Nucleic Acids Research

Survey and Summary:

Erica L. Mersfelder and Mark R. Parthun

The tale beyond the tail: histone core domain modifications and the regulation of chromatin structure
Nucl. Acids Res. 2006 34: 2653-2662; doi:10.1093/nar/gkl338 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Articles:

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

THUMP from archaeal tRNA:m²₂G10 methyltransferase, a genuine autonomously folding domain
Nucl. Acids Res. 2006 34: 2483-2494; doi:10.1093/nar/gkl145 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Rafael Dhalia, Nina Marinsek, Christian R. S. Reis, Rodolfo Katz, João R. C. Muniz, Nancy Standart, Mark Carrington, and Osvaldo P. de Melo Neto

The two eIF4A helicases in Trypanosoma brucei are functionally distinct
Nucl. Acids Res. 2006 34: 2495-2507; doi:10.1093/nar/gkl290 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Peter Burkovics, Valeria Szukacsov, Ildiko Unk, and Lajos Haracska

Human Ape2 protein has a 3'–5' exonuclease activity that acts preferentially on mismatched base pairs
Nucl. Acids Res. 2006 34: 2508-2515; doi:10.1093/nar/gkl259 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jiho Kim, Sören Doose, Hannes Neuweiler, and Markus Sauer

The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy
Nucl. Acids Res. 2006 34: 2516-2527; doi:10.1093/nar/gkl221 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Matthew Hogg, Wendy Cooper, Linda Reha-Krantz, and Susan S. Wallace

Kinetics of error generation in homologous B-family DNA polymerases
Nucl. Acids Res. 2006 34: 2528-2535; doi:10.1093/nar/gkl300 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Susanna Cogoi and Luigi E. Xodo

G-quadruplex formation within the promoter of the KRAS proto-oncogene and its effect on transcription
Nucl. Acids Res. 2006 34: 2536-2549; doi:10.1093/nar/gkl286 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Henrik Flyvbjerg, Steven A. Keatch, and David T.F. Dryden

Strong physical constraints on sequence-specific target location by proteins on DNA molecules
Nucl. Acids Res. 2006 34: 2550-2557; doi:10.1093/nar/gkl271 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Wigard P. Kloosterman, Florian A. Steiner, Eugene Berezikov, Ewart de Bruijn, Jose van de Belt, Mark Verheul, Edwin Cuppen, and Ronald H.A. Plasterk

Cloning and expression of new microRNAs from zebrafish
Nucl. Acids Res. 2006 34: 2558-2569; doi:10.1093/nar/gkl278 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Xiaofeng Ding, Changzheng Fan, Jianlin Zhou, Yingli Zhong, Rushi Liu, Kaiqun Ren, Xiang Hu, Chang Luo, Shunyong Xiao, Yeqi Wang, Du Feng, and Jian Zhang

GAS41 interacts with transcription factor AP-2ß and stimulates AP-2ß-mediated transactivation
Nucl. Acids Res. 2006 34: 2570-2578; doi:10.1093/nar/gkl319 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Leonid V. Gening, Svetlana A. Klincheva, Anastasia Reshetnjak, Arthur P. Grollman, and Holly Miller

RNA aptamers selected against DNA polymerase ß inhibit the polymerase activities of DNA polymerases ß and
Nucl. Acids Res. 2006 34: 2579-2586; doi:10.1093/nar/gkl326 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Adriana Antúnez de Mayolo, Michael Lisby, Naz Erdeniz, Tanja Thybo, Uffe H. Mortensen, and Rodney Rothstein

Multiple start codons and phosphorylation result in discrete Rad52 protein species
Nucl. Acids Res. 2006 34: 2587-2597; doi:10.1093/nar/gkl280 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. Panchenko, Teresa M. Przytycka, Paul A. Thiessen, and Stephen H. Bryant

Refining multiple sequence alignments with conserved core regions
Nucl. Acids Res. 2006 34: 2598-2606; doi:10.1093/nar/gkl274 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Michael Müller, Julia E. Weigand, Oliver Weichenrieder, and Beatrix Suess

