| | Articles SURVEY AND SUMMARY: Tracking EcoKI and DNA fifty years on: a golden story full of surprises Wil A. M. Loenen Nucleic Acids Res. 2003 December 15; 31(24): 7059–7069. doi: 10.1093/nar/gkg944.PMCID: PMC291878 In vitro characterization of a base pairing interaction between the primer binding site and the minimal packaging signal of avian leukosis virus genomic RNA Igor Kanevsky, Natalya Vasilenko, Hélène Dumay-Odelot, and Philippe Fossé Nucleic Acids Res. 2003 December 15; 31(24): 7070–7082. doi: 10.1093/nar/gkg942.PMCID: PMC291877 HMG-D and histone H1 alter the local accessibility of nucleosomal DNA Anan Ragab and Andrew Travers Nucleic Acids Res. 2003 December 15; 31(24): 7083–7089. doi: 10.1093/nar/gkg923.PMCID: PMC291865 Molecular genetic analysis of chloroplast gene promoters dependent on SIG2, a nucleus-encoded sigma factor for the plastid-encoded RNA polymerase, in Arabidopsis thaliana Mitsumasa Hanaoka, Kengo Kanamaru, Hideo Takahashi, and Kan Tanaka Nucleic Acids Res. 2003 December 15; 31(24): 7090–7098. doi: 10.1093/nar/gkg935.PMCID: PMC291874 Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps Michael Strong, Thomas G. Graeber, Morgan Beeby, Matteo Pellegrini, Michael J. Thompson, Todd O. Yeates, and David Eisenberg Nucleic Acids Res. 2003 December 15; 31(24): 7099–7109. doi: 10.1093/nar/gkg924.PMCID: PMC291866 Functional significance of intermediate cleavages in the 3′ETS of the pre-rRNA from Schizosaccharomyces pombe Evgueni Ivakine, Krasimir Spasov, David Frendewey, and Ross N. Nazar Nucleic Acids Res. 2003 December 15; 31(24): 7110–7116. doi: 10.1093/nar/gkg932.PMCID: PMC291872 Molecular model of SARS coronavirus polymerase: implications for biochemical functions and drug design Xiang Xu, Yunqing Liu, Susan Weiss, Eddy Arnold, Stefan G. Sarafianos, and Jianping Ding Nucleic Acids Res. 2003 December 15; 31(24): 7117–7130. doi: 10.1093/nar/gkg916.PMCID: PMC291860 Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening Yongping Pan and Alexander D. MacKerell, Jr Nucleic Acids Res. 2003 December 15; 31(24): 7131–7140. doi: 10.1093/nar/gkg941.PMCID: PMC291876 A novel allele of fission yeast rad11 that causes defects in DNA repair and telomere length regulation Yuuki Ono, Kazunori Tomita, Akira Matsuura, Takuro Nakagawa, Hisao Masukata, Masahiro Uritani, Takashi Ushimaru, and Masaru Ueno Nucleic Acids Res. 2003 December 15; 31(24): 7141–7149. doi: 10.1093/nar/gkg917.PMCID: PMC291861 The base pairing properties of 8-aza-7-deaza-2′-deoxyisoguanosine and 7-halogenated derivatives in oligonucleotide duplexes with parallel and antiparallel chain orientation Frank Seela and Rita Kröschel Nucleic Acids Res. 2003 December 15; 31(24): 7150–7158. doi: 10.1093/nar/gkg926.PMCID: PMC291867 Effects of sequence on repeat expansion during DNA replication Brooke L. Heidenfelder and Michael D. Topal Nucleic Acids Res. 2003 December 15; 31(24): 7159–7164. doi: 10.1093/nar/gkg920.PMCID: PMC291863 Twist2, a novel ADD1/SREBP1c interacting protein, represses the transcriptional activity of ADD1/SREBP1c Yun Sok Lee, Hyoung Ho Lee, Jiyoung Park, Eung Jae Yoo, Carlotta A. Glackin, Young Il Choi, Sung Ho Jeon, Rho Hyun Seong, Sang Dai Park, and Jae Bum Kim Nucleic Acids Res. 2003 December 15; 31(24): 7165–7174. doi: 10.1093/nar/gkg934.PMCID: PMC291873 A new, but old, nucleoside analog: the first synthesis of 1-deaza-2′-deoxyguanosine and its properties as a nucleoside and as oligodeoxynucleotides Naoshi Kojima, Kaori Inoue, Rina Nakajima-Shibata, Shun-ichi Kawahara, and Eiko Ohtsuka Nucleic Acids Res. 2003 December 15; 31(24): 7175–7188. doi: 10.1093/nar/gkh154.PMCID: PMC291881 Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins Susan Jones, Hugh P. Shanahan, Helen M. Berman, and Janet M. Thornton Nucleic Acids Res. 2003 December 15; 31(24): 7189–7198. doi: 10.1093/nar/gfg922.PMCID: PMC291864 The linker histone homolog Hho1p from Saccharomyces cerevisiae represents a winged helix–turn–helix fold as determined by NMR spectroscopy