| | Survey and Summary BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH) Bauke Ylstra, Paul van den IJssel, Beatriz Carvalho, Ruud H. Brakenhoff, and Gerrit A. Meijer PMCID: PMC1356528 Experimental approaches to identify non-coding RNAs Alexander Hüttenhofer and Jörg Vogel PMCID: PMC1351373 Degradation of RNA in bacteria: comparison of mRNA and stable RNA Murray P. Deutscher PMCID: PMC1360286 Post-transcriptional nucleotide modification and alternative folding of RNA Mark Helm PMCID: PMC1360285 Articles p66α and p66β of the Mi-2/NuRD complex mediate MBD2 and histone interaction Marc Brackertz, Zihua Gong, Jörg Leers, and Rainer Renkawitz PMCID: PMC1331983 Saccharomyces cerevisiae Est3p dimerizes in vitro and dimerization contributes to efficient telomere replication in vivo Cui-Ping Yang, Yong-Bin Chen, Fei-Long Meng, and Jin-Qiu Zhou PMCID: PMC1331985 Polη, Polζ and Rev1 together are required for G to T transversion mutations induced by the (+)- and (−)-trans-anti-BPDE-N2-dG DNA adducts in yeast cells Bo Zhao, Jillian Wang, Nicholas E. Geacintov, and Zhigang Wang PMCID: PMC1331986 Examination of an inverted repeat within the F factor origin of transfer: context dependence of F TraI relaxase DNA specificity Sarah L. Williams and Joel F. Schildbach PMCID: PMC1331984 Sub-plastidial localization of two different phage-type RNA polymerases in spinach chloroplasts Jacinthe Azevedo, Florence Courtois, and Silva Lerbs-Mache PMCID: PMC1342036 2′-Deoxy-2′-fluoro-β-d-arabinonucleic acid (2′F-ANA) modified oligonucleotides (ON) effect highly efficient, and persistent, gene silencing A. Kalota, L. Karabon, C. R. Swider, E. Viazovkina, M. Elzagheid, M. J. Damha, and A. M. Gewirtz PMCID: PMC1342038 Molecular characterization of geminivirus-derived small RNAs in different plant species Rashid Akbergenov, Azeddine Si-Ammour, Todd Blevins, Imran Amin, Claudia Kutter, Herve Vanderschuren, Peng Zhang, Wilhelm Gruissem, Frederick Meins, Jr, Thomas Hohn, and Mikhail M. Pooggin PMCID: PMC1342034 Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides Robert J. Fisher, Matthew J. Fivash, Andrew G. Stephen, Nathan A. Hagan, Shilpa R. Shenoy, Maxine V. Medaglia, Lindsey R. Smith, Karen M. Worthy, John T. Simpson, Robert Shoemaker, Karen L. McNitt, Donald G. Johnson, Catherine V. Hixson, Robert J. Gorelick, Daniele Fabris, Louis E. Henderson, and Alan Rein PMCID: PMC1351370 Nucleolin links to arsenic-induced stabilization of GADD45α mRNA Yadong Zhang, Deepak Bhatia, Hongfeng Xia, Vince Castranova, Xianglin Shi, and Fei Chen PMCID: PMC1342039 The Plasmodium selenoproteome Alexey V. Lobanov, Cesar Delgado, Stefan Rahlfs, Sergey V. Novoselov, Gregory V. Kryukov, Stephan Gromer, Dolph L. Hatfield, Katja Becker, and Vadim N. Gladyshev PMCID: PMC1342035 Evidence that the S.cerevisiae Sgs1 protein facilitates recombinational repair of telomeres during senescence Mahrukh Azam, Julia Y. Lee, Veena Abraham, Rebecca Chanoux, Kimberly A. Schoenly, and F. Brad Johnson PMCID: PMC1342037 Structure–function analysis of the kinase-CPD domain of yeast tRNA ligase (Trl1) and requirements for complementation of tRNA splicing by a plant Trl1 homolog Li Kai Wang, Beate Schwer, Markus Englert, Hildburg Beier, and Stewart Shuman PMCID: PMC1345694 Microarray-based DNA methylation profiling: technology and applications Axel Schumacher, Philipp Kapranov, Zachary Kaminsky, James Flanagan, Abbas Assadzadeh, Patrick Yau, Carl Virtanen, Neil Winegarden, Jill Cheng, Thomas Gingeras, and Arturas Petronis PMCID: PMC1345696 Regulation of the human p21(waf1/cip1) gene promoter via multiple binding sites for p53 and the vitamin D3 receptor Anna Saramäki, Claire M. Banwell, Moray J. Campbell, and Carsten Carlberg PMCID: PMC1351372 High throughput detection of M6P/IGF2R intronic hypermethylation and LOH in ovarian cancer Zhiqing Huang, Yaqing Wen, Ruby Shandilya, Jeffrey R. Marks, Andrew Berchuck, and Susan K. Murphy PMCID: PMC1345698 Base-stacking and base-pairing contributions into thermal stability of the DNA double helix Peter Yakovchuk, Ekaterina Protozanova, and Maxim D. Frank-Kamenetskii PMCID: PMC1360284 Engineered external guide sequences are highly effective in inducing RNase P for inhibition of gene expression and replication of human cytomegalovirus Yong-Hua Yang, Hongjian Li, Tianhong Zhou, Kihoon Kim, and Fenyong Liu PMCID: PMC1345693 Unbiased in vitro selection reveals the unique character of the self-cleaving antigenomic HDV RNA sequence Atef Nehdi and Jean-Pierre Perreault PMCID: PMC1345697 Nucleic acid binding and chaperone properties of HIV-1 Gag and nucleocapsid proteins Margareta Cruceanu, Maria A. Urbaneja, Catherine