Thermodynamic characterization of an engineered tetracycline-binding riboswitch
Nucl. Acids Res. 2006 34: 2607-2617; doi:10.1093/nar/gkl347 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Roland Ivanyi-Nagy, Igor Kanevsky, Caroline Gabus, Jean-Pierre Lavergne, Damien Ficheux, François Penin, Philippe Fossé, and Jean-Luc Darlix

Analysis of hepatitis C virus RNA dimerization and core–RNA interactions
Nucl. Acids Res. 2006 34: 2618-2633; doi:10.1093/nar/gkl240 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Song Cao and Shi-Jie Chen

Predicting RNA pseudoknot folding thermodynamics
Nucl. Acids Res. 2006 34: 2634-2652; doi:10.1093/nar/gkl346 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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

Long homopurine•homopyrimidine sequences are characteristic of genes expressed in brain and the pseudoautosomal region
Nucl. Acids Res. 2006 34: 2663-2675; doi:10.1093/nar/gkl354 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Anja Zemann, Anja op de Bekke, Martin Kiefmann, Jürgen Brosius, and Jürgen Schmitz

Evolution of small nucleolar RNAs in nematodes
Nucl. Acids Res. 2006 34: 2676-2685; doi:10.1093/nar/gkl359 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Ze-Chun Yuan, Rahat Zaheer, Richard Morton, and Turlough M. Finan

Genome prediction of PhoB regulated promoters in Sinorhizobium meliloti and twelve proteobacteria
Nucl. Acids Res. 2006 34: 2686-2697; doi:10.1093/nar/gkl365 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Mark A. Robinson, Jonathan P.A. Wood, Stephanie A. Capaldi, Andrew J. Baron, Christopher Gell, D. Alastair Smith, and Nicola J. Stonehouse

Affinity of molecular interactions in the bacteriophage 29 DNA packaging motor
Nucl. Acids Res. 2006 34: 2698-2709; doi:10.1093/nar/gkl318 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Olga Steinberg-Neifach and Neal F. Lue

Modulation of telomere terminal structure by telomerase components in Candida albicans
Nucl. Acids Res. 2006 34: 2710-2722; doi:10.1093/nar/gkl345 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Attila Ambrus, Ding Chen, Jixun Dai, Tiffanie Bialis, Roger A. Jones, and Danzhou Yang

Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution
Nucl. Acids Res. 2006 34: 2723-2735; doi:10.1093/nar/gkl348 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jeong Hoon Kim, Catherine K. Yang, and Michael R. Stallcup

Downstream signaling mechanism of the C-terminal activation domain of transcriptional coactivator CoCoA
Nucl. Acids Res. 2006 34: 2736-2750; doi:10.1093/nar/gkl361 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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

Collaboration of Werner syndrome protein and BRCA1 in cellular responses to DNA interstrand cross-links
Nucl. Acids Res. 2006 34: 2751-2760; doi:10.1093/nar/gkl362 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Patrick Hivin, Charlotte Arpin-André, Isabelle Clerc, Benoit Barbeau, and Jean-Michel Mesnard

A modified version of a Fos-associated cluster in HBZ affects Jun transcriptional potency
Nucl. Acids Res. 2006 34: 2761-2772; doi:10.1093/nar/gkl375 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Allison H. S. Hall, Jing Wan, April Spesock, Zinaida Sergueeva, Barbara Ramsay Shaw, and Kenneth A. Alexander

High potency silencing by single-stranded boranophosphate siRNA
Nucl. Acids Res. 2006 34: 2773-2781; doi:10.1093/nar/gkl339 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jennifer Li-Pook-Than and Linda Bonen

Multiple physical forms of excised group II intron RNAs in wheat mitochondria
Nucl. Acids Res. 2006 34: 2782-2790; doi:10.1093/nar/gkl328 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Brian Tjaden, Sarah S. Goodwin, Jason A. Opdyke, Maude Guillier, Daniel X. Fu, Susan Gottesman, and Gisela Storz

Target prediction for small, noncoding RNAs in bacteria
Nucl. Acids Res. 2006 34: 2791-2802; doi:10.1093/nar/gkl356 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

