| | Molecular Biology Transition from initiation to promoter proximal pausing requires the CTD of RNA polymerase II C. Lux, H. Albiez, R. D. Chapman, M. Heidinger, M. Meininghaus, R. Brack-Werner, A. Lang, M. Ziegler, T. Cremer, and D. Eick PMCID: PMC1214543 Trapping DNA–protein binding reactions with neutral osmolytes for the analysis by gel mobility shift and self-cleavage assays Nina Y. Sidorova, Shakir Muradymov, and Donald C. Rau PMCID: PMC1214545 Characterization of the SECIS binding protein 2 complex required for the co-translational insertion of selenocysteine in mammals Scott A. Kinzy, Kelvin Caban, and Paul R. Copeland PMCID: PMC1214547 An Sp1/KLF binding site is important for the activity of a Polycomb group response element from the Drosophila engrailed gene J. Lesley Brown, Daniel J. Grau, Sarah K. DeVido, and Judith A. Kassis PMCID: PMC1214548 Transcriptional repression of human cad gene by hypoxia inducible factor-1α Ko-Fan Chen, Yen-Yu Lai, H. Sunny Sun, and Shaw-Jenq Tsai PMCID: PMC1214551 Methylation patterns of histone H3 Lys 4, Lys 9 and Lys 27 in transcriptionally active and inactive Arabidopsis genes and in atx1 mutants Raul Alvarez-Venegas and Zoya Avramova PMCID: PMC1214549 Expression and regulation of the Msx1 natural antisense transcript during development Amélie E. Coudert, Laurence Pibouin, Brigitte Vi-Fane, Bethan L. Thomas, Mary Macdougall, Anuradha Choudhury, Benoît Robert, Paul T. Sharpe, Ariane Berdal, and Frédéric Lezot PMCID: PMC1214550 Genomics Comparative genomics analysis of NtcA regulons in cyanobacteria: regulation of nitrogen assimilation and its coupling to photosynthesis Zhengchang Su, Victor Olman, Fenglou Mao, and Ying Xu PMCID: PMC1214546 Chemistry The sacrificial role of easily oxidizable sites in the protection of DNA from damage Sriram Kanvah and Gary B. Schuster PMCID: PMC1214542 Articles Fluorescent properties of DNA base analogue tC upon incorporation into DNA — negligible influence of neighbouring bases on fluorescence quantum yield Peter Sandin, L. Marcus Wilhelmsson, Per Lincoln, Vicki E. C. Powers, Tom Brown, and Bo Albinsson PMCID: PMC1201328 Evidence that public database records for many cancer-associated genes reflect a splice form found in tumors and lack normal splice forms Meenakshi Roy, Qiang Xu, and Christopher Lee PMCID: PMC1201329 Open reading frames provide a rich pool of potential natural antisense transcripts in fungal genomes Stephan Steigele and Kay Nieselt PMCID: PMC1201330 Evidence that the Tfg1/Tfg2 dimer interface of TFIIF lies near the active center of the RNA polymerase II initiation complex M. Angeles Freire-Picos, Shankarling Krishnamurthy, Zu-Wen Sun, and Michael Hampsey PMCID: PMC1201334 Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes Jinhua Wang, Philip J. Smith, Adrian R. Krainer, and Michael Q. Zhang PMCID: PMC1201331 Discovery of new genes and deletion editing in Physarum mitochondria enabled by a novel algorithm for finding edited mRNAs Jonatha M. Gott, Neeta Parimi, and Ralf Bundschuh PMCID: PMC1201332 Human AP endonuclease suppresses DNA mismatch repair activity leading to microsatellite instability In-Youb Chang, Soo-Hyun Kim, Hyun-Ju Cho, Do Young Lee, Mi-Hwa Kim, Myung-Hee Chung, and Ho Jin You PMCID: PMC1201336 The influence of locked nucleic acid residues on the thermodynamic properties of 2′-O-methyl RNA/RNA heteroduplexes Elzbieta Kierzek, Anna Ciesielska, Karol Pasternak, David H. Mathews, Douglas H. Turner, and Ryszard Kierzek PMCID: PMC1201327 8-Oxoguanine incorporation into DNA repeats in vitro and mismatch recognition by MutSα Peter Macpherson, Flavia Barone, Giovanni Maga, Filomena Mazzei, Peter Karran, and Margherita Bignami PMCID: PMC1233161 Extended base pair complementarity between U1 snRNA and the 5′ splice site does not inhibit splicing in higher eukaryotes, but rather increases 5′ splice site recognition Marcel Freund, Martin J. Hicks, Carolin Konermann, Marianne Otte, Klemens J. Hertel, and Heiner Schaal PMCID: PMC1201333 RNase P: role of distinct protein cofactors in tRNA substrate recognition and RNA-based catalysis Ela Sharin, Aleks Schein, Hagit Mann, Yitzhak Ben-Asouli, and Nayef Jarrous PMCID: PMC1201335 Common and specific amino acid residues in the prokaryotic polypeptide release factors RF1 and RF2: possible functional implications Nina