants
Nucleic Acids Research Advance Access published on September 14, 2006
Nucl. Acids Res. 2006 34: 4846-4856; doi:10.1093/nar/gkl552 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Dylan Chivian and David Baker

Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection
Nucleic Acids Research Advance Access published on September 13, 2006
Nucl. Acids Res. 2006 34: e112; doi:10.1093/nar/gkl480 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Ting-Fung Chan, Connie Ha, Angie Phong, Dongmei Cai, Eunice Wan, Lucinda Leung, Pui-Yan Kwok, and Ming Xiao

A simple DNA stretching method for fluorescence imaging of single DNA molecules
Nucleic Acids Research Advance Access published on September 13, 2006
Nucl. Acids Res. 2006 34: e113; doi:10.1093/nar/gkl593 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tiziana Aucelli, Patrizia Contursi, Michele Girfoglio, Mosè Rossi, and Raffaele Cannio

A spreadable, non-integrative and high copy number shuttle vector for Sulfolobus solfataricus based on the genetic element pSSVx from Sulfolobus islandicus
Nucleic Acids Research Advance Access published on September 13, 2006
Nucl. Acids Res. 2006 34: e114; doi:10.1093/nar/gkl615 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Shuji Takada, Eugene Berezikov, Yoshihiro Yamashita, Mariana Lagos-Quintana, Wigard P. Kloosterman, Munehiro Enomoto, Hisashi Hatanaka, Shin-ichiro Fujiwara, Hideki Watanabe, Manabu Soda, Young Lim Choi, Ronald H. A. Plasterk, Edwin Cuppen, and Hiroyuki Mano

Mouse microRNA profiles determined with a new and sensitive cloning method
Nucleic Acids Research Advance Access published on September 14, 2006
Nucl. Acids Res. 2006 34: e115; doi:10.1093/nar/gkl653 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Guohong Hu, Hui-Yun Wang, Danielle M. Greenawalt, Marco A. Azaro, Minjie Luo, Irina V. Tereshchenko, Xiangfeng Cui, Qifeng Yang, Richeng Gao, Li Shen, and Honghua Li

AccuTyping: new algorithms for automated analysis of data from high-throughput genotyping with oligonucleotide microarrays
Nucleic Acids Research Advance Access published on September 18, 2006
Nucl. Acids Res. 2006 34: e116; doi:10.1093/nar/gkl601 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Michael Hiller, Rainer Pudimat, Anke Busch, and Rolf Backofen

Using RNA secondary structures to guide sequence motif finding towards single-stranded regions
Nucleic Acids Research Advance Access published on September 20, 2006
Nucl. Acids Res. 2006 34: e117; doi:10.1093/nar/gkl544 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

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