| | Articles Triplex targeted genomic crosslinks enter separable deletion and base substitution pathways Sally Richards, Su-Ting Liu, Alokes Majumdar, Ji-Lan Liu, Rodney S. Nairn, Michel Bernier, Veronica Maher, and Michael M. Seidman PMCID: PMC1236719 Real-time expression profiling of microRNA precursors in human cancer cell lines Jinmai Jiang, Eun Joo Lee, Yuriy Gusev, and Thomas D. Schmittgen PMCID: PMC1236977 The genes encoding Arabidopsis ORC subunits are E2F targets and the two ORC1 genes are differently expressed in proliferating and endoreplicating cells Sara Diaz-Trivino, María del Mar Castellano, María de la Paz Sanchez, Elena Ramirez-Parra, Bénédicte Desvoyes, and Crisanto Gutierrez PMCID: PMC1236721 Bacillus cereus DNA topoisomerase I and IIIα: purification, characterization and complementation of Escherichia coli TopoIII activity Zhiyu Li, Hiroshi Hiasa, and Russell DiGate PMCID: PMC1236973 Mutational analysis of BTAF1–TBP interaction: BTAF1 can rescue DNA-binding defective TBP mutants Marcin P. Klejman, Xuemei Zhao, Frederik M. A. van Schaik, Winship Herr, and H. Th. Marc Timmers PMCID: PMC1236718 Human-zebrafish non-coding conserved elements act in vivo to regulate transcription Jordan T. Shin, James R. Priest, Ivan Ovcharenko, Amy Ronco, Rachel K. Moore, C. Geoffrey Burns, and Calum A. MacRae PMCID: PMC1236720 A human-Tetrahymena pseudoknot chimeric telomerase RNA reconstitutes a nonprocessive enzyme in vitro that is defective in telomere elongation Delphine T. Marie-Egyptienne, Maria Antonietta Cerone, J. Arturo Londoño-Vallejo, and Chantal Autexier PMCID: PMC1236975 Characterization of E2F8, a novel E2F-like cell-cycle regulated repressor of E2F-activated transcription Jesper Christensen, Paul Cloos, Ulla Toftegaard, David Klinkenberg, Adrian P. Bracken, Emmanuelle Trinh, Mel Heeran, Luisa Di Stefano, and Kristian Helin PMCID: PMC1236722 Structure, internal motions and association–dissociation kinetics of the i-motif dimer of d(5mCCTCACTCC) Muriel Canalia and Jean Louis Leroy PMCID: PMC1243796 A diminutive and specific RNA binding site for L-tryptophan Irene Majerfeld and Michael Yarus PMCID: PMC1236723 Characterization of the metal ion binding site in the anti-terminator protein, HutP, of Bacillus subtilis Thirumananseri Kumarevel, Hiroshi Mizuno, and Penmetcha K. R. Kumar PMCID: PMC1236978 Analysis of the transcriptome of the protozoan Theileria parva using MPSS reveals that the majority of genes are transcriptionally active in the schizont stage Richard Bishop, Trushar Shah, Roger Pelle, David Hoyle, Terry Pearson, Lee Haines, Andrew Brass, Helen Hulme, Simon P. Graham, Evans L. N. Taracha, Simon Kanga, Charles Lu, Brian Hass, Jennifer Wortman, Owen White, Malcolm J. Gardner, Vishvanath Nene, and Etienne P. de Villiers PMCID: PMC1236717 Evolutionary conservation suggests a regulatory function of AUG triplets in 5′-UTRs of eukaryotic genes Alexander Churbanov, Igor B. Rogozin, Vladimir N. Babenko, Hesham Ali, and Eugene V. Koonin PMCID: PMC1236974 Regulation of multiple insulin-like growth factor binding protein genes by 1α,25-dihydroxyvitamin D3 Merja Matilainen, Marjo Malinen, Katri Saavalainen, and Carsten Carlberg PMCID: PMC1236724 Evidence for a preferential targeting of 3′-UTRs by cis-encoded natural antisense transcripts Miao Sun, Laurence D. Hurst, Gordon G. Carmichael, and Jianjun Chen PMCID: PMC1243798 Competition between trans-translation and termination or elongation of translation Krisana Asano, Daisuke Kurita, Kazuma Takada, Takayuki Konno, Akira Muto, and Hyouta Himeno PMCID: PMC1243801 UVA-visible photo-excitation of guanine radical cations produces sugar radicals in DNA and model structures Amitava Adhikary, Aramice Y. S. Malkhasian, Sean Collins, Jessica Koppen, David Becker, and Michael D. Sevilla PMCID: PMC1243799 Sub-array normalization subject to differentiation Chao Cheng and Lei M. Li PMCID: PMC1243797 The importance of being divisible by three in alternative splicing Alon Magen and Gil Ast PMCID: PMC1236976 Nucleic acid melting by Escherichia coli CspE Sangita Phadtare and Konstantin Severinov PMCID: PMC1251665 Evidence for a role of initiation factor 3 in recycling of ribosomal complexes stalled on mRNAs in Escherichia coli N. S. Singh, G. Das, A. Seshadri, R. Sangeetha, and U. Varshney PMCID: PMC1240113 In vitro selection of RNA aptamers against a composite small molecule-protein surface Kelly A. Plummer, James M. Carothers, Masahiro Yoshimura, Jack W. Szostak, and Gregory L. Verdine PMCID: PMC1240114 Non-EST based prediction of exon skipping and intron retention events using Pfam information Michael Hiller, Klaus Huse, Matthias Platzer, and