| | Molecular Biology Effects of Friedreich's ataxia (GAA)n·(TTC)n repeats on RNA synthesis and stability Maria M. Krasilnikova, Maria L. Kireeva, Vladimir Petrovic, Nelli Knijnikova, Mikhail Kashlev, and Sergei M. Mirkin PMCID: PMC1851639 Functional overlap between conserved and diverged KH domains in Saccharomyces cerevisiae SCP160 Melissa A. Brykailo, Anita H. Corbett, and Judith L. Fridovich-Keil PMCID: PMC1994781 Meiotic association between Spo11 regulated by Rec102, Rec104 and Rec114 Hiroyuki Sasanuma, Hajime Murakami, Tomoyuki Fukuda, Takehiko Shibata, Alain Nicolas, and Kunihiro Ohta PMCID: PMC1851646 Sumoylation delays the ATF7 transcription factor subcellular localization and inhibits its transcriptional activity Pierre-Jacques Hamard, Michaël Boyer-Guittaut, Barbara Camuzeaux, Denis Dujardin, Charlotte Hauss, Thomas Oelgeschläger, Marc Vigneron, Claude Kedinger, and Bruno Chatton PMCID: PMC1851647 A Col9a1 enhancer element activated by two interdependent SOX9 dimers Mary Ann Genzer and Laura C. Bridgewater PMCID: PMC1851653 Caf1 regulates translocation of ribonucleotide reductase by releasing nucleoplasmic Spd1–Suc22 assembly Shinya Takahashi, Kenji Kontani, Yasuhiro Araki, and Toshiaki Katada PMCID: PMC1851654 Cruciform extrusion propensity of human translocation-mediating palindromic AT-rich repeats Hiroshi Kogo, Hidehito Inagaki, Tamae Ohye, Takema Kato, Beverly S. Emanuel, and Hiroki Kurahashi PMCID: PMC1851657 Interactions between the RepB initiator protein of plasmid pMV158 and two distant DNA regions within the origin of replication José A. Ruiz-Masó, Rudi Lurz, Manuel Espinosa, and Gloria del Solar PMCID: PMC1851628 Dual role of DNA methylation inside and outside of CTCF-binding regions in the transcriptional regulation of the telomerase hTERT gene S. Renaud, D. Loukinov, Z. Abdullaev, I. Guilleret, F. T. Bosman, V. Lobanenkov, and J. Benhattar PMCID: PMC1851636 Rpm2p, a protein subunit of mitochondrial RNase P, physically and genetically interacts with cytoplasmic processing bodies Vilius Stribinskis and Kenneth S. Ramos PMCID: PMC1851656 ATF2 is required for amino acid-regulated transcription by orchestrating specific histone acetylation Alain Bruhat, Yoan Chérasse, Anne-Catherine Maurin, Wolfgang Breitwieser, Laurent Parry, Christiane Deval, Nic Jones, Céline Jousse, and Pierre Fafournoux PMCID: PMC1851658 Arabidopsis thaliana telomeric DNA-binding protein 1 is required for telomere length homeostasis and its Myb-extension domain stabilizes plant telomeric DNA binding Moo Gak Hwang and Myeon Haeng Cho PMCID: PMC1851659 DNA supercoiling suppresses real-time PCR: a new approach to the quantification of mitochondrial DNA damage and repair Jinsong Chen, Fred F. Kadlubar, and Junjian Z. Chen PMCID: PMC1851651 RNA Inhibition of MDR1 expression with altritol-modified siRNAs Michael Fisher, Mikhail Abramov, Arthur Van Aerschot, Dong Xu, Rudolph L. Juliano, and Piet Herdewijn PMCID: PMC1851637 CRD-BP shields c-myc and MDR-1 RNA from endonucleolytic attack by a mammalian endoribonuclease Dan Sparanese and Chow H. Lee PMCID: PMC1851641 RNA chaperone activity and RNA-binding properties of the E. coli protein StpA Oliver Mayer, Lukas Rajkowitsch, Christina Lorenz, Robert Konrat, and Renée Schroeder PMCID: PMC1851640 Recognition of pyrrolysine tRNA by the Desulfitobacterium hafniense pyrrolysyl-tRNA synthetase Stephanie Herring, Alexandre Ambrogelly, Carla R. Polycarpo, and Dieter Söll PMCID: PMC1851642 Sigma E controls biogenesis of the antisense RNA MicA Klas I. Udekwu and E. Gerhart H. Wagner PMCID: PMC1851643 The gateway pDEST17 expression vector encodes a −1 ribosomal frameshifting sequence Eric J. Belfield, Richard K. Hughes, Nicolas Tsesmetzis, Mike J. Naldrett, and Rod Casey PMCID: PMC1851650 Yeast Rrp14p is required for ribosomal subunit synthesis and for correct positioning of the mitotic spindle during mitosis Marlene Oeffinger, Alessandro Fatica, Michael P. Rout, and David Tollervey PMCID: PMC1849896 Structural Biology High-resolution crystal structure of the intramolecular d(TpA) thymine–adenine photoadduct and its mechanistic implications R. Jeremy H. Davies, John F. Malone, Yu Gan, Christine J. Cardin, Michael P.H. Lee, and Stephen Neidle PMCID: PMC1851629 DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein Ming-Rui Duan, Jie Nan, Yu-He Liang, Peng Mao, Lu Lu, Lanfen Li, Chunhong Wei, Luhua Lai, Yi Li, and Xiao-Dong Su PMCID: PMC1851648 Raman and Raman optical activity (ROA) analysis of RNA structural motifs in Domain I of the EMCV IRES Alison J. Hobro, Mansour Rouhi, Ewan W. Blanch, and Graeme L. Conn PMCID: PMC1851652 Release Factors 2 from Escherichia coli and Thermus thermophilus: structural, spectroscopic and microcalorimetric studies Gabriel Zoldák, Lars Redecke, Dmitri I. Svergun, Peter V. Konarev, C. Stefan Voertler, Holger Dobbek, Erik Sedlák, and Mathias Sprinzl PMCID: PMC1849895 Genomics Identifying synergistic regulation involving c-Myc and sp1 in human tissues Fabio Parisi, Pratyaksha Wirapati, and Felix Naef PMCID: PMC1851645 Identification and characterization of human Mex-3 proteins, a novel family of evolutionarily conserved RNA-binding proteins differentially localized to processing bodies Karine Buchet-Poyau, Julien Courchet, Hervé Le Hir, Bertrand Séraphin, Jean-Yves Scoazec, Laurent Duret, Claire Domon-Dell, Jean-Noël Freund, and Marc Billaud PMCID: PMC1851655 Chemistry Design and synthesis of boronic-acid-labeled thymidine triphosphate for incorporation into DNA Na Lin, Jun Yan, Zhen Huang, Craig Altier, Minyong Li, Nicolas Carrasco, Mitsu Suyemoto, Lynette Johnston, Siming Wang, Qian Wang, Hao Fang, Julianne Caton-Williams, and Binghe Wang PMCID: PMC1851626 Methods Online Use of signal sequences as an in situ removable sequence element to stimulate protein synthesis in cell-free extracts Jin-Ho Ahn, Mi-Yeon Hwang, Kyung-Ho Lee, Cha-Yong Choi, and Dong-Myung Kim PMCID: PMC1849898 An inducible system for expression and validation of the specificity of short hairpin RNA in mammalian cells Hoi Tang Ma, Kin Fan On, Yiu Huen Tsang, and Randy Y.C. Poon PMCID: PMC1851631 Dry-reagent disposable dipstick test for visual screening of seven leukemia-related chromosomal translocations Despina P. Kalogianni, Vasiliki Bravou, Theodore K. Christopoulos, Penelope C. Ioannou, and Nicholas C. Zoumbos PMCID: PMC1851627 Automated parallel isolation of multiple species of non-coding RNAs by the reciprocal circulating chromatography method Kenjyo Miyauchi, Tomoya Ohara, and Tsutomu Suzuki PMCID: PMC1851638 Reversible site-specific tagging of enzymatically synthesized RNAs using aldehyde–hydrazine chemistry and protease-cleavable linkers Stephanie Pfander, Roberto Fiammengo, Srećko I. Kirin, Nils Metzler-Nolte, and Andres Jäschke PMCID: PMC1851632 High-yield production of short GpppA- and 7MeGpppA-capped RNAs and HPLC-monitoring of methyltransfer reactions at the guanine-N7 and adenosine-2′O positions F. Peyrane, B. Selisko, E. Decroly, J. J. Vasseur, D. Benarroch, B. Canard, and K. Alvarez PMCID: PMC1851634 Specific residues at every third position of siRNA shape its efficient RNAi activity Takayuki Katoh and Tsutomu Suzuki PMCID: PMC1851635 Electrospray ionisation-cleavable tandem nucleic acid mass tag–peptide nucleic acid conjugates: synthesis and applications to quantitative genomic analysis using electrospray ionisation-MS/MS Andrew Thompson, Mark Prescott, Noorhan Chelebi, John Smith, Tom Brown, and Günter Schmidt PMCID: PMC1994780 Computational Biology Energetics of protein–DNA interactions Jason E. Donald, William W. Chen, and Eugene I. Shakhnovich PMCID: PMC1851630 Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry Trevor W. Siggers and Barry Honig PMCID: PMC1851644 Nucleic Acid Enzymes DNA polymerase δ-dependent repair of DNA single strand breaks containing 3′-end proximal lesions Jason L. Parsons, Bradley D. Preston, Timothy R. O'Connor, and Grigory L. Dianov PMCID: PMC1851633 The active site residue Valine 867 in human telomerase reverse transcriptase influences nucleotide incorporation and fidelity William C. Drosopoulos and Vinayaka R. Prasad PMCID: PMC1851649 DNA strand displacement, strand annealing and strand swapping by the Drosophila Bloom's syndrome helicase Brian T. Weinert and Donald C. Rio PMCID: PMC1849897 Corrigendum Survey and Summary: Alu elements as regulators of gene expression Julien Häsler and Katharina Strub PMCID: PMC1851660 Corrects: Julien Häsler, et al. Survey and Summary: Alu elements as regulators of gene expression. Nucleic Acids Res. 2007 February; 35(4): 1389. |
