| | Chemistry and Synthetic Biology Kinetics of charge transfer in DNA containing a mismatch Yasuko Osakada, Kiyohiko Kawai, Mamoru Fujitsuka, and Tetsuro Majima PMCID: PMC2553589 Chiral metallo-supramolecular complexes selectively recognize human telomeric G-quadruplex DNA Haijia Yu, Xiaohui Wang, Manliang Fu, Jinsong Ren, and Xiaogang Qu PMCID: PMC2553577 Gene regulation, Chromatin and Epigenetics The transcription factor Sox5 modulates Sox10 function during melanocyte development C. Claus Stolt, Petra Lommes, Simone Hillgärtner, and Michael Wegner PMCID: PMC2553580 Activated transcription via mammalian amino acid response elements does not require enhanced recruitment of the Mediator complex Michelle M. Thiaville, Elizabeth E. Dudenhausen, Keytam S. Awad, Altin Gjymishka, Can Zhong, and Michael S. Kilberg PMCID: PMC2553592 Genome Integrity, Repair and Replication Viral AlkB proteins repair RNA damage by oxidative demethylation Erwin van den Born, Marina V. Omelchenko, Anders Bekkelund, Vibeke Leihne, Eugene V. Koonin, Valerian V. Dolja, and Pål Ø. Falnes PMCID: PMC2553587 DNA replication timing is deterministic at the level of chromosomal domains but stochastic at the level of replicons in Xenopus egg extracts Hélène Labit, Irène Perewoska, Thomas Germe, Olivier Hyrien, and Kathrin Marheineke PMCID: PMC2553594 Evidence for lesion bypass by yeast replicative DNA polymerases during DNA damage Nasim Sabouri, Jörgen Viberg, Dinesh Kumar Goyal, Erik Johansson, and Andrei Chabes PMCID: PMC2553575 Molecular Biology Biochemical analysis of the N-terminal domain of human RAD54B Naoyuki Sarai, Wataru Kagawa, Norie Fujikawa, Kengo Saito, Juri Hikiba, Kozo Tanaka, Kiyoshi Miyagawa, Hitoshi Kurumizaka, and Shigeyuki Yokoyama PMCID: PMC2553597 Helical coherence of DNA in crystals and solution Aaron Wynveen, Dominic J. Lee, Alexei A. Kornyshev, and Sergey Leikin PMCID: PMC2553576 Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3′-end of genes Ju Youn Lee, Zhe Ji, and Bin Tian PMCID: PMC2553571 Non-conservative homologous recombination in human B lymphocytes is promoted by activation-induced cytidine deaminase and transcription Maren Mierau, Guido A. Drexler, André Kutzera, Kerstin Braunschmidt, Joachim Ellwart, Friederike Eckardt-Schupp, Eberhard Fritz, Jürgen Bachl, and Berit Jungnickel PMCID: PMC2553578 A single mutation in the 729 residue modulates human DNA topoisomerase IB DNA binding and drug resistance Carmen Losasso, Erica Cretaio, Paola Fiorani, Ilda D’Annessa, Giovanni Chillemi, and Piero Benedetti PMCID: PMC2553582 Thr729 in human topoisomerase I modulates anti-cancer drug resistance by altering protein domain communications as suggested by molecular dynamics simulations Giovanni Chillemi, Ilda D’Annessa, Paola Fiorani, Carmen Losasso, Piero Benedetti, and Alessandro Desideri PMCID: PMC2553568 Kinetics and thermodynamics of salt-dependent T7 gene 2.5 protein binding to single- and double-stranded DNA Leila Shokri, Boriana Marintcheva, Mootaz Eldib, Andreas Hanke, Ioulia Rouzina, and Mark C. Williams PMCID: PMC2553585 LINE-1 methylation patterns of different loci in normal and cancerous cells Chureerat Phokaew, Supakit Kowudtitham, Keskanya Subbalekha, Shanop Shuangshoti, and Apiwat Mutirangura PMCID: PMC2553567 RNA Core flexibility of a truncated metazoan mitochondrial tRNA Ashley A. Frazer-Abel and Paul J. Hagerman PMCID: PMC2553581 A manganese-dependent ribozyme in