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Volume 36(1);  January 2008
Molecular Biology
The ERCC1/XPF endonuclease is required for efficient single-strand annealing and gene conversion in mammalian cells
Ali Z. Al-Minawi, Nasrollah Saleh-Gohari, and Thomas Helleday
Nucleic Acids Res. 2008 January; 36(1): 1–9. Published online 2008 January. doi: 10.1093/nar/gkm888.
PMCID: PMC2248766
Nuclear receptor interaction protein, a coactivator of androgen receptors (AR), is regulated by AR and Sp1 to feed forward and activate its own gene expression through AR protein stability
Pei-Hong Chen, Yeou-Ping Tsao, Chih-Chiang Wang, and Show-Li Chen
Nucleic Acids Res. 2008 January; 36(1): 51–66. Published online 2008 January. doi: 10.1093/nar/gkm942.
PMCID: PMC2248731
Mismatch Repair proteins are recruited to replicating DNA through interaction with Proliferating Cell Nuclear Antigen (PCNA)
Prerna Jasmine Masih, Dimiter Kunnev, and Thomas Melendy
Nucleic Acids Res. 2008 January; 36(1): 67–75. Published online 2008 January. doi: 10.1093/nar/gkm943.
PMCID: PMC2248749
The process of displacing the single-stranded DNA-binding protein from single-stranded DNA by RecO and RecR proteins
Jin Inoue, Masayoshi Honda, Shukuko Ikawa, Takehiko Shibata, and Tsutomu Mikawa
Nucleic Acids Res. 2008 January; 36(1): 94–109. Published online 2008 January. doi: 10.1093/nar/gkm1004.
PMCID: PMC2248737
Dynamic structures of Bacillus subtilis RecN–DNA complexes
Humberto Sanchez, Paula P. Cardenas, Shige H. Yoshimura, Kunio Takeyasu, and Juan C. Alonso
Nucleic Acids Res. 2008 January; 36(1): 110–120. Published online 2008 January. doi: 10.1093/nar/gkm759.
PMCID: PMC2248758
Distinct HDACs regulate the transcriptional response of human cyclin-dependent kinase inhibitor genes to trichostatin A and 1α,25-dihydroxyvitamin D3
Marjo Malinen, Anna Saramäki, Antti Ropponen, Tatjana Degenhardt, Sami Väisänen, and Carsten Carlberg
Nucleic Acids Res. 2008 January; 36(1): 121–132. Published online 2008 January. doi: 10.1093/nar/gkm913.
PMCID: PMC2248733
The C-terminal domain of Escherichia coli Hfq is required for regulation
Branislav Večerek, Lukas Rajkowitsch, Elisabeth Sonnleitner, Renée Schroeder, and Udo Bläsi
Nucleic Acids Res. 2008 January; 36(1): 133–143. Published online 2008 January. doi: 10.1093/nar/gkm985.
PMCID: PMC2248732
SMAD3 prevents binding of NKX2.1 and FOXA1 to the SpB promoter through its MH1 and MH2 domains
Parviz Minoo, Lingyan Hu, Nianling Zhu, Zea Borok, Saverio Bellusci, John Groffen, Dimitris Kardassis, and Changgong Li
Nucleic Acids Res. 2008 January; 36(1): 179–188. Published online 2008 January. doi: 10.1093/nar/gkm871.
PMCID: PMC2248754
Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes
Ryoko Harada, Charles Vadnais, Laurent Sansregret, Lam Leduy, Ginette Bérubé, François Robert, and Alain Nepveu
Nucleic Acids Res. 2008 January; 36(1): 189–202. Published online 2008 January. doi: 10.1093/nar/gkm970.
PMCID: PMC2248751
Nucleolin regulates c-Jun/Sp1-dependent transcriptional activation of cPLA2α in phorbol ester-treated non-small cell lung cancer A549 cells
Jen-Hui Tsou, Kwang-Yu Chang, Wei-Chiao Wang, Joseph T. Tseng, Wu-Chou Su, Liang-Yi Hung, Wen-Chang Chang, and Ben-Kuen Chen
Nucleic Acids Res. 2008 January; 36(1): 217–227. Published online 2008 January. doi: 10.1093/nar/gkm1027.
