| | Survey and Summary The tale beyond the tail: histone core domain modifications and the regulation of chromatin structure Erica L. Mersfelder and Mark R. Parthun PMCID: PMC1464108 Articles THUMP from archaeal tRNA:m22G10 methyltransferase, a genuine autonomously folding domain Guillaume Gabant, Sylvie Auxilien, Irina Tuszynska, Marie Locard, Michal J. Gajda, Guylaine Chaussinand, Bernard Fernandez, Alain Dedieu, Henri Grosjean, Béatrice Golinelli-Pimpaneau, Janusz M. Bujnicki, and Jean Armengaud PMCID: PMC1459410 The two eIF4A helicases in Trypanosoma brucei are functionally distinct Rafael Dhalia, Nina Marinsek, Christian R. S. Reis, Rodolfo Katz, João R. C. Muniz, Nancy Standart, Mark Carrington, and Osvaldo P. de Melo Neto PMCID: PMC1459412 Human Ape2 protein has a 3′–5′ exonuclease activity that acts preferentially on mismatched base pairs Peter Burkovics, Valeria Szukacsov, Ildiko Unk, and Lajos Haracska PMCID: PMC1459411 The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy Jiho Kim, Sören Doose, Hannes Neuweiler, and Markus Sauer PMCID: PMC1459409 Kinetics of error generation in homologous B-family DNA polymerases Matthew Hogg, Wendy Cooper, Linda Reha-Krantz, and Susan S. Wallace PMCID: PMC1459414 G-quadruplex formation within the promoter of the KRAS proto-oncogene and its effect on transcription Susanna Cogoi and Luigi E. Xodo PMCID: PMC1459413 RNA aptamers selected against DNA polymerase β inhibit the polymerase activities of DNA polymerases β and κ Leonid V. Gening, Svetlana A. Klincheva, Anastasia Reshetnjak, Arthur P. Grollman, and Holly Miller PMCID: PMC1463896 Multiple start codons and phosphorylation result in discrete Rad52 protein species Adriana Antúnez de Mayolo, Michael Lisby, Naz Erdeniz, Tanja Thybo, Uffe H. Mortensen, and Rodney Rothstein PMCID: PMC1463902 Refining multiple sequence alignments with conserved core regions Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. Panchenko, Teresa M. Przytycka, Paul A. Thiessen, and Stephen H. Bryant PMCID: PMC1463900 Thermodynamic characterization of an engineered tetracycline-binding riboswitch Michael Müller, Julia E. Weigand, Oliver Weichenrieder, and Beatrix Suess PMCID: PMC1463898 Analysis of hepatitis C virus RNA dimerization and core–RNA interactions Roland Ivanyi-Nagy, Igor Kanevsky, Caroline Gabus, Jean-Pierre Lavergne, Damien Ficheux, François Penin, Philippe Fossé, and Jean-Luc Darlix PMCID: PMC1463901 Predicting RNA pseudoknot folding thermodynamics Song Cao and Shi-Jie Chen PMCID: PMC1463895 Long homopurine•homopyrimidine sequences are characteristic of genes expressed in brain and the pseudoautosomal region Albino Bacolla, Jack R. Collins, Bert Gold, Nadia Chuzhanova, Ming Yi, Robert M. Stephens, Stefan Stefanov, Adam Olsh, John P. Jakupciak, Michael Dean, Richard A. Lempicki, David N. Cooper, and Robert D. Wells PMCID: PMC1464109 Evolution of small nucleolar RNAs in nematodes Anja Zemann, Anja op de Bekke, Martin Kiefmann, Jürgen Brosius, and Jürgen Schmitz PMCID: PMC1464110 Genome prediction of PhoB regulated promoters in Sinorhizobium meliloti and twelve proteobacteria Ze-Chun Yuan, Rahat Zaheer, Richard Morton, and Turlough M. Finan PMCID: PMC1464414 Affinity of molecular interactions in the bacteriophage ![[var phi]](corehtml/pmc/pmcents/x03C6.gif) 29 DNA packaging motor Mark A. Robinson, Jonathan P.A. Wood, Stephanie A. Capaldi, Andrew J. Baron, Christopher Gell, D. Alastair Smith, and Nicola J. Stonehouse PMCID: PMC1464111 Modulation of telomere terminal structure by telomerase components in Candida albicans Olga Steinberg-Neifach and Neal F. Lue PMCID: PMC1464115 Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution Attila Ambrus, Ding Chen, Jixun Dai, Tiffanie Bialis, Roger A. Jones, and Danzhou Yang PMCID: PMC1464114 