the 3′-untranslated region of Xenopus Vg1 mRNA Nikolay G. Kolev, Emilia I. Hartland, and Paul W. Huber PMCID: PMC2553595 A mosaic of RNA binding and protein interaction motifs in a bifunctional mitochondrial tRNA import factor from Leishmania tropica Pratik Home, Saikat Mukherjee, and Samit Adhya PMCID: PMC2553583 Thermodynamic analysis of 5′ and 3′ single- and 3′ double-nucleotide overhangs neighboring wobble terminal base pairs Stacy Miller, Laura E. Jones, Karen Giovannitti, Dan Piper, and Martin J. Serra PMCID: PMC2553593 Structural Biology Stability and kinetics of G-quadruplex structures Andrew N. Lane, J. Brad Chaires, Robert D. Gray, and John O. Trent PMCID: PMC2553573 A thermodynamic overview of naturally occurring intramolecular DNA quadruplexes Niti Kumar and Souvik Maiti PMCID: PMC2553590 Survey and Summary γ-H2AX in recognition and signaling of DNA double-strand breaks in the context of chromatin Andrea Kinner, Wenqi Wu, Christian Staudt, and George Iliakis PMCID: PMC2553572 Methods Online Mix and measure fluorescence screening for selective quadruplex binders Sattanathan Paramasivan and Philip H. Bolton PMCID: PMC2553591 De novo DNA synthesis using single molecule PCR Tuval Ben Yehezkel, Gregory Linshiz, Hen Buaron, Shai Kaplan, Uri Shabi, and Ehud Shapiro PMCID: PMC2553596 Consolidated strategy for the analysis of microarray spike-in data Matthew N. McCall and Rafael A. Irizarry PMCID: PMC2553586 A probabilistic generative model for GO enrichment analysis Yong Lu, Roni Rosenfeld, Itamar Simon, Gerard J. Nau, and Ziv Bar-Joseph PMCID: PMC2553574 An approach of orthology detection from homologous sequences under minimum evolution Kyung Mo Kim, Samsun Sung, Gustavo Caetano-Anollés, Jae Yong Han, and Heebal Kim PMCID: PMC2553584 Homogeneity and persistence of transgene expression by omitting antibiotic selection in cell line isolation Weimin L. Kaufman, Ibrahim Kocman, Vishal Agrawal, Hans-Peter Rahn, Daniel Besser, and Manfred Gossen PMCID: PMC2553579 Analysis of copy number variation using quantitative interspecies competitive PCR Nigel M. Williams, Hywel Williams, Elisa Majounie, Nadine Norton, Beate Glaser, Huw R. Morris, Michael J. Owen, and Michael C. O’Donovan PMCID: PMC2553599 Efficient transfer of two large secondary metabolite pathway gene clusters into heterologous hosts by transposition Jun Fu, Silke C. Wenzel, Olena Perlova, Junping Wang, Frank Gross, Zhiru Tang, Yulong Yin, A. Francis Stewart, Rolf Müller, and Youming Zhang PMCID: PMC2553598 Nucleic Acid Enzymes Cell type differences in activity of the Streptomyces bacteriophage ϕC31 integrase Christof Maucksch, Manish Kumar Aneja, Elisabeth Hennen, Alexander Bohla, Florian Hoffmann, Markus Elfinger, Joseph Rosenecker, and Carsten Rudolph PMCID: PMC2553569 Clerocidin selectively modifies the gyrase-DNA gate to induce irreversible and reversible DNA damage Xiao Su Pan, Miriam Dias, Manlio Palumbo, and L. Mark Fisher PMCID: PMC2553588 Thermoplasma acidophilum Cdc6 protein stimulates MCM helicase activity by regulating its ATPase activity Gyri Teien Haugland, Nozomi Sakakibara, Angel L. Pey, Claire R. Rollor, Nils-Kåre Birkeland, and Zvi Kelman PMCID: PMC2553600 Evidence for an inositol hexakisphosphate-dependent role for Ku in mammalian nonhomologous end joining that is independent of its role in the DNA-dependent protein kinase Joyce C.Y. Cheung, Brenda Salerno, and Les A. Hanakahi PMCID: PMC2553570 |