Rolf Backofen PMCID: PMC1243800 Characterization of the bisintercalative DNA binding mode of a bifunctional platinum–acridine agent Jayati Roy Choudhury and Ulrich Bierbach PMCID: PMC1236979 The replacement histone H2A.Z in a hyperacetylated form is a feature of active genes in the chicken Kimberley Bruce, Fiona A. Myers, Evangelia Mantouvalou, Pascal Lefevre, Ian Greaves, Constanze Bonifer, David J. Tremethick, Alan W. Thorne, and Colyn Crane-Robinson PMCID: PMC1243646 The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological system A. Michael Sismour and Steven A. Benner PMCID: PMC1236980 A new mechanism for mtDNA pathogenesis: impairment of post-transcriptional maturation leads to severe depletion of mitochondrial tRNASer(UCN) caused by T7512C and G7497A point mutations Myriam Möllers, Katharina Maniura-Weber, Emina Kiseljakovic, Maria Bust, Armine Hayrapetyan, Michaela Jaksch, Mark Helm, Rudolf J. Wiesner, and Jürgen-Christoph von Kleist-Retzow PMCID: PMC1240115 Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles Zhengyan Kan, Philip W. Garrett-Engele, Jason M. Johnson, and John C. Castle PMCID: PMC1240112 Mechanistic features of CAG•CTG repeat contractions in cultured cells revealed by a novel genetic assay Richard Pelletier, Brian T. Farrell, Juan José Miret, and Robert S. Lahue PMCID: PMC1240116 Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding Boris François, Rupert J. M. Russell, James B. Murray, Fareed Aboul-ela, Benoît Masquida, Quentin Vicens, and Eric Westhof PMCID: PMC1251667 The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes Ross Overbeek, Tadhg Begley, Ralph M. Butler, Jomuna V. Choudhuri, Han-Yu Chuang, Matthew Cohoon, Valérie de Crécy-Lagard, Naryttza Diaz, Terry Disz, Robert Edwards, Michael Fonstein, Ed D. Frank, Svetlana Gerdes, Elizabeth M. Glass, Alexander Goesmann, Andrew Hanson, Dirk Iwata-Reuyl, Roy Jensen, Neema Jamshidi, Lutz Krause, Michael Kubal, Niels Larsen, Burkhard Linke, Alice C. McHardy, Folker Meyer, Heiko Neuweger, Gary Olsen, Robert Olson, Andrei Osterman, Vasiliy Portnoy, Gordon D. Pusch, Dmitry A. Rodionov, Christian Rückert, Jason Steiner, Rick Stevens, Ines Thiele, Olga Vassieva, Yuzhen Ye, Olga Zagnitko, and Veronika Vonstein PMCID: PMC1251668 PCNA–MutSα-mediated binding of MutLα to replicative DNA with mismatched bases to induce apoptosis in human cells Masumi Hidaka, Yasumitsu Takagi, Tomoko Y. Takano, and Mutsuo Sekiguchi PMCID: PMC1243802 Methods Online Combining SELEX with quantitative assays to rapidly obtain accurate models of protein–DNA interactions Jiajian Liu and Gary D. Stormo PMCID: PMC1236725 PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays Jesper Brohede, Rob Dunne, James D. McKay, and Garry N. Hannan PMCID: PMC1240117 Genome-wide estimation of transcript concentrations from spotted cDNA microarray data Arnoldo Frigessi, Mark A. van de Wiel, Marit Holden, Debbie H. Svendsrud, Ingrid K. Glad, and Heidi Lyng PMCID: PMC1243803 A post-processing method for optimizing synthesis strategy for oligonucleotide microarrays Kang Ning, Kwok Pui Choi, Hon Wai Leong, and Louxin Zhang PMCID: PMC1236981 Expressible molecular colonies Timur R. Samatov, Helena V. Chetverina, and Alexander B. Chetverin PMCID: PMC1243806 End invasion of peptide nucleic acids (PNAs) with mixed-base composition into linear DNA duplexes Irina V. Smolina, Vadim V. Demidov, Viatcheslav A. Soldatenkov, Sergey G. Chasovskikh, and Maxim D. Frank-Kamenetskii PMCID: PMC1243805 Reproducible doxycycline-inducible transgene expression at specific loci generated by Cre-recombinase mediated cassette exchange Ee Tsin Wong, John L Kolman, Yao-Cheng Li, Larry D Mesner, Wolfgang Hillen, Christian Berens, and Geoffrey M Wahl PMCID: PMC1243804 Isolation of mRNA from specific tissues of Drosophila by mRNA tagging Zhiyong Yang, Howard J. Edenberg, and Ronald L. Davis PMCID: PMC1243647 Detection of ApoE E2, E3 and E4 alleles using MALDI-TOF mass spectrometry and the homogeneous mass-extend technology Nader Ghebranious, Lynn Ivacic, Jamie Mallum, and Charles Dokken PMCID: PMC1243648 PCR amplification from single DNA molecules on magnetic beads in emulsion: application for high-throughput screening of transcription factor targets Takaaki Kojima, Yoshiaki Takei, Miharu Ohtsuka, Yasuaki Kawarasaki, Tsuneo Yamane, and Hideo Nakano PMCID: PMC1251669 Corrigendum Conservation versus parallel gains in intron evolution Alexander V. Sverdlov, Igor B. Rogozin, Vladimir N. Babenko, and Eugene V. Koonin PMCID: PMC1251666 Corrects: Alexander V. Sverdlov, et al. Conservation versus parallel gains in intron evolution. Nucleic Acids Res. 2005; 33(6): 1741–1748. |
