| | Molecular Biology Uracil–DNA glycosylases SMUG1 and UNG2 coordinate the initial steps of base excision repair by distinct mechanisms Henrik Sahlin Pettersen, Ottar Sundheim, Karin Margaretha Gilljam, Geir Slupphaug, Hans Einar Krokan, and Bodil Kavli PMCID: PMC1919486 A new connection of mRNP biogenesis and export with transcription-coupled repair Hélène Gaillard, Ralf Erik Wellinger, and Andrés Aguilera PMCID: PMC1919492 Cellular antisense activity of peptide nucleic acid (PNAs) targeted to HIV-1 polypurine tract (PPT) containing RNA Fatima Boutimah-Hamoudi, Erwan Leforestier, Catherine Sénamaud-Beaufort, Peter E. Nielsen, Carine Giovannangeli, and Tula Ester Saison-Behmoaras PMCID: PMC1919497 Characterization of the sequence specificity of the R1Bm endonuclease domain by structural and biochemical studies Nobuo Maita, Hideyuki Aoyagi, Mizuko Osanai, Masahiro Shirakawa, and Haruhiko Fujiwara PMCID: PMC1919474 Efficient and exclusive induction of Tet repressor by the oligopeptide Tip results from co-variation of their interaction site Marcus Klotzsche, Dagmar Goeke, Christian Berens, and Wolfgang Hillen PMCID: PMC1919500 The selenoproteome exhibits widely varying, tissue-specific dependence on selenoprotein P for selenium supply Peter R. Hoffmann, Simone C. Höge, Ping-An Li, Fukun W. Hoffmann, Ann C. Hashimoto, and Marla J. Berry PMCID: PMC1919489 Effects of nucleic acid local structure and magnesium ions on minus-strand transfer mediated by the nucleic acid chaperone activity of HIV-1 nucleocapsid protein Tiyun Wu, Susan L. Heilman-Miller, and Judith G. Levin PMCID: PMC1919501 Effects of nucleoid proteins on DNA repression loop formation in Escherichia coli Nicole A. Becker, Jason D. Kahn, and L. James Maher, III PMCID: PMC1919473 Synthesis and investigation of deoxyribonucleic acid/locked nucleic acid chimeric molecular beacons Chaoyong James Yang, Lin Wang, Yanrong Wu, Youngmi Kim, Colin D. Medley, Hui Lin, and Weihong Tan PMCID: PMC1919502 Relative abundance of the human mitochondrial transcription system and distinct roles for h-mtTFB1 and h-mtTFB2 in mitochondrial biogenesis and gene expression Justin Cotney, Zhibo Wang, and Gerald S. Shadel PMCID: PMC1919481 DSIF contributes to transcriptional activation by DNA-binding activators by preventing pausing during transcription elongation Wenyan Zhu, Tadashi Wada, Sachiko Okabe, Takuya Taneda, Yuki Yamaguchi, and Hiroshi Handa PMCID: PMC1919491 Nuclear interactions of topoisomerase II α and β with phospholipid scramblase 1 Jessica P. Wyles, Zhongqin Wu, Shelagh E.L. Mirski, and Susan P.C. Cole PMCID: PMC1919507 Regulation of DNA nucleases by molecular crowding Yoshiharu Sasaki, Daisuke Miyoshi, and Naoki Sugimoto PMCID: PMC1919490 RNA Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors Yen-I G. Chen, Roger E. Moore, Helen Y. Ge, Mary K. Young, Terry D. Lee, and Scott W. Stevens PMCID: PMC1919476 Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA Filip Rázga, Jaroslav Koča, Ali Mokdad, and Jiří Šponer PMCID: PMC1919483 Functional genetic selection of Helix 66 in Escherichia coli 23S rRNA identified the eukaryotic-binding sequence for ribosomal protein L2 Kei Kitahara, Akimasa Kajiura, Neuza Satomi Sato, and Tsutomu Suzuki PMCID: PMC1919495 Explaining differences in saturation levels for Affymetrix GeneChip® arrays Dmitriy Skvortsov, Diana Abdueva, Christina Curtis, Betty Schaub, and Simon Tavaré PMCID: PMC1919478 PLP/DM20 ratio is regulated by hnRNPH and F and a novel G-rich enhancer in oligodendrocytes Erming Wang, Neviana Dimova, and Franca Cambi PMCID: PMC1919487 Tetracycline aptamer-controlled regulation of pre-mRNA splicing in yeast Julia E. Weigand and Beatrix Suess PMCID: PMC1919484 In vitro selection of a 5′-purine ribonucleotide transferase ribozyme Taek Jin Kang and Hiroaki Suga PMCID: PMC1919479 Functional analysis of Saccharomyces cerevisiae ribosomal protein Rpl3p in ribosome synthesis Iván V. Rosado, Dieter Kressler, and Jesús de la Cruz PMCID: PMC1919493 Structural