| | Editorial Editorial Johannes Grillari and William Dynan Nucleic Acids Res. 2007 December; 35(22): 7397–7398. Published online 2007 December. doi: 10.1093/nar/gkm1164.PMCID: PMC2190702 Molecular Biology Site-directed gene mutation at mixed sequence targets by psoralen-conjugated pseudo-complementary peptide nucleic acids Ki-Hyun Kim, Peter E. Nielsen, and Peter M. Glazer Nucleic Acids Res. 2007 December; 35(22): 7604–7613. Published online 2007 December. doi: 10.1093/nar/gkm666.PMCID: PMC2190703 Exploring the sequence space of a DNA aptamer using microarrays Evaldas Katilius, Carole Flores, and Neal W. Woodbury Nucleic Acids Res. 2007 December; 35(22): 7626–7635. Published online 2007 December. doi: 10.1093/nar/gkm922.PMCID: PMC2190713 Feedback-regulated poly(ADP-ribosyl)ation by PARP-1 is required for rapid response to DNA damage in living cells Oliver Mortusewicz, Jean-Christophe Amé, Valérie Schreiber, and Heinrich Leonhardt Nucleic Acids Res. 2007 December; 35(22): 7665–7675. Published online 2007 December. doi: 10.1093/nar/gkm933.PMCID: PMC2190722 Base excision repair processing of abasic site/single-strand break lesions within clustered damage sites associated with XRCC1 deficiency Sophie Mourgues, Martine E. Lomax, and Peter O’Neill Nucleic Acids Res. 2007 December; 35(22): 7676–7687. Published online 2007 December. doi: 10.1093/nar/gkm947.PMCID: PMC2190709 Characterization of the G-quadruplexes in the duplex nuclease hypersensitive element of the PDGF-A promoter and modulation of PDGF-A promoter activity by TMPyP4 Yong Qin, Evonne M. Rezler, Vijay Gokhale, Daekyu Sun, and Laurence H. Hurley Nucleic Acids Res. 2007 December; 35(22): 7698–7713. Published online 2007 December. doi: 10.1093/nar/gkm538.PMCID: PMC2190695 Characterization of DNA-binding activity of Zα domains from poxviruses and the importance of the β-wing regions in converting B-DNA to Z-DNA Dong Van Quyen, Sung Chul Ha, Ky Lowenhaupt, Alexander Rich, Kyeong Kyu Kim, and Yang-Gyun Kim Nucleic Acids Res. 2007 December; 35(22): 7714–7720. Published online 2007 December. doi: 10.1093/nar/gkm748.PMCID: PMC2190711 RNA Regulatory mechanisms for 3′-end alternative splicing and polyadenylation of the Glial Fibrillary Acidic Protein, GFAP, transcript Jenny Blechingberg, Søren Lykke-Andersen, Torben Heick Jensen, Arne Lund Jørgensen, and Anders Lade Nielsen Nucleic Acids Res. 2007 December; 35(22): 7636–7650. Published online 2007 December. doi: 10.1093/nar/gkm931.PMCID: PMC2190720 Characterization of the role of ribonucleases in Salmonella small RNA decay Sandra C. Viegas, Verena Pfeiffer, Alexandra Sittka, Inês J. Silva, Jörg Vogel, and Cecília M. Arraiano Nucleic Acids Res. 2007 December; 35(22): 7651–7664. Published online 2007 December. doi: 10.1093/nar/gkm916.PMCID: PMC2190706 Saccharomyces cerevisiae Ebs1p is a putative ortholog of human Smg7 and promotes nonsense-mediated mRNA decay Brian Luke, Claus M. Azzalin, Nele Hug, Anna Deplazes, Matthias Peter, and Joachim Lingner Nucleic Acids Res. 2007 December; 35(22): 7688–7697. Published online 2007 December. doi: 10.1093/nar/gkm912.PMCID: PMC2190716 Survey and Summary The ageing mitochondrial genome Kim J. Krishnan, Laura C. Greaves, Amy K. Reeve, and Doug Turnbull Nucleic