| | Molecular Biology Dynamics of Dnmt1 interaction with the replication machinery and its role in postreplicative maintenance of DNA methylation Lothar Schermelleh, Andrea Haemmer, Fabio Spada, Nicole Rösing, Daniela Meilinger, Ulrich Rothbauer, M. Cristina Cardoso, and Heinrich Leonhardt PMCID: PMC1934996 Different structural states in oligonucleosomes are required for early versus late steps of base excision repair Shima Nakanishi, Rajendra Prasad, Samuel H. Wilson, and Michael Smerdon PMCID: PMC1934998 Interplay of polyethyleneimine molecular weight and oligonucleotide backbone chemistry in the dynamics of antisense activity Sumati Sundaram, Li Kim Lee, and Charles M. Roth PMCID: PMC1935005 Nearest-neighbor non-additivity versus long-range non-additivity in TATA-box structure and its implications for TBP-binding mechanism Hana Faiger, Marina Ivanchenko, and Tali E. Haran PMCID: PMC1935006 Transcriptional co-activator protein p100 interacts with snRNP proteins and facilitates the assembly of the spliceosome Jie Yang, Tuuli Välineva, Jingxin Hong, Tianxu Bu, Zhi Yao, Ole N. Jensen, Mikko J. Frilander, and Olli Silvennoinen PMCID: PMC1935017 Efficient splicing correction by PNA conjugation to an R6-Penetratin delivery peptide Saïd Abes, John J. Turner, Gabriela D. Ivanova, David Owen, Donna Williams, Andrey Arzumanov, Philippe Clair, Michael J. Gait, and Bernard Lebleu PMCID: PMC1934994 Functional conservation between structurally diverse ribosomal proteins from Drosophila melanogaster and Saccharomyces cerevisiae: fly L23a can substitute for yeast L25 in ribosome assembly and function Carrie L. N. Ross, Ranoo R. Patel, Tamra C. Mendelson, and Vassie C. Ware PMCID: PMC1934995 The novel PIAS-like protein hZimp10 is a transcriptional co-activator of the p53 tumor suppressor Jane Lee, Jason Beliakoff, and Zijie Sun PMCID: PMC1935018 Cytotoxic G-rich oligodeoxynucleotides: putative protein targets and required sequence motif Amber Goodchild, Andrew King, Mary Margaret Gozar, Toby Passioura, Carly Tucker, and Laurent Rivory PMCID: PMC1935016 RNA A systematic analysis of the effect of target RNA structure on RNA interference Ellen M. Westerhout and Ben Berkhout PMCID: PMC1934999 In vitro analysis of the interaction between the small RNA SR1 and its primary target ahrC mRNA Nadja Heidrich, Isabella Moll, and Sabine Brantl PMCID: PMC1935000 Manipulation of P-TEFb control machinery by HIV: recruitment of P-TEFb from the large form by Tat and binding of HEXIM1 to TAR Stanley C. Sedore, Sarah A. Byers, Sebastian Biglione, Jason P. Price, Wendy J. Maury, and David H. Price PMCID: PMC1935001 SR protein-mediated inhibition of CFTR exon 9 inclusion: molecular characterization of the intronic splicing silencer Emanuele Buratti, Cristiana Stuani, Greta De Prato, and Francisco E. Baralle PMCID: PMC1935002 RNA structure is a key regulatory element in pathological ATM and CFTR pseudoexon inclusion events Emanuele Buratti, Ashish Dhir, Marzena A. Lewandowska, and Francisco E. Baralle PMCID: PMC1935003 Processing of Bacillus subtilis small cytoplasmic RNA: evidence for an additional endonuclease cleavage site Shiyi Yao, Joshua B. Blaustein, and David H. Bechhofer PMCID: PMC1935012 The abundance of RNPS1, a protein component of the exon junction complex, can determine the variability in efficiency of the Nonsense Mediated Decay pathway Marcelo H. Viegas, Niels H. Gehring, Stephen Breit, Matthias W. Hentze, and Andreas E. Kulozik PMCID: PMC1935013 Structural Biology Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC S. Sunita, Elzbieta Purta, Malgorzata Durawa, Karolina