| | Survey and Summary In vitro selection, characterization, and application of deoxyribozymes that cleave RNA Scott K. Silverman PMCID: PMC1283523 Articles Expansion of the BioCyc collection of pathway/genome databases to 160 genomes Peter D. Karp, Christos A. Ouzounis, Caroline Moore-Kochlacs, Leon Goldovsky, Pallavi Kaipa, Dag Ahrén, Sophia Tsoka, Nikos Darzentas, Victor Kunin, and Núria López-Bigas PMCID: PMC1266070 Binding of herpes simplex virus-1 US11 to specific RNA sequences Kevin F. Bryant, J. Colin Cox, Hongming Wang, James M. Hogle, Andrew D. Ellington, and Donald M. Coen PMCID: PMC1266072 Rearranging the centromere of the human Y chromosome with ![[var phi]](corehtml/pmc/pmcents/x03C6.gif) C31 integrase Sunir Malla, Felix Dafhnis-Calas, John F. Y. Brookfield, Margaret C. M. Smith, and William R. A. Brown PMCID: PMC1266074 Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation Xingyuan Li, Zhili He, and Jizhong Zhou PMCID: PMC1266071 Transgene-induced CCWGG methylation does not alter CG methylation patterning in human kidney cells Taras Shevchuk, Leo Kretzner, Kristofer Munson, John Axume, Jarrod Clark, Olga V. Dyachenko, Marie Caudill, Yaroslav Buryanov, and Steven S. Smith PMCID: PMC1266073 In vivo and in vitro studies of Mgs1 suggest a link between genome instability and Okazaki fragment processing Jeong-Hoon Kim, Young-Hoon Kang, Hyo-Jin Kang, Do-Hyung Kim, Gi-Hyuck Ryu, Min-Jung Kang, and Yeon-Soo Seo PMCID: PMC1275582 Correlation between sequence conservation and the genomic context after gene duplication Richard A. Notebaart, Martijn A. Huynen, Bas Teusink, Roland J. Siezen, and Berend Snel PMCID: PMC1275583 Information theory based T7-like promoter models: classification of bacteriophages and differential evolution of promoters and their polymerases Zehua Chen and Thomas D. Schneider PMCID: PMC1275584 8-Methyl-2′-deoxyguanosine incorporation into parallel DNA quadruplex structures Antonella Virgilio, Veronica Esposito, Antonio Randazzo, Luciano Mayol, and Aldo Galeone PMCID: PMC1275585 Mutagenic effects of abasic and oxidized abasic lesions in Saccharomyces cerevisiae Yoke W. Kow, Gaobin Bao, Brenda Minesinger, Sue Jinks-Robertson, Wolfram Siede, Yu Lin Jiang, and Marc M. Greenberg PMCID: PMC1275587 SegH and Hef: two novel homing endonucleases whose genes replace the mobC and mobE genes in several T4-related phages Linus Sandegren, David Nord, and Britt-Marie Sjöberg PMCID: PMC1275590 Role of stacking interactions in the binding sequence preferences of DNA bis-intercalators: insight from thermodynamic integration free energy simulations Esther Marco, Ana Negri, F. Javier Luque, and Federico Gago PMCID: PMC1283521 A single catalytic domain of the junction-resolving enzyme T7 endonuclease I is a non-specific nicking endonuclease Chudi Guan and Sanjay Kumar PMCID: PMC1277808 Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome Yasunari Ogihara, Yukiko Yamazaki, Koji Murai, Akira Kanno, Toru Terachi, Takashi Shiina, Naohiko Miyashita, Shuhei Nasuda, Chiharu Nakamura, Naoki Mori, Shigeo Takumi, Minoru Murata, Satoshi Futo, and Koichiro Tsunewaki PMCID: PMC1275586 Identification of RecQL1 as a Holliday junction processing enzyme in human cell lines Gary LeRoy, Robert Carroll, Saw Kyin, Masayuki Seki, and Michael D. Cole PMCID: PMC1275589 Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes Norman E. Watkins, Jr and John SantaLucia, Jr PMCID: PMC1277807 Detection of low-level promoter activity within open reading frame sequences of Escherichia coli Mitsuoki Kawano, Gisela Storz, B. Sridhar Rao, Judah L. Rosner, and Robert G. Martin PMCID: PMC1275588 The POU protein Oct-6 is a nucleocytoplasmic shuttling protein Constanze Baranek, Elisabeth Sock, and Michael Wegner PMCID: PMC1275591 Binding of the Bacillus subtilis LexA protein to the SOS operator Eli S. Groban, Martha B. Johnson, Poopak Banky, Peta-Gaye G. Burnett, Georgina L. Calderon, Erica C. Dwyer, Shakierah N. Fuller, Biniam Gebre, Leah M. King, Ila N. Sheren, Lindi D. Von Mutius, Thomas M. O'Gara, and Charles M. Lovett PMCID: PMC1277809 Tracking of microinjected DNA in live cells reveals the intracellular behavior and elimination of extrachromosomal genetic material Noriaki Shimizu, Fumie Kamezaki, and Shiho Shigematsu PMCID: PMC1277811 Farm animal genomics and informatics: an update Ahmed Fadiel, Ifeanyi Anidi, and Kenneth D. Eichenbaum PMCID: PMC1278942 Duplication processes in Saccharomyces cerevisiae haploid strains Joseph Schacherer, Jacky de Montigny, Anne Welcker, Jean-Luc Souciet, and Serge Potier PMCID: PMC1277810 FOB1 affects DNA topoisomerase I in vivo cleavages in the enhancer region of the Saccharomyces cerevisiae ribosomal DNA locus Francesca Di Felice, Francesco Cioci, and Giorgio Camilloni PMCID: PMC1277812 Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs Irmtraud M. Meyer and István Miklós PMCID: PMC1278941 Structure–function analysis of yeast RNA debranching enzyme (Dbr1), a manganese-dependent phosphodiesterase M. Fahad Khalid, Masad J. Damha, Stewart Shuman, and Beate Schwer PMCID: PMC1278944 A coarse graining approach to determine nucleic acid structures from small angle neutron scattering profiles in solution J. Zhou, S. Krueger, and S. K. Gregurick PMCID: PMC1283524 Shared RNA-binding sites for interacting members of the Drosophila ELAV family of neuronal proteins Claudia D. Borgeson and Marie-Laure Samson PMCID: PMC1283526 DNA damage and replication stress induced transcription of RNR genes is dependent on the Ccr4–Not complex Klaas W. Mulder, G. Sebastiaan Winkler, and H. Th. Marc Timmers PMCID: PMC1278945 T:G mismatch-specific thymine-DNA glycosylase (TDG) as a coregulator of transcription interacts with SRC1 family members through a novel tyrosine repeat motif Marie J. Lucey, Dongsheng Chen, Jorge Lopez-Garcia, Stephen M. Hart, Fladia Phoenix, Rajai Al-Jehani, John P. Alao, Roger White, Karin B. Kindle, Régine Losson, Pierre Chambon, Malcolm G. Parker, Primo Schär, David M. Heery, Lakjaya Buluwela, and Simak Ali PMCID: PMC1283525 Silencing of retrotransposons in Dictyostelium by DNA methylation and RNAi Markus Kuhlmann, Branimira E. Borisova, Markus Kaller, Pontus Larsson, Dirk Stach, Jianbo Na, Ludwig Eichinger, Frank Lyko, Victor Ambros, Fredrik Söderbom, Christian Hammann, and Wolfgang Nellen PMCID: PMC1283529 Invariant amino acids essential for decoding function of polypeptide release factor eRF1 Petr Kolosov, Ludmila Frolova, Alim Seit-Nebi, Vera Dubovaya, Artem Kononenko, Nina Oparina, Just Justesen, Alexandr Efimov, and Lev Kisselev PMCID: PMC1283522 Pyrimido[1,2-a]-purin-10(3H)-one, M1G, is less prone to artifact than base oxidation Yo-Chan Jeong, Jun Nakamura, Patricia B. Upton, and James A. Swenberg PMCID: PMC1283527 Crystal structure and RNA binding of the Rpb4/Rpb7 subunits of human RNA polymerase II Hedije Meka, Finn Werner, Suzanne C. Cordell, Silvia Onesti, and Peter Brick PMCID: PMC1283528 Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery Fan Yang, Jian Yang, Xiaobing Zhang, Lihong Chen, Yan Jiang, Yongliang Yan, Xudong Tang, Jing Wang, Zhaohui Xiong, Jie Dong, Ying Xue, Yafang Zhu, Xingye Xu, Lilian Sun, Shuxia Chen, Huan Nie, Junping Peng, Jianguo Xu, Yu Wang, Zhenghong Yuan, Yumei Wen, Zhijian Yao, Yan Shen, Boqin Qiang, Yunde Hou, Jun Yu, and Qi Jin PMCID: PMC1278947 Methods Online Two-photon fluorescence cross-correlation spectroscopy as a potential tool for high-throughput screening of DNA repair activity Maddalena Collini, Michele Caccia, Giuseppe Chirico, Flavia Barone, Eugenia Dogliotti, and Filomena Mazzei PMCID: PMC1266075 Position of the fluorescent label is a crucial factor determining signal intensity in microarray hybridizations Lei Zhang, Thomas Hurek, and Barbara Reinhold-Hurek PMCID: PMC1275592 A method to find tissue-specific novel sites of selective adenosine deamination Johan Ohlson, Mats Ensterö, Britt-Marie Sjöberg, and Marie Öhman PMCID: PMC1275595 A colorimetric method for point mutation detection using high-fidelity DNA ligase Jishan Li, Xia Chu, Yali Liu, Jian-Hui Jiang, Zhimin He, Zhiwei Zhang, Guoli Shen, and Ru-Qin Yu PMCID: PMC1275593 A new generation of vectors with increased induction ratios by overimposing a second regulatory level by attenuation Jose Luis Royo, Hamid Manyani, Angel Cebolla, and Eduardo Santero PMCID: PMC1275594 In vitro non-viral gene delivery with nanofibrous scaffolds Dehai Liang, Yen K. Luu, Kwangsok Kim, Benjamin S. Hsiao, Michael Hadjiargyrou, and Benjamin Chu PMCID: PMC1277813 An analysis of the feasibility of short read sequencing Nava Whiteford, Niall Haslam, Gerald Weber, Adam Prügel-Bennett, Jonathan W. Essex, Peter L. Roach, Mark Bradley, and Cameron Neylon PMCID: PMC1278949 Protocols for the assurance of microarray data quality and process control L. D. Burgoon, J. E. Eckel-Passow, C. Gennings, D. R. Boverhof, J. W. Burt, C. J. Fong, and T. R. Zacharewski PMCID: PMC1278948 Parameters determining the efficiency of gene targeting in the moss Physcomitrella patens Yasuko Kamisugi, Andrew C. Cuming, and David J. Cove PMCID: PMC1283530 Corrigenda 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: PMC1278943 Corrects: Irina V. Smolina, et al. End invasion of peptide nucleic acids (PNAs) with mixed-base composition into linear DNA duplexes. Nucleic Acids Res. 2005; 33(17): e146. 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: PMC1278946 Corrects: In-Youb Chang, et al. Human AP endonuclease suppresses DNA mismatch repair activity leading to microsatellite instability. Nucleic Acids Res. 2005; 33(16): 5073–5081. |