Biology Intramolecular DNA quadruplexes with different arrangements of short and long loops Phillip A. Rachwal, I. Stuart Findlow, Joern M. Werner, Tom Brown, and Keith R. Fox PMCID: PMC1919480 Chemistry A chemical synthesis of LNA-2,6-diaminopurine riboside, and the influence of 2′-O-methyl-2,6-diaminopurine and LNA-2,6-diaminopurine ribosides on the thermodynamic properties of 2′-O-methyl RNA/RNA heteroduplexes Anna Pasternak, Elzbieta Kierzek, Karol Pasternak, Douglas H. Turner, and Ryszard Kierzek PMCID: PMC1919511 Methods Online s-RT-MELT for rapid mutation scanning using enzymatic selection and real time DNA-melting: new potential for multiplex genetic analysis Jin Li, Ross Berbeco, Robert J. Distel, Pasi A. Jänne, Lilin Wang, and G. Mike Makrigiorgos PMCID: PMC1919510 Novel zinc-based fixative for high quality DNA, RNA and protein analysis Dimitrios Lykidis, Susan Van Noorden, Alan Armstrong, Bradley Spencer-Dene, Jie Li, Zhengping Zhuang, and Gordon W. H. Stamp PMCID: PMC1919503 Nuclear accumulation of plasmid DNA can be enhanced by non-selective gating of the nuclear pore Roosmarijn E. Vandenbroucke, Bart Lucas, Joseph Demeester, Stefaan C. De Smedt, and Niek N. Sanders PMCID: PMC1919477 Generation of an inducible and optimized piggyBac transposon system Juan Cadiñanos and Allan Bradley PMCID: PMC1919496 Small multicopy, non-integrative shuttle vectors based on the plasmid pRN1 for Sulfolobus acidocaldarius and Sulfolobus solfataricus, model organisms of the (cren-)archaea Silvia Berkner, Dennis Grogan, Sonja-Verena Albers, and Georg Lipps PMCID: PMC1919505 A 96-well DNase I footprinting screen for drug–DNA interactions Tom Ellis, David A. Evans, Christopher R. H. Martin, and John A. Hartley PMCID: PMC1919508 Conditional brain-specific knockdown of MAPK using Cre/loxP regulated RNA interference Christiane Hitz, Wolfgang Wurst, and Ralf Kühn PMCID: PMC1919482 Computational Biology A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case G.X. Yu, E.E. Snyder, S.M. Boyle, O.R. Crasta, M. Czar, S.P. Mane, A. Purkayastha, B. Sobral, and J.C. Setubal PMCID: PMC1919506 A statistical learning approach to the modeling of chromatographic retention of oligonucleotides incorporating sequence and secondary structure data Marc Sturm, Sascha Quinten, Christian G. Huber, and Oliver Kohlbacher PMCID: PMC1919494 Nucleic Acid Enzymes Phosphorylation in the serine/threonine 2609–2647 cluster promotes but is not essential for DNA-dependent protein kinase-mediated nonhomologous end joining in human whole-cell extracts Lawrence F. Povirk, Rui-Zhe Zhou, Dale A. Ramsden, Susan P. Lees-Miller, and Kristoffer Valerie PMCID: PMC1919499 ‘In-line attack’ conformational effect plays a modest role in an enzyme-catalyzed RNA cleavage: a free energy simulation study Donghong Min, Song Xue, Hong Li, and Wei Yang PMCID: PMC1919504 Molecular interactions of Escherichia coli ExoIX and identification of its associated 3′–5′ exonuclease activity Michael R. G. Hodskinson, Lee M. Allen, Duncan P. Thomson, and Jon R. Sayers PMCID: PMC1919509 Cockayne syndrome B protein stimulates apurinic endonuclease 1 activity and protects against agents that introduce base excision repair intermediates Heng-Kuan Wong, Meltem Muftuoglu, Gad Beck, Syed Z. Imam, Vilhelm A. Bohr, and David M. Wilson, III PMCID: PMC1919475 Multiple functions for the N-terminal region of Msh6 Alan B. Clark, Leesa Deterding, Kenneth B. Tomer, and Thomas A. Kunkel PMCID: PMC1919485 Rad51 and Rad54 ATPase activities are both required to modulate Rad51-dsDNA filament dynamics Xuan Li, Xiao-Ping Zhang, Jachen A. Solinger, Konstantin Kiianitsa, Xiong Yu, Edward H. Egelman, and Wolf-Dietrich Heyer PMCID: PMC1919488 The −11A of promoter DNA and two conserved amino acids in the melting region of σ70 both directly affect the rate limiting step in formation of the stable RNA polymerase-promoter complex, but they do not necessarily interact Lisa A. Schroeder, Ae-Jin Choi, and Pieter L. deHaseth PMCID: PMC1919498 |