Katsuki Ono, Osamu Kusano, Sakurako Shimotakahara, Mitsuhiro Shimizu, Toshimasa Yamazaki, and Heisaburo Shindo Nucleic Acids Res. 2003 December 15; 31(24): 7199–7207. doi: 10.1093/nar/gkg931.PMCID: PMC291871 A conserved chloramphenicol binding site at the entrance to the ribosomal peptide exit tunnel Katherine S. Long and Bo T. Porse Nucleic Acids Res. 2003 December 15; 31(24): 7208–7215. doi: 10.1093/nar/gkg945.PMCID: PMC291879 Substitutions at tyrosine 66 of Escherichia coli uracil DNA glycosylase lead to characterization of an efficient enzyme that is recalcitrant to product inhibition Narottam Acharya, Ramappa K. Talawar, K. Saikrishnan, M. Vijayan, and Umesh Varshney Nucleic Acids Res. 2003 December 15; 31(24): 7216–7226. doi: 10.1093/nar/gkg918.PMCID: PMC291862 Repair of a minimal DNA double-strand break by NHEJ requires DNA-PKcs and is controlled by the ATM/ATR checkpoint Christian Kühne, Marie-Louise Tjörnhammar, Sándor Pongor, Lawrence Banks, and András Simoncsits Nucleic Acids Res. 2003 December 15; 31(24): 7227–7237. doi: 10.1093/nar/gkg937.PMCID: PMC291875 The role of DNA dependent protein kinase in synapsis of DNA ends Eric Weterings, Nicole S. Verkaik, Hennie T. Brüggenwirth, Jan H. J. Hoeijmakers, and Dik C. van Gent Nucleic Acids Res. 2003 December 15; 31(24): 7238–7246. doi: 10.1093/nar/gkg889.PMCID: PMC291856 Discovery and characterization of a thermostable bacteriophage RNA ligase homologous to T4 RNA ligase 1 Thorarinn Blondal, Sigridur H. Hjorleifsdottir, Olafur F. Fridjonsson, Arnthor Ævarsson, Sigurlaug Skirnisdottir, Anna Gudny Hermannsdottir, Gudmundur O. Hreggvidsson, Albert Vernon Smith, and Jakob K. Kristjansson Nucleic Acids Res. 2003 December 15; 31(24): 7247–7254. doi: 10.1093/nar/gkg914.PMCID: PMC291858 Residues 190–210 of human topoisomerase I are required for enzyme activity in vivo but not in vitro Morten O. Christensen, Hans U. Barthelmes, Fritz Boege, and Christian Mielke Nucleic Acids Res. 2003 December 15; 31(24): 7255–7263. doi: 10.1093/nar/gkg927.PMCID: PMC291868 Transcription factor ZBP-89 is required for STAT1 constitutive expression Longchuan Bai and Juanita L. Merchant Nucleic Acids Res. 2003 December 15; 31(24): 7264–7270. doi: 10.1093/nar/gkg929.PMCID: PMC291869 Gene structure prediction in syntenic DNA segments Jonathan E. Moore and James A. Lake Nucleic Acids Res. 2003 December 15; 31(24): 7271–7279. doi: 10.1093/nar/gkg905.PMCID: PMC291857 A statistical sampling algorithm for RNA secondary structure prediction Ye Ding and Charles E. Lawrence Nucleic Acids Res. 2003 December 15; 31(24): 7280–7301. doi: 10.1093/nar/gkg938.PMCID: PMC297010 The poly(A) binding protein Hfq protects RNA from RNase E and exoribonucleolytic degradation Marc Folichon, Véronique Arluison, Olivier Pellegrini, Eric Huntzinger, Philippe Régnier, and Eliane Hajnsdorf Nucleic Acids Res. 2003 December 15; 31(24): 7302–7310. doi: 10.1093/nar/gkg915.PMCID: PMC291859 Effect of G-1 on histidine tRNA microhelix conformation Mahadevan Seetharaman, Caroline Williams, Christopher J. Cramer, and Karin Musier-Forsyth Nucleic Acids Res. 2003 December 15; 31(24): 7311–7321. doi: 10.1093/nar/gkg930.PMCID: PMC291870 NAR Methods Online A PCR primer bank for quantitative gene expression analysis Xiaowei Wang and Brian Seed Nucleic Acids Res. 2003 December 15; 31(24): e154. doi: 10.1093/nar/gng154.PMCID: PMC291882 A novel MALDI–TOF based methodology for genotyping single nucleotide polymorphisms Thorarinn Blondal, Benedikt G. Waage, Sigurdur V. Smarason, Frosti Jonsson, Sigridur B. Fjalldal, Kari Stefansson, Jeffery Gulcher, and Albert V. Smith Nucleic Acids Res. 2003 December 15; 31(24): e155. doi: 10.1093/nar/gng156.PMCID: PMC291883 Erratum Nucleic Acids Res. 2003 December 15; 31(24): 7322. doi: 10.1093/nar/gkg946.PMCID: PMC291880 Corrects: Kazuyuki Takai, et al. SURVEY AND SUMMARY: Roles of 5-substituents of tRNA wobble uridines in the recognition of purine-ending codons. Nucleic Acids Res. 2003 November 15; 31(22): 6383–6391. |