V. Hixson, Donald G. Johnson, Siddhartha A. Datta, Matthew J. Fivash, Andrew G. Stephen, Robert J. Fisher, Robert J. Gorelick, Jose R. Casas-Finet, Alan Rein, Ioulia Rouzina, and Mark C. Williams PMCID: PMC1356529 Induction of the lac promoter in the absence of DNA loops and the stoichiometry of induction Stefan Oehler, Siegfried Alberti, and Benno Müller-Hill PMCID: PMC1345695 Rampant polyuridylylation of plastid gene transcripts in the dinoflagellate Lingulodinium Yunling Wang and David Morse PMCID: PMC1351369 Deletion of the Tetrahymena thermophila rDNA replication fork barrier region disrupts macronuclear rDNA excision and creates a fragile site in the micronuclear genome J. S. Yakisich and G. M. Kapler PMCID: PMC1356531 Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes Ikuo Uchiyama PMCID: PMC1351371 HEN1 recognizes 21–24 nt small RNA duplexes and deposits a methyl group onto the 2′ OH of the 3′ terminal nucleotide Zhiyong Yang, Yon W. Ebright, Bin Yu, and Xuemei Chen PMCID: PMC1356533 Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site Jiro Kondo, Alexandre Urzhumtsev, and Eric Westhof PMCID: PMC1360289 Similarities and differences in interaction of K+ and Na+ with condensed ordered DNA. A molecular dynamics computer simulation study Yuhua Cheng, Nikolay Korolev, and Lars Nordenskiöld PMCID: PMC1356527 Molecular dynamics simulations of sarcin–ricin rRNA motif Nad'a Špačková and Jiří Šponer PMCID: PMC1360246 Hfq variant with altered RNA binding functions Katarzyna Ziolkowska, Philippe Derreumaux, Marc Folichon, Olivier Pellegrini, Philippe Régnier, Irina V. Boni, and Eliane Hajnsdorf PMCID: PMC1356530 Growth inhibition and apoptosis induced by daunomycin-conjugated triplex-forming oligonucleotides targeting the c-myc gene in prostate cancer cells Sara Napoli, Umberto Negri, Federico Arcamone, Massimo L. Capobianco, Giuseppina M. Carbone, and Carlo V. Catapano PMCID: PMC1356532 The Werner syndrome protein operates in base excision repair and cooperates with DNA polymerase β Jeanine A. Harrigan, David M. Wilson, III, Rajendra Prasad, Patricia L. Opresko, Gad Beck, Alfred May, Samuel H. Wilson, and Vilhelm A. Bohr PMCID: PMC1356534 Sequence effects of aminofluorene-modified DNA duplexes: thermodynamic and circular dichroism properties Srinivasa Rao Meneni, Rhijuta D'Mello, Gregory Norigian, Gregory Baker, Lan Gao, M. Paul Chiarelli, and Bongsup P. Cho PMCID: PMC1356535 Methods Online Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons Bettina Harr and Christian Schlötterer PMCID: PMC1345700 MicroRNA expression profiling of single whole embryonic stem cells Fuchou Tang, Petra Hajkova, Sheila C. Barton, Kaiqin Lao, and M. Azim Surani PMCID: PMC1351374 Genetic manipulation of an exogenous non-immunoglobulin protein by gene conversion machinery in a chicken B cell line Naoki Kanayama, Kagefumi Todo, Satoko Takahashi, Masaki Magari, and Hitoshi Ohmori PMCID: PMC1342040 A simple and effective chromosome modification method for large-scale deletion of genome sequences and identification of essential genes in fission yeast Kyotaro Hirashima, Tomoko Iwaki, Kaoru Takegawa, Yuko Giga-Hama, and Hideki Tohda PMCID: PMC1351375 Detection of rare mutant K-ras DNA in a single-tube reaction using peptide nucleic acid as both PCR clamp and sensor probe Ji-Dung Luo, Err-Cheng Chan, Chun-Liang Shih, Tai-Long Chen, Ying Liang, Tsann-Long Hwang, and Chiuan-Chian Chiou PMCID: PMC1345699 Thorough validation of siRNA-induced cell death phenotypes defines new anti-apoptotic protein Weilin Wu, Emily Hodges, and Christer Höög PMCID: PMC1345702 Sequence- and structural-selective nucleic acid binding revealed by the melting of mixtures Xiaochun Shi and Jonathan B. Chaires PMCID: PMC1345701 A general method for manipulating DNA sequences from any organism with optical tweezers Derek N. Fuller, Gregory J. Gemmen, John Peter Rickgauer, Aurelie Dupont, Rachel Millin, Pierre Recouvreux, and Douglas E. Smith PMCID: PMC1360288 Therapeutic protein transduction of mammalian cells and mice by nucleic acid-free lentiviral nanoparticles Nils Link, Corinne Aubel, Jens M. Kelm, René R. Marty, David Greber, Valentin Djonov, Jean Bourhis, Wilfried Weber, and Martin Fussenegger PMCID: PMC1356536 Erratum The genetic map and comparative analysis with the physical map of Trypanosoma brucei Annette MacLeod, Alison Tweedie, Sarah McLellan, Sonya Taylor, Neil Hall, Matthew Berriman, Najib M. El-Sayed, Michelle Hope, C. Michael R. Turner, and Andy Tait PMCID: PMC1360287 Corrects: Annette MacLeod, et al. The genetic map and comparative analysis with the physical map of Trypanosoma brucei. Nucleic Acids Res. 2005; 33(21): 6688–6693. |