PMCID: PMC2248756
Incorporation of extracellular 8-oxodG into DNA and RNA requires purine nucleoside phosphorylase in MCF-7 cells
Janna M. Mundt, Sang Soo Hah, Rhoda A. Sumbad, Vern Schramm, and Paul T. Henderson
Nucleic Acids Res. 2008 January; 36(1): 228–236. Published online 2008 January. doi: 10.1093/nar/gkm1032.
PMCID: PMC2248762
Ex vivo correction of selenoprotein N deficiency in rigid spine muscular dystrophy caused by a mutation in the selenocysteine codon
M. Rederstorff, V. Allamand, P. Guicheney, C. Gartioux, P. Richard, D. Chaigne, A. Krol, and A. Lescure
Nucleic Acids Res. 2008 January; 36(1): 237–244. Published online 2008 January. doi: 10.1093/nar/gkm1033.
PMCID: PMC2248747
SUMO1 negatively regulates BRCA1-mediated transcription, via modulation of promoter occupancy
Mi Ae Park, Yeong-Jae Seok, Gajin Jeong, and Jong-Soo Lee
Nucleic Acids Res. 2008 January; 36(1): 263–283. Published online 2008 January. doi: 10.1093/nar/gkm969.
PMCID: PMC2248730
Measurement of the salt-dependent stabilization of partially open DNA by Escherichia coli SSB protein
K. Hatch, C. Danilowicz, V. Coljee, and M. Prentiss
Nucleic Acids Res. 2008 January; 36(1): 294–299. Published online 2008 January. doi: 10.1093/nar/gkm1014.
PMCID: PMC2248746
Unconventional GIY-YIG homing endonuclease encoded in group I introns in closely related strains of the Bacillus cereus group
David Nord and Britt-Marie Sjöberg
Nucleic Acids Res. 2008 January; 36(1): 300–310. Published online 2008 January. doi: 10.1093/nar/gkm1016.
PMCID: PMC2248736
CpG methylation plays a vital role in determining tissue- and cell-specific expression of the human cell-death-inducing DFF45-like effector A gene through the regulation of Sp1/Sp3 binding
Dong Li, Liang Da, Hong Tang, Tsaiping Li, and Mujun Zhao
Nucleic Acids Res. 2008 January; 36(1): 330–341. Published online 2008 January. doi: 10.1093/nar/gkm1028.
PMCID: PMC2248752
Activation of DNA strand exchange by cationic comb-type copolymers: effect of cationic moieties of the copolymers
Sung Won Choi, Arihiro Kano, and Atsushi Maruyama
Nucleic Acids Res. 2008 January; 36(1): 342–351. Published online 2008 January. doi: 10.1093/nar/gkm1035.
PMCID: PMC2248768
RNA
RNA secondary structure regulates the translation of sxy and competence development in Haemophilus influenzae
Andrew D.S. Cameron, Milica Volar, Laura A. Bannister, and Rosemary J. Redfield
Nucleic Acids Res. 2008 January; 36(1): 10–20. Published online 2008 January. doi: 10.1093/nar/gkm915.
PMCID: PMC2248739
The presence of the TAR RNA structure alters the programmed -1 ribosomal frameshift efficiency of the human immunodeficiency virus type 1 (HIV-1) by modifying the rate of translation initiation
Karine Gendron, Johanie Charbonneau, Dominic Dulude, Nikolaus Heveker, Gerardo Ferbeyre, and Léa Brakier-Gingras
Nucleic Acids Res. 2008 January; 36(1): 30–40. Published online 2008 January. doi: 10.1093/nar/gkm906.
PMCID: PMC2248755
The eIF4G homolog DAP5/p97 supports the translation of select mRNAs during endoplasmic reticulum stress
Stephen M. Lewis, Sonia Cerquozzi, Tyson E. Graber, Nicoleta Hosszu Ungureanu, Meghan Andrews, and Martin Holcik
Nucleic Acids Res. 2008 January; 36(1): 168–178. Published online 2008 January. doi: 10.1093/nar/gkm1007.
PMCID: PMC2248753
Two RNA editing sites with cis-acting elements of moderate sequence identity are recognized by an identical site-recognition protein in tobacco chloroplasts
Yusuke Kobayashi, Mitsuhiro Matsuo, Koji Sakamoto, Tatsuya Wakasugi, Kyoji Yamada, and Junichi Obokata
Nucleic Acids Res. 2008 January; 36(1): 311–318. Published online 2008 January. doi: 10.1093/nar/gkm1026.