Acids Res. 2007 December; 35(22): 7399–7405. Published online 2007 December. doi: 10.1093/nar/gkm635.PMCID: PMC2190723 Human diseases of telomerase dysfunction: insights into tissue aging Christine Kim Garcia, Woodring E. Wright, and Jerry W. Shay Nucleic Acids Res. 2007 December; 35(22): 7406–7416. Published online 2007 December. doi: 10.1093/nar/gkm644.PMCID: PMC2190725 DNA damage, cellular senescence and organismal ageing: causal or correlative? Jian-Hua Chen, C. Nicholes Hales, and Susan E. Ozanne Nucleic Acids Res. 2007 December; 35(22): 7417–7428. Published online 2007 December. doi: 10.1093/nar/gkm681.PMCID: PMC2190714 Human telomere, oncogenic promoter and 5′-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics Dinshaw J. Patel, Anh Tuân Phan, and Vitaly Kuryavyi Nucleic Acids Res. 2007 December; 35(22): 7429–7455. Published online 2007 December. doi: 10.1093/nar/gkm711.PMCID: PMC2190718 Poly(ADP-ribosyl)ation in mammalian ageing Sascha Beneke and Alexander Bürkle Nucleic Acids Res. 2007 December; 35(22): 7456–7465. Published online 2007 December. doi: 10.1093/nar/gkm735.PMCID: PMC2190698 Changes in DNA repair during aging Vera Gorbunova, Andrei Seluanov, Zhiyong Mao, and Christpher Hine Nucleic Acids Res. 2007 December; 35(22): 7466–7474. Published online 2007 December. doi: 10.1093/nar/gkm756.PMCID: PMC2190694 Two faces of p53: aging and tumor suppression Francis Rodier, Judith Campisi, and Dipa Bhaumik Nucleic Acids Res. 2007 December; 35(22): 7475–7484. Published online 2007 December. doi: 10.1093/nar/gkm744.PMCID: PMC2190721 Caloric restriction and genomic stability Ahmad R. Heydari, Archana Unnikrishnan, Lisa Ventrella Lucente, and Arlan Richardson Nucleic Acids Res. 2007 December; 35(22): 7485–7496. Published online 2007 December. doi: 10.1093/nar/gkm860.PMCID: PMC2190719 Oxidative DNA damage in mild cognitive impairment and late-stage Alzheimer's disease Mark A. Lovell and William R. Markesbery Nucleic Acids Res. 2007 December; 35(22): 7497–7504. Published online 2007 December. doi: 10.1093/nar/gkm821.PMCID: PMC2190704 DNA damage in telomeres and mitochondria during cellular senescence: is there a connection? João F. Passos, Gabriele Saretzki, and Thomas von Zglinicki Nucleic Acids Res. 2007 December; 35(22): 7505–7513. Published online 2007 December. doi: 10.1093/nar/gkm893.PMCID: PMC2190715 Yeast mother cell-specific ageing, genetic (in)stability, and the somatic mutation theory of ageing Peter Laun, Carlo V. Bruschi, J. Richard Dickinson, Mark Rinnerthaler, Gino Heeren, Richard Schwimbersky, Raphaela Rid, and Michael Breitenbach Nucleic Acids Res. 2007 December; 35(22): 7514–7526. Published online 2007 December. doi: 10.1093/nar/gkm919.PMCID: PMC2190697 Human premature aging, DNA repair and RecQ helicases Robert M. Brosh, Jr and Vilhelm A. Bohr Nucleic Acids Res. 2007 December; 35(22): 7527–7544. Published online 2007 December. doi: 10.1093/nar/gkm1008.PMCID: PMC2190726 DNA replication stress, genome instability and aging William C. Burhans and Martin Weinberger Nucleic Acids Res. 2007 December; 35(22): 7545–7556. Published online 2007 December. doi: 10.1093/nar/gkm1059.PMCID: PMC2190710 The role of DNA damage repair in aging of adult stem cells Jonathan Kenyon