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

Structure-based prediction of insertion-site preferences of transposons into chromosomes
Nucl. Acids Res. 2006 34: 2803-2811; doi:10.1093/nar/gkl301 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

André X. C. N. Valente and Michael E. Cusick

Yeast Protein Interactome topology provides framework for coordinated-functionality
Nucl. Acids Res. 2006 34: 2812-2819; doi:10.1093/nar/gkl325 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Mindy Steiniger, Christian D. Adams, John F. Marko, and William S. Reznikoff

Defining characteristics of Tn5 Transposase non-specific DNA binding
Nucl. Acids Res. 2006 34: 2820-2832; doi:10.1093/nar/gkl179 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Claudia Wiese, John M. Hinz, Robert S. Tebbs, Peter B. Nham, Salustra S. Urbin, David W. Collins, Larry H. Thompson, and David Schild

Disparate requirements for the Walker A and B ATPase motifs of human RAD51D in homologous recombination
Nucl. Acids Res. 2006 34: 2833-2843; doi:10.1093/nar/gkl366 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Corrigendum:

Michiel Wels, Christof Francke, Robert Kerkhoven, Michiel Kleerebezem, and Roland J. Siezen

Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups
Nucl. Acids Res. 2006 34: 2844; doi:10.1093/nar/gkl370 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

M. Abul Kalam, Kazuhiro Haraguchi, Sushil Chandani, Edward L. Loechler, Maasaki Moriya, Marc M. Greenberg, and Ashis K. Basu

Genetic effects of oxidative DNA damages: comparative mutagenesis of the imidazole ring-opened formamidopyrimidines (Fapy lesions) and 8-oxo-purines in simian kidney cells
Nucl. Acids Res. 2006 34: 2845; doi:10.1093/nar/gkl399 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

T. Tran, P. Havlak, and J. Miller

MicroRNA enrichment among short ‘ultraconserved’ sequences in insects
Nucl. Acids Res. 2006 34: e65; doi:10.1093/nar/gkl173 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Alex Pozhitkov, Peter A. Noble, Tomislav Domazet-Loso, Arne W. Nolte, Rainer Sonnenberg, Peer Staehler, Markus Beier, and Diethard Tautz

Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted
Nucl. Acids Res. 2006 34: e66; doi:10.1093/nar/gkl133 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Anton Buzdin, Elena Kovalskaya-Alexandrova, Elena Gogvadze, and Eugene Sverdlov

GREM, a technique for genome-wide isolation and quantitative analysis of promoter active repeats
Nucl. Acids Res. 2006 34: e67; doi:10.1093/nar/gkl335 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Cedric Le Caignec, Claudia Spits, Karen Sermon, Martine De Rycke, Bernard Thienpont, Sophie Debrock, Catherine Staessen, Yves Moreau, Jean-Pierre Fryns, Andre Van Steirteghem, Inge Liebaers, and Joris R. Vermeesch

Single-cell chromosomal imbalances detection by array CGH
Nucl. Acids Res. 2006 34: e68; doi:10.1093/nar/gkl336 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Jin Inoue, Yasushi Shigemori, and Tsutomu Mikawa

Improvements of rolling circle amplification (RCA) efficiency and accuracy using Thermus thermophilus SSB mutant protein
Nucl. Acids Res. 2006 34: e69; doi:10.1093/nar/gkl350 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

G. A. Held, G. Grinstein, and Y. Tu

Relationship between gene expression and observed intensities in DNA microarrays—a modeling study
Nucl. Acids Res. 2006 34: e70; doi:10.1093/nar/gkl122 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Xiao-Zhou Zhang, Xin Yan, Zhong-Li Cui, Qing Hong, and Shun-Peng Li

mazF, a novel counter-selectable marker for unmarked chromosomal manipulation in Bacillus subtilis
Nucl. Acids Res. 2006 34: e71; doi:10.1093/nar/gkl358 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Colin T. Dolphin and Ian A. Hope

Caenorhabditis elegans reporter fusion genes generated by seamless modification of large genomic DNA clones
Nucl. Acids Res. 2006 34: e72; doi:10.1093/nar/gkl352 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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