PMCID: PMC2248765
Roles for TbDSS-1 in RNA surveillance and decay of maturation by-products from the 12S rRNA locus
Jonelle L. Mattiacio and Laurie K. Read
Nucleic Acids Res. 2008 January; 36(1): 319–329. Published online 2008 January. doi: 10.1093/nar/gkm690.
PMCID: PMC2248759
Structural Biology
DNA oligonucleotides with A, T, G or C opposite an abasic site: structure and dynamics
Jingyang Chen, François-Yves Dupradeau, David A. Case, Christopher J. Turner, and JoAnne Stubbe
Nucleic Acids Res. 2008 January; 36(1): 253–262. Published online 2008 January. doi: 10.1093/nar/gkm622.
PMCID: PMC2248740
Genomics
Mechanisms of primary and secondary estrogen target gene regulation in breast cancer cells
Véronique Bourdeau, Julie Deschênes, David Laperrière, Malika Aid, John H. White, and Sylvie Mader
Nucleic Acids Res. 2008 January; 36(1): 76–93. Published online 2008 January. doi: 10.1093/nar/gkm945.
PMCID: PMC2248750
Genomic distribution and functional analyses of potential G-quadruplex-forming sequences in Saccharomyces cerevisiae
Steve G. Hershman, Qijun Chen, Julia Y. Lee, Marina L. Kozak, Peng Yue, Li-San Wang, and F. Brad Johnson
Nucleic Acids Res. 2008 January; 36(1): 144–156. Published online 2008 January. doi: 10.1093/nar/gkm986.
PMCID: PMC2248735
Chemistry
Characterization and use of an unprecedentedly bright and structurally non-perturbing fluorescent DNA base analogue
Peter Sandin, Karl Börjesson, Hong Li, Jerker Mårtensson, Tom Brown, L. Marcus Wilhelmsson, and Bo Albinsson
Nucleic Acids Res. 2008 January; 36(1): 157–167. Published online 2008 January. doi: 10.1093/nar/gkm1006.
PMCID: PMC2248743
Dehydration, deamination and enzymatic repair of cytosine glycols from oxidized poly(dG-dC) and poly(dI-dC)
Sébastien Tremblay and J. Richard Wagner
Nucleic Acids Res. 2008 January; 36(1): 284–293. Published online 2008 January. doi: 10.1093/nar/gkm1013.
PMCID: PMC2248729
Methods Online
Protein evolution by hypermutation and selection in the B cell line DT40
Hiroshi Arakawa, Hiroaki Kudo, Vera Batrak, Randolph B. Caldwell, Michael A. Rieger, Joachim W. Ellwart, and Jean-Marie Buerstedde
Nucleic Acids Res. 2008 January; 36(1): e1. Published online 2008 January. doi: 10.1093/nar/gkm616.
PMCID: PMC2248763
siRNA nanoformulation against the Ret/PTC1 junction oncogene is efficient in an in vivo model of papillary thyroid carcinoma
Henri de Martimprey, Jean-Remi Bertrand, Alfredo Fusco, Massimo Santoro, Patrick Couvreur, Christine Vauthier, and Claude Malvy
Nucleic Acids Res. 2008 January; 36(1): e2. Published online 2008 January. doi: 10.1093/nar/gkm1094.
PMCID: PMC2248757
Comprehensive viral oligonucleotide probe design using conserved protein regions
Omar J. Jabado, Yang Liu, Sean Conlan, P. Lan Quan, Hédi Hegyi, Yves Lussier, Thomas Briese, Gustavo Palacios, and W. I. Lipkin
Nucleic Acids Res. 2008 January; 36(1): e3. Published online 2008 January. doi: 10.1093/nar/gkm1106.
PMCID: PMC2248741
Recombineering with tolC as a Selectable/Counter-selectable Marker: remodeling the rRNA Operons of Escherichia coli
Joseph A. DeVito
Nucleic Acids Res. 2008 January; 36(1): e4. Published online 2008 January. doi: 10.1093/nar/gkm1084.