and Stanton L. Gerson Nucleic Acids Res. 2007 December; 35(22): 7557–7565. Published online 2007 December. doi: 10.1093/nar/gkm1064.PMCID: PMC2190724 Contributions of DNA interstrand cross-links to aging of cells and organisms Johannes Grillari, Hermann Katinger, and Regina Voglauer Nucleic Acids Res. 2007 December; 35(22): 7566–7576. Published online 2007 December. doi: 10.1093/nar/gkm1065.PMCID: PMC2190700 Multidimensional annotation of the Escherichia coli K-12 genome Peter D. Karp, Ingrid M. Keseler, Alexander Shearer, Mario Latendresse, Markus Krummenacker, Suzanne M. Paley, Ian Paulsen, Julio Collado-Vides, Socorro Gama-Castro, Martin Peralta-Gil, Alberto Santos-Zavaleta, Mónica I. Peñaloza-Spínola, César Bonavides-Martinez, and John Ingraham Nucleic Acids Res. 2007 December; 35(22): 7577–7590. Published online 2007 December. doi: 10.1093/nar/gkm740.PMCID: PMC2190727 Genomics The origins and early evolution of DNA mismatch repair genes—multiple horizontal gene transfers and co-evolution Zhenguo Lin, Masatoshi Nei, and Hong Ma Nucleic Acids Res. 2007 December; 35(22): 7591–7603. Published online 2007 December. doi: 10.1093/nar/gkm921.PMCID: PMC2190696 Methods Online Lentivirus-mediated antagomir expression for specific inhibition of miRNA function Michaela Scherr, Letizia Venturini, Karin Battmer, Michael Schaller-Schoenitz, Daniel Schaefer, Iris Dallmann, Arnold Ganser, and Matthias Eder Nucleic Acids Res. 2007 December; 35(22): e149. Published online 2007 December. doi: 10.1093/nar/gkm971.PMCID: PMC2190705 STRALCP—structure alignment-based clustering of proteins Adam Zemla, Brian Geisbrecht, Jason Smith, Marisa Lam, Bonnie Kirkpatrick, Mark Wagner, Tom Slezak, and Carol Ecale Zhou Nucleic Acids Res. 2007 December; 35(22): e150. Published online 2007 December. doi: 10.1093/nar/gkm1049.PMCID: PMC2190701 Polony analysis of gene expression in ES cells and blastocysts C. Rieger, R. Poppino, R. Sheridan, K. Moley, R. Mitra, and D. Gottlieb Nucleic Acids Res. 2007 December; 35(22): e151. Published online 2007 December. doi: 10.1093/nar/gkm1076.PMCID: PMC2190707 Small-scale extracts for the study of nucleotide excision repair and non-homologous end joining Michael B. Smeaton, Paul S. Miller, Gary Ketner, and Les A. Hanakahi Nucleic Acids Res. 2007 December; 35(22): e152. Published online 2007 December. doi: 10.1093/nar/gkm974.PMCID: PMC2190712 Computational Biology Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements Buyong Ma and Arnold J. Levine Nucleic Acids Res. 2007 December; 35(22): 7733–7747. Published online 2007 December. doi: 10.1093/nar/gkm890.PMCID: PMC2190717 Nucleic Acid Enzymes Ribonuclease P processes polycistronic tRNA transcripts in Escherichia coli independent of ribonuclease E Bijoy K. Mohanty and Sidney R. Kushner Nucleic Acids Res. 2007 December; 35(22): 7614–7625. Published online 2007 December. doi: 10.1093/nar/gkm917.PMCID: PMC2190699 Characterization of the 2′,3′ cyclic phosphodiesterase activities of Clostridium thermocellum polynucleotide kinase-phosphatase and bacteriophage λ phosphatase Niroshika Keppetipola and Stewart Shuman Nucleic Acids Res. 2007 December; 35(22): 7721–7732. Published online 2007 December. doi: 10.1093/nar/gkm868.PMCID: PMC2190708 |