| | Obituary OBITUARY Gerhart Wagner, Wolfgang Nellen, Alfredo Berzal-Herranz, and Georg Sczakiel PMCID: PMC1142347 Articles A monoclonal antibody that inhibits mycobacterial DNA gyrase by a novel mechanism Ujjini H. Manjunatha, Anthony Maxwell, and Valakunja Nagaraja PMCID: PMC1142348 UNR translation can be driven by an IRES element that is negatively regulated by polypyrimidine tract binding protein Sigrid Cornelis, Sandrine A. Tinton, Bert Schepens, Yanik Bruynooghe, and Rudi Beyaert PMCID: PMC1142345 Structural and functional characterizations reveal the importance of a zinc binding domain in Bloom's syndrome helicase Rong-bin Guo, Pascal Rigolet, Loussiné Zargarian, Serge Fermandjian, and Xu Guang Xi PMCID: PMC1142346 Recognizing the pseudogenes in bacterial genomes Emmanuelle Lerat and Howard Ochman PMCID: PMC1142405 Reconstitution of archaeal H/ACA small ribonucleoprotein complexes active in pseudouridylation Bruno Charpentier, Sébastien Muller, and Christiane Branlant PMCID: PMC1142404 NMR structure and Mg2+ binding of an RNA segment that underlies the L7/L12 stalk in the E.coli 50S ribosomal subunit Qin Zhao, Uma Nagaswamy, Hunjoong Lee, Youlin Xia, Hung-Chung Huang, Xiaolian Gao, and George E. Fox PMCID: PMC1143578 oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes Shannan J. Ho Sui, James R. Mortimer, David J. Arenillas, Jochen Brumm, Christopher J. Walsh, Brian P. Kennedy, and Wyeth W. Wasserman PMCID: PMC1142402 Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes Aditi Kanhere and Manju Bansal PMCID: PMC1143579 Sequence determination of nucleic acids containing 5-methylisocytosine and isoguanine: identification and insight into polymerase replication of the non-natural nucleobases J. David Ahle, Stephen Barr, A. Michael Chin, and Thomas R. Battersby PMCID: PMC1142403 Covalent ligation studies on the human telomere quadruplex Jianying Qi and Richard H. Shafer PMCID: PMC1142406 Prediction of solvent accessibility and sites of deleterious mutations from protein sequence Huiling Chen and Huan-Xiang Zhou PMCID: PMC1142490 Cell-type-specific epigenetic marking of the IL2 gene at a distal cis-regulatory region in competent, nontranscribing T-cells Satoko Adachi and Ellen V. Rothenberg PMCID: PMC1142491 Functional analysis of the N- and C-terminus of mammalian G9a histone H3 methyltransferase Pierre-Olivier Estève, Debasis Patnaik, Hang Gyeong Chin, Jack Benner, Michael A. Teitell, and Sriharsa Pradhan PMCID: PMC1143580 Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication Morgan N. Price, Eric J. Alm, and Adam P. Arkin PMCID: PMC1143696 DNA bending by M.EcoKI methyltransferase is coupled to nucleotide flipping Tsueu-Ju Su, Mark R. Tock, Stefan U. Egelhaaf, Wilson C. K. Poon, and David T. F. Dryden PMCID: PMC1143692 Visualizing the dynamic behavior of poliovirus plus-strand RNA in living host cells Zong-Qiang Cui, Zhi-Ping Zhang, Xian-En Zhang, Ji-Kai Wen, Ya-Feng Zhou, and Wei-Hong Xie PMCID: PMC1143693 A universally applicable method of operon map prediction on minimally annotated genomes using conserved genomic context Martin T. Edwards, Stuart C. G. Rison, Neil G. Stoker, and Lorenz Wernisch PMCID: PMC1143694 Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming Pål Sætrom, Ragnhild Sneve, Knut I. Kristiansen, Ola Snøve, Jr, Thomas Grünfeld, Torbjørn Rognes, and Erling Seeberg PMCID: PMC1143698 Phosphorylation of human oxoguanine DNA glycosylase (α-OGG1) modulates its function Jingping Hu, Syed Z. Imam, Kazunari Hashiguchi, Nadja C. de Souza-Pinto, and Vilhelm A. Bohr PMCID: PMC1143695 The XPF-ERCC1 endonuclease and homologous recombination contribute to the repair of minor groove DNA interstrand crosslinks in mammalian cells produced by the pyrrolo[2,1-c][1,4]benzodiazepine dimer SJG-136 Peter H. Clingen, Inusha U. De Silva, Peter J. McHugh, Farid J Ghadessy, Michael J. Tilby, David E. Thurston, and John A. Hartley PMCID: PMC1145189 Human Rad51 filaments on double- and single-stranded DNA: correlating regular and irregular forms with recombination function Dejan Ristic, Mauro Modesti, Thijn van der Heijden, John van Noort, Cees Dekker, Roland Kanaar, and Claire Wyman PMCID: PMC1145190 Analysis of nuclear transport signals in the human apurinic/apyrimidinic endonuclease (APE1/Ref1) Elias B. Jackson, Corey A. Theriot, Ranajoy Chattopadhyay, Sankar Mitra, and Tadahide Izumi PMCID: PMC1143697 Formation of a large, complex domain of histone hyperacetylation at human 14q32.1 requires the serpin locus control region Euan W. Baxter, W. Jason Cummings, and R. E. K. Fournier PMCID: PMC1143699 MSH2 missense mutations alter cisplatin cytotoxicity and promote cisplatin-induced genome instability Jill E. Clodfelter, Michael B. Gentry, and Karin Drotschmann PMCID: PMC1148170 Excision of formamidopyrimidine lesions by endonucleases III and VIII is not a major DNA repair pathway in Escherichia coli