Downstream signaling mechanism of the C-terminal activation domain of transcriptional coactivator CoCoA Jeong Hoon Kim, Catherine K. Yang, and Michael R. Stallcup PMCID: PMC1464418 Collaboration of Werner syndrome protein and BRCA1 in cellular responses to DNA interstrand cross-links Wen-Hsing Cheng, Rika Kusumoto, Patricia L. Opresko, XiuFen Sui, Shurong Huang, Matthew L. Nicolette, Tanya T. Paull, Judith Campisi, Michael Seidman, and Vilhelm A. Bohr PMCID: PMC1464112 A modified version of a Fos-associated cluster in HBZ affects Jun transcriptional potency Patrick Hivin, Charlotte Arpin-André, Isabelle Clerc, Benoit Barbeau, and Jean-Michel Mesnard PMCID: PMC1464409 High potency silencing by single-stranded boranophosphate siRNA Allison H. S. Hall, Jing Wan, April Spesock, Zinaida Sergueeva, Barbara Ramsay Shaw, and Kenneth A. Alexander PMCID: PMC1464415 Multiple physical forms of excised group II intron RNAs in wheat mitochondria Jennifer Li-Pook-Than and Linda Bonen PMCID: PMC1464410 Target prediction for small, noncoding RNAs in bacteria Brian Tjaden, Sarah S. Goodwin, Jason A. Opdyke, Maude Guillier, Daniel X. Fu, Susan Gottesman, and Gisela Storz PMCID: PMC1464411 Structure-based prediction of insertion-site preferences of transposons into chromosomes Aron M. Geurts, Christopher S. Hackett, Jason B. Bell, Tracy L. Bergemann, Lara S. Collier, Corey M. Carlson, David A. Largaespada, and Perry B. Hackett PMCID: PMC1464413 Yeast Protein Interactome topology provides framework for coordinated-functionality André X. C. N. Valente and Michael E. Cusick PMCID: PMC1464412 Defining characteristics of Tn5 Transposase non-specific DNA binding Mindy Steiniger, Christian D. Adams, John F. Marko, and William S. Reznikoff PMCID: PMC1464417 Disparate requirements for the Walker A and B ATPase motifs of human RAD51D in homologous recombination Claudia Wiese, John M. Hinz, Robert S. Tebbs, Peter B. Nham, Salustra S. Urbin, David W. Collins, Larry H. Thompson, and David Schild PMCID: PMC1464408 Methods Online Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted Alex Pozhitkov, Peter A. Noble, Tomislav Domazet-Lošo, Arne W. Nolte, Rainer Sonnenberg, Peer Staehler, Markus Beier, and Diethard Tautz PMCID: PMC1463897 Improvements of rolling circle amplification (RCA) efficiency and accuracy using Thermus thermophilus SSB mutant protein Jin Inoue, Yasushi Shigemori, and Tsutomu Mikawa PMCID: PMC1463899 Relationship between gene expression and observed intensities in DNA microarrays—a modeling study G. A. Held, G. Grinstein, and Y. Tu PMCID: PMC1472623 mazF, a novel counter-selectable marker for unmarked chromosomal manipulation in Bacillus subtilis Xiao-Zhou Zhang, Xin Yan, Zhong-Li Cui, Qing Hong, and Shun-Peng Li PMCID: PMC1464113 Caenorhabditis elegans reporter fusion genes generated by seamless modification of large genomic DNA clones Colin T. Dolphin and Ian A. Hope PMCID: PMC1464416 Corrigenda Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups Michiel Wels, Christof Francke, Robert Kerkhoven, Michiel Kleerebezem, and Roland J. Siezen PMCID: PMC1472624 Corrects: Michiel Wels, et al. Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups. Nucleic Acids Res. 2006; 34(7): 1947–1958. Genetic effects of oxidative DNA damages: comparative mutagenesis of the imidazole ring-opened formamidopyrimidines (Fapy lesions) and 8-oxo-purines in simian kidney cells M. Abul Kalam, Kazuhiro Haraguchi, Sushil Chandani, Edward L. Loechler, Maasaki Moriya, Marc M. Greenberg, and Ashis K. Basu PMCID: PMC1472625 Corrects: M. Abul Kalam, et al. Genetic effects of oxidative DNA damages: comparative mutagenesis of the imidazole ring-opened formamidopyrimidines (Fapy lesions) and 8-oxo-purines in simian kidney cells. Nucleic Acids Res. 2006; 34(8): 2305–2315. |
