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Volume 31(17);  September 1, 2003
Articles
Poly(ADP-ribose) polymerase (PARP-1) has a controlling role in homologous recombination
Niklas Schultz, Elena Lopez, Nasrollah Saleh-Gohari, and Thomas Helleday
Nucleic Acids Res. 2003 September 1; 31(17): 4959–4964. doi: 10.1093/nar/gkg703.
PMCID: PMC212803
Differences in replication of a DNA template containing an ethyl phosphotriester by T4 DNA polymerase and Escherichia coli DNA polymerase I
Laura Tsujikawa, Michael Weinfield, and Linda J. Reha-Krantz
Nucleic Acids Res. 2003 September 1; 31(17): 4965–4972. doi: 10.1093/nar/gkg722.
PMCID: PMC212818
Developmental defects by antisense-mediated inactivation of micro-RNAs 2 and 13 in Drosophila and the identification of putative target genes
Alexandra Boutla, Christos Delidakis, and Martin Tabler
Nucleic Acids Res. 2003 September 1; 31(17): 4973–4980. doi: 10.1093/nar/gkg707.
PMCID: PMC212806
Ribozyme-mediated REV1 inhibition reduces the frequency of UV-induced mutations in the human HPRT gene
Denise R. Clark, Wolfgang Zacharias, Luminita Panaitescu, and W. Glenn McGregor
Nucleic Acids Res. 2003 September 1; 31(17): 4981–4988. doi: 10.1093/nar/gkg725.
PMCID: PMC212819
Thermodynamic criteria for high hit rate antisense oligonucleotide design
O. V. Matveeva, D. H. Mathews, A. D. Tsodikov, S. A. Shabalina, R. F. Gesteland, J. F. Atkins, and S. M. Freier
Nucleic Acids Res. 2003 September 1; 31(17): 4989–4994. doi: 10.1093/nar/gkg710.
PMCID: PMC212809
Functional conservation of Dhh1p, a cytoplasmic DExD/H-box protein present in large complexes
Stephanie S.-I Tseng-Rogenski, Jean-Leon Chong, Christopher B. Thomas, Shinichiro Enomoto, Judith Berman, and Tien-Hsien Chang
Nucleic Acids Res. 2003 September 1; 31(17): 4995–5002. doi: 10.1093/nar/gkg712.
PMCID: PMC212811
Structural motifs in the RNA encoded by the early nodulation gene enod40 of soybean
Geneviève Girard, Andreas Roussis, Alexander P. Gultyaev, Cornelis W. A. Pleij, and Herman P. Spaink
Nucleic Acids Res. 2003 September 1; 31(17): 5003–5015. doi: 10.1093/nar/gkg721.
PMCID: PMC212817
Elongation by RNA polymerase II on chromatin templates requires topoisomerase activity
Neelima Mondal, Ye Zhang, Zophonias Jonsson, Suman Kumar Dhar, Madhu Kannapiran, and Jeffrey D. Parvin
Nucleic Acids Res. 2003 September 1; 31(17): 5016–5024. doi: 10.1093/nar/gkg705.
PMCID: PMC212805
Construction and analysis of cells lacking the HMGA gene family
Brett Beitzel and Frederic Bushman
Nucleic Acids Res. 2003 September 1; 31(17): 5025–5032. doi: 10.1093/nar/gkg684.
PMCID: PMC212792
Promoter choice affects the potency of HIV-1 specific RNA interference
Daniel Boden, Oliver Pusch, Fredrick Lee, Lynne Tucker, Peter R. Shank, and Bharat Ramratnam
Nucleic Acids Res. 2003 September 1; 31(17): 5033–5038. doi: 10.1093/nar/gkg704.
PMCID: PMC212804
Import of mitochondrial transcription factor A (TFAM) into rat liver mitochondria stimulates transcription of mitochondrial DNA
Heike L. Garstka, Wolfgang E. Schmitt, Jeanette Schultz, Bettina Sogl, Barbara Silakowski, Acisclo Pérez-Martos, Julio Montoya, and Rudolf J. Wiesner
Nucleic Acids Res. 2003 September 1; 31(17): 5039–5047. doi: 10.1093/nar/gkg717.
PMCID: PMC212813
Enzymatic repair of an expanded genetic information system
Michael J. Moser and James R. Prudent
Nucleic Acids Res. 2003 September 1; 31(17): 5048–5053. doi: 10.1093/nar/gkg709.
