| | Articles Molecular requirements for degradation of a modified sense RNA strand by Escherichia coli ribonuclease H1 Daniel R. Yazbeck, Kyung-Lyum Min, and Masad J. Damha PMCID: PMC135749 Transfer RNA-mediated antitermination in vitro Harald Putzer, Ciarán Condon, Dominique Brechemier-Baey, Renata Brito, and Marianne Grunberg-Manago PMCID: PMC135736 Functional interaction between TATA and upstream CACGTG elements regulates the temporally specific expression of Otx mRNAs during early embryogenesis of the sea urchin, Hemicentrotus pulcherrimus Akiko Kobayashi, Koji Akasaka, Masashi Kawaichi, and Tetsuro Kokubo PMCID: PMC135759 The effect of ICAD-S on the formation and intracellular distribution of a nucleolytically active caspase-activated DNase Sebastian Richard Scholz, Christian Korn, Oleg Gimadutdinow, Michael Knoblauch, Alfred Pingoud, and Gregor Meiss PMCID: PMC135751 Alternate exon insertion controls selective ubiquitination and degradation of different AUF1 protein isoforms Gaurav Laroia and Robert J. Schneider PMCID: PMC135764 MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform Kazutaka Katoh, Kazuharu Misawa, Kei-ichi Kuma, and Takashi Miyata PMCID: PMC135756 A genetic screen identifies novel non-compatible loxP sites Stephen J. Langer, A. Paiman Ghafoori, Marshall Byrd, and Leslie Leinwand PMCID: PMC135742 The role of TFIIB–RNA polymerase II interaction in start site selection in yeast cells Dong-Yi Zhang, Daniel J. Carson, and Jun Ma PMCID: PMC135743 Effects of mutations at tyrosine 66 and asparagine 123 in the active site pocket of Escherichia coli uracil DNA glycosylase on uracil excision from synthetic DNA oligomers: evidence for the occurrence of long-range interactions between the enzyme and substrate Priya Handa, Narottam Acharya, and Umesh Varshney PMCID: PMC135746 Selective down-regulation of tyrosinase family gene TYRP1 by inhibition of the activity of melanocyte transcription factor, MITF Dong Fang, Yoshiaki Tsuji, and Vijayasaradhi Setaluri PMCID: PMC135745 Bone morphogenetic protein-4-induced activation of Xretpos is mediated by Smads and Olf-1/EBF associated zinc finger (OAZ) Sangwoo Shim, Narina Bae, and Jin-Kwan Han PMCID: PMC135757 The role of template-primer in protection of reverse transcriptase from thermal inactivation Gary F. Gerard, R. Jason Potter, Michael D. Smith, Kim Rosenthal, Gulshan Dhariwal, Jun Lee, and Deb. K. Chatterjee PMCID: PMC135738 Mammalian metal response element-binding transcription factor-1 functions as a zinc sensor in yeast, but not as a sensor of cadmium or oxidative stress Patrick J. Daniels, Doug Bittel, Irina V. Smirnova, Dennis R. Winge, and Glen K. Andrews PMCID: PMC135752 Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation Alexey G. Vitreschak, Dmitry A. Rodionov, Andrey A. Mironov, and Mikhail S. Gelfand PMCID: PMC135753 Identification of 113 conserved essential genes using a high-throughput gene disruption system in Streptococcus pneumoniae Jane A. Thanassi, Sandra L. Hartman-Neumann, Thomas J. Dougherty, Brian A. Dougherty, and Michael J. Pucci PMCID: PMC135739 NotI flanking sequences: a tool for gene discovery and verification of the human genome Alexey S. Kutsenko, Rinat Z. Gizatullin, Ali N. Al-Amin, Fuli Wang, Sergei M. Kvasha, Raf M. Podowski, Yuri G. Matushkin, Anita Gyanchandani, Olga V. Muravenko, Viktor G. Levitsky, Nikolay A. Kolchanov, Alexei I. Protopopov, Vladimir I. Kashuba, Lev L. Kisselev, Wyeth Wasserman, Claes Wahlestedt, and Eugene R. Zabarovsky PMCID: PMC135748 Thermodynamic and hydration effects for the incorporation of a cationic 3-aminopropyl chain into DNA Ana Maria Soto, Besik I. Kankia, Prasad Dande, Barry Gold, and Luis A. Marky PMCID: PMC135750 A comparative genomic method for computational identification of prokaryotic translation initiation sites Megon Walker, Vladimir Pavlovic, and Simon Kasif PMCID: PMC135744 Preformed hexamers of SV40 T antigen are active in RNA and origin-DNA unwinding Heike Uhlmann-Schiffler, Stephanie Seinsoth, and Hans Stahl PMCID: PMC135737 Identification of Sox-2 regulatory region which is under the control of Oct-3/4–Sox-2 complex Mizuho Tomioka, Masazumi Nishimoto, Satoru