L. Tkaczuk, J. Swaathi, Janusz M. Bujnicki, and J. Sivaraman PMCID: PMC1934991 Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase Pingna Xu, Lida Oum, Lorena S. Beese, Nicholas E. Geacintov, and Suse Broyde PMCID: PMC1934992 Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms Masaru Tsunoda, Yoshio Kusakabe, Nobutada Tanaka, Satoshi Ohno, Masashi Nakamura, Toshiya Senda, Tomohisa Moriguchi, Norio Asai, Mitsuo Sekine, Takashi Yokogawa, Kazuya Nishikawa, and Kazuo T. Nakamura PMCID: PMC1934993 Conformational and thermodynamic changes of the repressor/DNA operator complex upon monomerization shed new light on regulation mechanisms of bacterial resistance against β-lactam antibiotics Julien Boudet, Valérie Duval, Hélène Van Melckebeke, Martin Blackledge, Ana Amoroso, Bernard Joris, and Jean-Pierre Simorre PMCID: PMC1935004 Fine-tuning of intrinsic N-Oct-3 POU domain allostery by regulatory DNA targets Robert Alazard, Lionel Mourey, Christine Ebel, Peter V. Konarev, Maxim V. Petoukhov, Dmitri I. Svergun, and Monique Erard PMCID: PMC1935007 The structure of the CstF-77 homodimer provides insights into CstF assembly Pierre Legrand, Noël Pinaud, Lionel Minvielle-Sébastia, and Sébastien Fribourg PMCID: PMC1935011 Survey and Summary Miniaturized PCR chips for nucleic acid amplification and analysis: latest advances and future trends Chunsun Zhang and Da Xing PMCID: PMC1934988 Genomics Aberrant 5′ splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization Emanuele Buratti, Martin Chivers, Jana Královičová, Maurizio Romano, Marco Baralle, Adrian R. Krainer, and Igor Vořechovský PMCID: PMC1934990 Adaptation in bacterial flagellar and motility systems: from regulon members to ‘foraging’-like behavior in E. coli Kai Zhao, Mingzhu Liu, and Richard R. Burgess PMCID: PMC1935009 Aberrant allele frequencies of the SNPs located in microRNA target sites are potentially associated with human cancers Zhenbao Yu, Zhen Li, Normand Jolicoeur, Linhua Zhang, Yves Fortin, Edwin Wang, Meiqun Wu, and Shi-Hsiang Shen PMCID: PMC1935019 Methods Online DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations Christian Hoffmann, Nana Minkah, Jeremy Leipzig, Gary Wang, Max Q. Arens, Pablo Tebas, and Frederic D. Bushman PMCID: PMC1934997 Analytical biochemistry of DNA–protein assemblies from crude cell extracts Nadia Hégarat, Gildas Mouta Cardoso, Filippo Rusconi, Jean-Christophe François, and Danièle Praseuth PMCID: PMC1935021 Engineered apoptotic nucleases for chromatin research Fei Xiao, Piotr Widlak, and William T. Garrard PMCID: PMC1935020 Computational Biology A new systematic computational approach to predicting target genes of transcription factors Xinbin Dai, Ji He, and Xuechun Zhao PMCID: PMC1935008 Nucleic Acid Enzymes Enzymatic incorporation of a third nucleobase pair Zunyi Yang, A. Michael Sismour, Pinpin Sheng, Nyssa L. Puskar, and Steven A. Benner PMCID: PMC1934989 A novel endonuclease activity associated with the Arabidopsis ortholog of the 30-kDa subunit of cleavage and polyadenylation specificity factor Balasubrahmanyam Addepalli and Arthur G. Hunt PMCID: PMC1935010 Novel high-throughput electrochemiluminescent assay for identification of human tyrosyl-DNA phosphodiesterase (Tdp1) inhibitors and characterization of furamidine (NSC 305831) as an inhibitor of Tdp1 Smitha Antony, Christophe Marchand, Andrew G. Stephen, Laurent Thibaut, Keli K. Agama, Robert J. Fisher, and Yves Pommier PMCID: PMC1935015 YtqI from Bacillus subtilis has both oligoribonuclease and pAp-phosphatase activity Undine Mechold, Gang Fang, Saravuth Ngo, Vasily Ogryzko, and Antoine Danchin PMCID: PMC1935014 |