PMCID: PMC212808
Fission yeast Rhp51 is required for the maintenance of telomere structure in the absence of the Ku heterodimer
Tatsuya Kibe, Kazunori Tomita, Akira Matsuura, Daisuke Izawa, Tsutomu Kodaira, Takashi Ushimaru, Masahiro Uritani, and Masaru Ueno
Nucleic Acids Res. 2003 September 1; 31(17): 5054–5063. doi: 10.1093/nar/gkg718.
PMCID: PMC212814
Nuclear factories for signalling and repairing DNA double strand breaks in living fission yeast
Peter Meister, Mickaël Poidevin, Stefania Francesconi, Isabelle Tratner, Patrick Zarzov, and Giuseppe Baldacci
Nucleic Acids Res. 2003 September 1; 31(17): 5064–5073. doi: 10.1093/nar/gkg719.
PMCID: PMC212815
Effect of polyamines on the inhibition of peptidyltransferase by antibiotics: revisiting the mechanism of chloramphenicol action
Maria A. Xaplanteri, Athanasios Andreou, George P. Dinos, and Dimitrios L. Kalpaxis
Nucleic Acids Res. 2003 September 1; 31(17): 5074–5083. doi: 10.1093/nar/gkg686.
PMCID: PMC212793
Determination of DNA minor groove width in distamycin-DNA complexes by solid-state NMR
Greg L. Olsen, Elizabeth A. Louie, Gary P. Drobny, and Snorri Th. Sigurdsson
Nucleic Acids Res. 2003 September 1; 31(17): 5084–5089. doi: 10.1093/nar/gkg720.
PMCID: PMC212816
Analysis of the DNA joining repertoire of Chlorella virus DNA ligase and a new crystal structure of the ligase–adenylate intermediate
Mark Odell, Lucy Malinina, Verl Sriskanda, Marianna Teplova, and Stewart Shuman
Nucleic Acids Res. 2003 September 1; 31(17): 5090–5100. doi: 10.1093/nar/gkg665.
PMCID: PMC212790
Mg2+-induced triplex formation of an equimolar mixture of poly(rA) and poly(rU)
Besik I. Kankia
Nucleic Acids Res. 2003 September 1; 31(17): 5101–5107. doi: 10.1093/nar/gkg698.
PMCID: PMC212798
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
Xiang-Jun Lu and Wilma K. Olson
Nucleic Acids Res. 2003 September 1; 31(17): 5108–5121. doi: 10.1093/nar/gkg680.
PMCID: PMC212791
Novel chimeric immunomodulatory compounds containing short CpG oligodeoxyribonucleotides have differential activities in human cells
Jason D. Marshall, Edith M. Hessel, Josh Gregorio, Christina Abbate, Priscilla Yee, Mabel Chu, Gary Van Nest, Robert L. Coffman, and Karen L. Fearon
Nucleic Acids Res. 2003 September 1; 31(17): 5122–5133. doi: 10.1093/nar/gkg700.
PMCID: PMC212800
Solution measurement of DNA curvature in papillomavirus E2 binding sites
Jeff M. Zimmerman and L. James Maher, III
Nucleic Acids Res. 2003 September 1; 31(17): 5134–5139. doi: 10.1093/nar/gkg697.
PMCID: PMC212797
Activation of site-specific DNA integration in human cells by a single chain integration host factor
Teresa Corona, Qiuye Bao, Nicole Christ, Thomas Schwartz, Jinming Li, and Peter Dröge
Nucleic Acids Res. 2003 September 1; 31(17): 5140–5148. doi: 10.1093/nar/gkg711.
PMCID: PMC212810
Clerocidin alkylates DNA through its epoxide function: evidence for a fine tuned mechanism of action
Sara Richter, Barbara Gatto, Daniele Fabris, Ken-ichi Takao, Susumu Kobayashi, and Manlio Palumbo
Nucleic Acids Res. 2003 September 1; 31(17): 5149–5156. doi: 10.1093/nar/gkg696.
PMCID: PMC212796
Simultaneous gene expression analysis of steady-state and actively translated mRNA populations from osteosarcoma MG-63 cells in response to IL-1α via an open expression analysis platform
Jingfang Ju, Chunli Huang, Stacey A. Minskoff, Jane E. Mayotte, Bruce E. Taillon, and Jan F. Simons
Nucleic Acids Res. 2003 September 1; 31(17): 5157–5166. doi: 10.1093/nar/gkg702.
PMCID: PMC212802
A positively charged side chain at position 154 on the β8–αE loop of HIV-1 RT is required for stable ternary complex formation
Bechan Sharma, Neerja Kaushik, Alok Upadhyay, Snehlata Tripathi, Kamalendra Singh, and Virendra N. Pandey
Nucleic Acids Res. 2003 September 1; 31(17): 5167–5174. doi: 10.1093/nar/gkg708.