Miyagi, Tomoko Katayanagi, Nobutaka Fukui, Hitoshi Niwa, Masami Muramatsu, and Akihiko Okuda PMCID: PMC135755 Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences Martin C. Frith, John L. Spouge, Ulla Hansen, and Zhiping Weng PMCID: PMC135758 Mutagenic scan of the H-N-H motif of colicin E9: implications for the mechanistic enzymology of colicins, homing enzymes and apoptotic endonucleases David C. Walker, Theonie Georgiou, Ansgar J. Pommer, Daniel Walker, Geoffrey R. Moore, Colin Kleanthous, and Richard James PMCID: PMC135741 Analysis of repeatability in spotted cDNA microarrays Tor-Kristian Jenssen, Mette Langaas, Winston P. Kuo, Birgitte Smith-Sørensen, Ola Myklebost, and Eivind Hovig PMCID: PMC135761 SOX9 interacts with a component of the human thyroid hormone receptor-associated protein complex Rongjia Zhou, Nathalie Bonneaud, Chao-Xing Yuan, Pascal de Santa Barbara, Brigitte Boizet, Schomber Tibor, Gerd Scherer, Robert G. Roeder, Francis Poulat, and Philippe Berta PMCID: PMC135763 Selective stimulation of translational expression by Alu RNA Carol M. Rubin, Richard H. Kimura, and Carl W. Schmid PMCID: PMC135740 A novel gene organization: intronic snoRNA gene clusters from Oryza sativa Dan Liang, Hui Zhou, Peng Zhang, Yue-Qin Chen, Xiao Chen, Chun-Long Chen, and Liang-Hu Qu PMCID: PMC135747 Vertebrate cells lacking FEN-1 endonuclease are viable but hypersensitive to methylating agents and H2O2 Yasuo Matsuzaki, Noritaka Adachi, and Hideki Koyama PMCID: PMC135760 Quantitative analysis of DNA demethylation and transcriptional reactivation of the FMR1 gene in fragile X cells treated with 5-azadeoxycytidine Roberta Pietrobono, Maria Grazia Pomponi, Elisabetta Tabolacci, Ben Oostra, Pietro Chiurazzi, and Giovanni Neri PMCID: PMC135754 Regulation of ribonuclease expression by estradiol in Rana catesbeiana (Bullfrog) Pin-Chi Tang, Huey-Chung Huang, Sui-Chi Wang, Jen-Chong Jeng, and You-Di Liao PMCID: PMC135762 NAR Methods Online Rapid parallel mutation scanning of gene fragments using a microelectronic protein–DNA chip format Heike A. Behrensdorf, Marc Pignot, Norbert Windhab, and Andreas Kappel PMCID: PMC135765 Detection of promoter activity by flow cytometric analysis of GFP reporter expression Anne-Lyse Ducrest, Mario Amacker, Joachim Lingner, and Markus Nabholz PMCID: PMC135766 Real-time monitoring of rolling-circle amplification using a modified molecular beacon design Mats Nilsson, Mats Gullberg, Fredrik Dahl, Karoly Szuhai, and Anton K. Raap PMCID: PMC135767 Re-sequencing of multiple single nucleotide polymorphisms by liquid chromatography–electrospray ionization mass spectrometry H. Oberacher, P. J. Oefner, G. Hölzl, A. Premstaller, K. Davis, and C. G. Huber PMCID: PMC135768 Detection and quantification of mitochondrial DNA deletions in individual cells by real-time PCR Langping He, Patrick F. Chinnery, Steve E. Durham, Emma L. Blakely, Theresa M. Wardell, Gillian M. Borthwick, Robert W. Taylor, and Douglass M. Turnbull PMCID: PMC135769 DNA affinity capture and protein profiling by SELDI-TOF mass spectrometry: effect of DNA methylation Thomas K. Bane, James F. LeBlanc, Terry D. Lee, and Arthur D. Riggs PMCID: PMC135770 Multiplex SNP genotyping in pooled DNA samples by a four-colour microarray system Katarina Lindroos, Snaevar Sigurdsson, Karin Johansson, Lars Rönnblom, and Ann-Christine Syvänen PMCID: PMC135771 Genome-wide comparison of differences in the integration sites of interspersed repeats between closely related genomes Ilgar Mamedov, Anastasia Batrak, Anton Buzdin, Elena Arzumanyan, Yuri Lebedev, and Eugene D. Sverdlov PMCID: PMC135772 Detection of oligonucleotide hybridization at femtomolar level and sequence-specific gene analysis of the Arabidopsis thaliana leaf extract with an ultrasensitive surface plasmon resonance spectrometer Fayi Song, Feimeng Zhou, Jun Wang, Nongjian Tao, Jianqiao Lin, Robert L. Vellanoweth, Yvonne Morquecho, and Janel Wheeler-Laidman PMCID: PMC135773 Binary system for selective photoaffinity labeling of base excision repair DNA polymerases Olga I. Lavrik, Dmitry M. Kolpashchikov, Rajendra Prasad, Robert W. Sobol, and Samuel H. Wilson PMCID: PMC135774 |