J. Oparina, Olga V. Kalinina, Mikhail S. Gelfand, and Lev L. Kisselev PMCID: PMC1214553 Viral mutations enhance the Max binding properties of the vMyc b-HLH-LZ domain D. H. Crouch, F. Fisher, S. A. La Rocca, C. R. Goding, and D. A. F. Gillespie PMCID: PMC1216337 Inverted repeat-stimulated sister-chromatid exchange events are RAD1-independent but reduced in a msh2 mutant Dilip K. Nag, Michael Fasullo, Zheng Dong, and Ashlie Tronnes PMCID: PMC1216339 RNase III cleavage demonstrates a long range RNA: RNA duplex element flanking the hepatitis C virus internal ribosome entry site Nerea Beguiristain, Hugh D. Robertson, and Jordi Gómez PMCID: PMC1216335 Localization, mobility and fidelity of retrotransposed Group II introns in rRNA genes Lori H. Conlan, Matthew J. Stanger, Kenji Ichiyanagi, and Marlene Belfort PMCID: PMC1216334 Binding of serum response factor to cystic fibrosis transmembrane conductance regulator CArG-like elements, as a new potential CFTR transcriptional regulation pathway Céline René, Magali Taulan, Florence Iral, Julien Doudement, Aurore L'Honoré, Catherine Gerbon, Jacques Demaille, Mireille Claustres, and Marie-Catherine Romey PMCID: PMC1216340 Deacylated tRNA is released from the E site upon A site occupation but before GTP is hydrolyzed by EF-Tu George Dinos, Dimitrios L. Kalpaxis, Daniel N. Wilson, and Knud H. Nierhaus PMCID: PMC1216338 Stabilizing contributions of sulfur-modified nucleotides: crystal structure of a DNA duplex with 2′-O-[2-(methoxy)ethyl]-2-thiothymidines Benjamin Diop-Frimpong, Thazha P. Prakash, Kallanthottathil G. Rajeev, Muthiah Manoharan, and Martin Egli PMCID: PMC1216336 NF-κB controls the global pro-inflammatory response in endothelial cells: evidence for the regulation of a pro-atherogenic program Sybille Kempe, Hans Kestler, Andrea Lasar, and Thomas Wirth PMCID: PMC1226313 Non-homologous end joining, but not homologous recombination, enables survival for cells exposed to a histone deacetylase inhibitor Mariana Yaneva, Han Li, Teresa Marple, and Paul Hasty PMCID: PMC1226312 GATA-1 mediates auto-regulation of Gfi-1B transcription in K562 cells Duen-Yi Huang, Yuan-Yeh Kuo, and Zee-Fen Chang PMCID: PMC1226314 Gibbs sampling and helix-cap motifs Erik Kruus, Peter Thumfort, Chao Tang, and Ned S. Wingreen PMCID: PMC1234247 Phosphorylation of human DNA polymerase λ by the cyclin-dependent kinase Cdk2/cyclin A complex is modulated by its association with proliferating cell nuclear antigen Isabelle Frouin, Magali Toueille, Elena Ferrari, Igor Shevelev, and Ulrich Hübscher PMCID: PMC1226315 Modulation of ADAR1 editing activity by Z-RNA in vitro Michael Koeris, Lars Funke, Jay Shrestha, Alexander Rich, and Stefan Maas PMCID: PMC1226316 Mechanistic studies on DNA damage by minor groove binding copper–phenanthroline conjugates Brian C. Bales, Tetsuya Kodama, Yvonne N. Weledji, Marguerite Pitié, Bernard Meunier, and Marc M. Greenberg PMCID: PMC1235636 Methods Online A novel transcriptome subtraction method for the detection of differentially expressed genes in highly complex eukaryotes L. Li, D. Techel, N. Gretz, and A. Hildebrandt PMCID: PMC1201337 Stringent doxycycline-dependent control of gene activities using an episomal one-vector system Georg W. Bornkamm, Christian Berens, Conny Kuklik-Roos, Jean-Marie Bechet, Gerhard Laux, Jürgen Bachl, Martin Korndoerfer, Martin Schlee, Michael Hölzel, Anastassia Malamoussi, Rob D. Chapman, Falk Nimmerjahn, Josef Mautner, Wolfgang Hillen, Hermann Bujard, and Jean Feuillard PMCID: PMC1201338 Thermal difference spectra: a specific signature for nucleic acid structures Jean-Louis Mergny, Jing Li, Laurent Lacroix, Samir Amrane, and Jonathan B. Chaires PMCID: PMC1201377 Transformation of isolated mammalian mitochondria by bacterial conjugation Young Geol Yoon and Michael D. Koob PMCID: PMC1201378 Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools Brian D. Peyser, Rafael A. Irizarry, Carol W. Tiffany, Ou Chen, Daniel S. Yuan, Jef D. Boeke, and Forrest A. Spencer PMCID: PMC1216341 Computational Biology Constraining ribosomal RNA conformational space Paola Favaretto, Arjun Bhutkar, and Temple F. Smith PMCID: PMC1214544 Nucleic Acid Enzymes High fidelity TNA synthesis by Therminator polymerase Justin K. Ichida, Allen Horhota, Keyong Zou, Larry W. McLaughlin, and Jack W. Szostak PMCID: PMC1214552 |