PMCID: PMC212807
MFP1 is a thylakoid-associated, nucleoid-binding protein with a coiled-coil structure
Sun Yong Jeong, Annkatrin Rose, and Iris Meier
Nucleic Acids Res. 2003 September 1; 31(17): 5175–5185. doi: 10.1093/nar/gkg693.
PMCID: PMC212795
On the importance of the primer activation signal for initiation of tRNAlys3-primed reverse transcription of the HIV-1 RNA genome
Hendrik Huthoff, Katarzyna Bugala, Jan Barciszewski, and Ben Berkhout
Nucleic Acids Res. 2003 September 1; 31(17): 5186–5194. doi: 10.1093/nar/gkg714.
PMCID: PMC212812
Comparative analysis of the base biases at the gene terminal portions in seven eukaryote genomes
Yoshihito Niimura, Mahito Terabe, Takashi Gojobori, and Kin-ichiro Miura
Nucleic Acids Res. 2003 September 1; 31(17): 5195–5201. doi: 10.1093/nar/gkg701.
PMCID: PMC212801
Phosphorylation of the PCNA binding domain of the large subunit of replication factor C on Thr506 by cyclin-dependent kinases regulates binding to PCNA
Isabelle Salles-Passador, Anil Munshi, Dominique Cannella, Vincent Pennaneach, Stephane Koundrioukoff, Michel Jacquinod, Eric Forest, Vladimir Podust, Arun Fotedar, and Rati Fotedar
Nucleic Acids Res. 2003 September 1; 31(17): 5202–5211. doi: 10.1093/nar/gkg692.
PMCID: PMC212794
Isochores and tissue-specificity
Alexander E. Vinogradov
Nucleic Acids Res. 2003 September 1; 31(17): 5212–5220. doi: 10.1093/nar/gkg699.
PMCID: PMC212799
NAR Methods Online
An enhanced U6 promoter for synthesis of short hairpin RNA
Xu Gang Xia, Hongxia Zhou, Hongliu Ding, El Bashir Affar, Yang Shi, and Zuoshang Xu
Nucleic Acids Res. 2003 September 1; 31(17): e100. doi: 10.1093/nar/gng098.
PMCID: PMC212820
Improved generation of recombinant baculovirus genomes in Escherichia coli
Kari J. Airenne, Erik Peltomaa, Vesa P. Hytönen, Olli H. Laitinen, and Seppo Ylä-Herttuala
Nucleic Acids Res. 2003 September 1; 31(17): e101. doi: 10.1093/nar/gng102.
PMCID: PMC212821
mRNA fusion constructs serve in a general cell-based assay to profile oligonucleotide activity
Dieter Hüsken, Fred Asselbergs, Bernd Kinzel, Francois Natt, Jan Weiler, Pierre Martin, Robert Häner, and Jonathan Hall
Nucleic Acids Res. 2003 September 1; 31(17): e102. doi: 10.1093/nar/gng103.
PMCID: PMC212822
Parallel gene analysis with allele-specific padlock probes and tag microarrays
Johan Banér, Anders Isaksson, Erik Waldenström, Jonas Jarvius, Ulf Landegren, and Mats Nilsson
Nucleic Acids Res. 2003 September 1; 31(17): e103. doi: 10.1093/nar/gng104.
PMCID: PMC212823
Quantitation of intracellular NAD(P)H can monitor an imbalance of DNA single strand break repair in base excision repair deficient cells in real time
Jun Nakamura, Shoji Asakura, Susan D. Hester, Gilbert de Murcia, Keith W. Caldecott, and James A. Swenberg
Nucleic Acids Res. 2003 September 1; 31(17): e104. doi: 10.1093/nar/gng105.
PMCID: PMC212824
Kinetic Outlier Detection (KOD) in real-time PCR
Tzachi Bar, Anders Ståhlberg, Anders Muszta, and Mikael Kubista
Nucleic Acids Res. 2003 September 1; 31(17): e105. doi: 10.1093/nar/gng106.
PMCID: PMC212825
MGView: an alignment and visualization tool to enhance gap closure of microbial genomes
Lisa Herron-Olson, John Freeman, Qing Zhang, Ernest F. Retzel, and Vivek Kapur
Nucleic Acids Res. 2003 September 1; 31(17): e106. doi: 10.1093/nar/gng107.
PMCID: PMC212826
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