PMCID: PMC2248734
From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing
Matthias Meyer, Adrian W. Briggs, Tomislav Maricic, Barbara Höber, Barbara Höffner, Johannes Krause, Antje Weihmann, Svante Pääbo, and Michael Hofreiter
Nucleic Acids Res. 2008 January; 36(1): e5. Published online 2008 January. doi: 10.1093/nar/gkm1095.
PMCID: PMC2248761
The translation of recombinant proteins in E. coli can be improved by in silico generating and screening random libraries of a −70/+96 mRNA region with respect to the translation initiation codon
S. Care, C. Bignon, M. C. Pelissier, E. Blanc, B. Canard, and B. Coutard
Nucleic Acids Res. 2008 January; 36(1): e6. Published online 2008 January. doi: 10.1093/nar/gkm1097.
PMCID: PMC2248745
In situ oligonucleotide synthesis on carbon materials: stable substrates for microarray fabrication
Margaret F. Phillips, Matthew R. Lockett, Matthew J. Rodesch, Michael R. Shortreed, Franco Cerrina, and Lloyd M. Smith
Nucleic Acids Res. 2008 January; 36(1): e7. Published online 2008 January. doi: 10.1093/nar/gkm1103.
PMCID: PMC2248760
Genome wide screens in yeast to identify potential binding sites and target genes of DNA-binding proteins
Jue Zeng, Jizhou Yan, Ting Wang, Deborah Mosbrook-Davis, Kyle T. Dolan, Ryan Christensen, Gary D. Stormo, David Haussler, Richard H. Lathrop, Rainer K. Brachmann, and Shawn M. Burgess
Nucleic Acids Res. 2008 January; 36(1): e8. Published online 2008 January. doi: 10.1093/nar/gkm1117.
PMCID: PMC2248728
Site-specific recombination in Schizosaccharomyces pombe and systematic assembly of a 400kb transgene array in mammalian cells using the integrase of Streptomyces phage ϕBT1
Zhengyao Xu, Nicholas C. O. Lee, Felix Dafhnis-Calas, Sunir Malla, Margaret C. M. Smith, and William R. A. Brown
Nucleic Acids Res. 2008 January; 36(1): e9. Published online 2008 January. doi: 10.1093/nar/gkm1123.
PMCID: PMC2248738
Computational Biology
Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations
Sarah A. Harris, Charles A. Laughton, and Tanniemola B. Liverpool
Nucleic Acids Res. 2008 January; 36(1): 21–29. Published online 2008 January. doi: 10.1093/nar/gkm891.
PMCID: PMC2248748
Nucleic Acid Enzymes
Mutation of the arginine finger in the active site of Escherichia coli DbpA abolishes ATPase and helicase activity and confers a dominant slow growth phenotype
Lisa M. Sharpe Elles and Olke C. Uhlenbeck
Nucleic Acids Res. 2008 January; 36(1): 41–50. Published online 2008 January. doi: 10.1093/nar/gkm926.
PMCID: PMC2248767
Identification of functional domains in Arabidopsis thaliana mRNA decapping enzyme (AtDcp2)
Dilantha Gunawardana, Heung-Chin Cheng, and Kenwyn R. Gayler
Nucleic Acids Res. 2008 January; 36(1): 203–216. Published online 2008 January. doi: 10.1093/nar/gkm1002.
PMCID: PMC2248764
The RNA polymerase factory: a robotic in vitro assembly platform for high-throughput production of recombinant protein complexes
Sven Nottebaum, Lin Tan, Dominika Trzaska, Hannah C. Carney, and Robert O. J. Weinzierl
Nucleic Acids Res. 2008 January; 36(1): 245–252. Published online 2008 January. doi: 10.1093/nar/gkm1044.
PMCID: PMC2248744
Corrigendum
Elk1 and SRF transcription factors convey basal transcription and mediate glucose response via their binding sites in the human LXRB gene promoter
Maria Nilsson, Karin Dahlman-Wright, Charlotta Karelmo, Martin Ebeling, Jan-Åke Gustafsson, and Knut R. Steffensen
Nucleic Acids Res. 2008 January; 36(1): 352. Published online 2008 January. doi: 10.1093/nar/gkm1155.
PMCID: PMC2248742
Corrects: Maria Nilsson, et al. Elk1 and SRF transcription factors convey basal transcription and mediate glucose response via their binding sites in the human LXRB gene promoter. Nucleic Acids Res. 2007 July; 35(14): 4858–4868.
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