Carissa J. Wiederholt, Jennifer N. Patro, Yu Lin Jiang, Kazuhiro Haraguchi, and Marc M. Greenberg PMCID: PMC1145193 Effect on DNA relaxation of the single Thr718Ala mutation in human topoisomerase I: a functional and molecular dynamics study Giovanni Chillemi, Paola Fiorani, Silvia Castelli, Alessandro Bruselles, Piero Benedetti, and Alessandro Desideri PMCID: PMC1145191 Gene targeting using randomly inserted group II introns (targetrons) recovered from an Escherichia coli gene disruption library Jun Yao, Jin Zhong, and Alan M. Lambowitz PMCID: PMC1148171 A real-time semi-quantitative RT–PCR assay demonstrates that the pilE sequence dictates the frequency and characteristics of pilin antigenic variation in Neisseria gonorrhoeae Melissa S. Rohrer, Matthew P. Lazio, and H. Steven Seifert PMCID: PMC1148172 A spontaneous tRNA suppressor of a mutation in the Chlamydomonas reinhardtii nuclear MCD1 gene required for stability of the chloroplast petD mRNA Shinya Murakami, Katrin Kuehnle, and David B. Stern PMCID: PMC1148173 Inferring the connectivity of a regulatory network from mRNA quantification in Synechocystis PCC6803 Sylvain Lemeille, Amel Latifi, and Johannes Geiselmann PMCID: PMC1145192 Protein length in eukaryotic and prokaryotic proteomes Luciano Brocchieri and Samuel Karlin PMCID: PMC1150220 cAMP-responsive element in TATA-less core promoter is essential for haploid-specific gene expression in mouse testis Pranee Somboonthum, Hiroshi Ohta, Shuichi Yamada, Masayoshi Onishi, Akiko Ike, Yoshitake Nishimune, and Masami Nozaki PMCID: PMC1150221 Structure of RadB recombinase from a hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1: an implication for the formation of a near-7-fold helical assembly Toshihiko Akiba, Noriyuki Ishii, Naeem Rashid, Masaaki Morikawa, Tadayuki Imanaka, and Kazuaki Harata PMCID: PMC1150280 Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle Yasuo Tsunaka, Naoko Kajimura, Shin-ichi Tate, and Kosuke Morikawa PMCID: PMC1150222 Loss of G–A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif Vlad Cojocaru, Reinhard Klement, and Thomas M. Jovin PMCID: PMC1150281 Methods Online Direct molecular haplotyping by melting curve analysis of hybridization probes: beta 2-adrenergic receptor haplotypes as an example Genevieve Pont-Kingdon and Elaine Lyon PMCID: PMC1142492 DNA microarrays on a dendron-modified surface improve significantly the detection of single nucleotide variations in the p53 gene Soon Jin Oh, Jimin Ju, Byung Chul Kim, Eunsil Ko, Bong Jin Hong, Jae-Gahb Park, Joon Won Park, and Kwan Yong Choi PMCID: PMC1143581 Genome amplification of single sperm using multiple displacement amplification Zhengwen Jiang, Xingqi Zhang, Ranjan Deka, and Li Jin PMCID: PMC1143700 RNA interference by mixtures of siRNAs prepared using custom oligonucleotide arrays Andrew V. Oleinikov, Jun Zhao, and Matthew D. Gray PMCID: PMC1143701 MSRE-PCR for analysis of gene-specific DNA methylation Anatoliy A. Melnikov, Ronald B. Gartenhaus, Anait S. Levenson, Natalia A. Motchoulskaia, and Victor V. Levenson (Chernokhvostov) PMCID: PMC1145194 A complementation method for functional analysis of mammalian genes Juana Maria Gonzalez-Santos, Huibi Cao, Anan Wang, David R. Koehler, Bernard Martin, Roya Navab, and Jim Hu PMCID: PMC1145195 Single nucleotide extension technology for quantitative site-specific evaluation of metC/C in GC-rich regions Zachary A. Kaminsky, Abbas Assadzadeh, James Flanagan, and Arturas Petronis PMCID: PMC1150895 Real-time monitoring of enzymatic DNA hydrolysis by electrospray ionization mass spectrometry Robert H. H. van den Heuvel, Sara Gato, Cees Versluis, Pascal Gerbaux, Colin Kleanthous, and Albert J. R. Heck PMCID: PMC1150282 |
