| | Articles Distant sequences determine 5′ end formation of cox3 transcripts in Arabidopsis thaliana ecotype C24 Joachim Forner, Bärbel Weber, Caterina Wiethölter, Rhonda C. Meyer, and Stefan Binder PMCID: PMC1187949 A unique tRNA recognition mechanism of Caenorhabditis elegans mitochondrial EF-Tu2 Takuma Suematsu, Aya Sato, Masayuki Sakurai, Kimitsuna Watanabe, and Takashi Ohtsuki PMCID: PMC1188084 Saccharomyces cerevisiae Mre11 is a high-affinity G4 DNA-binding protein and a G-rich DNA-specific endonuclease: implications for replication of telomeric DNA Gargi Ghosal and K. Muniyappa PMCID: PMC1188515 Tolerated wobble mutations in siRNAs decrease specificity, but can enhance activity in vivo Torgeir Holen, Svein Erik Moe, Jan Gunnar Sørbø, Trine J. Meza, Ole Petter Ottersen, and Arne Klungland PMCID: PMC1188085 Isolation of a small molecule inhibitor of DNA base excision repair Srinivasan Madhusudan, Fiona Smart, Paul Shrimpton, Jason L. Parsons, Laurence Gardiner, Sue Houlbrook, Denis C. Talbot, Timothy Hammonds, Paul A. Freemont, Michael J. E. Sternberg, Grigory L. Dianov, and Ian D. Hickson PMCID: PMC1188083 Structural and functional characterizations of mung bean mitochondrial nucleoids Hwa Dai, Yih-Shan Lo, Alexandra Litvinchuk, Yuh-Tai Wang, Wann-Neng Jane, Lin-June Hsiao, and Kwen-Sheng Chiang PMCID: PMC1188516 Characterization of cis- and trans-acting elements in the imprinted human SNURF-SNRPN locus Sara Rodriguez-Jato, Robert D. Nicholls, Daniel J. Driscoll, and Thomas P. Yang PMCID: PMC1188517 Specific roles of 5′ RNA secondary structures in stabilizing transcripts in chloroplasts Loreto Suay, Maria L. Salvador, Emnet Abesha, and Uwe Klein PMCID: PMC1188514 Characterization of SpPol4, a unique X-family DNA polymerase in Schizosaccharomyces pombe Sergio González-Barrera, Arancha Sánchez, José F. Ruiz, Raquel Juárez, Angel J. Picher, Gloria Terrados, Paula Andrade, and Luis Blanco PMCID: PMC1192829 Characterization of the Type III restriction endonuclease PstII from Providencia stuartii Alice Sears, Luke J. Peakman, Geoffrey G. Wilson, and Mark D. Szczelkun PMCID: PMC1192830 Subunit assembly modulates the activities of the Type III restriction–modification enzyme PstII in vitro Alice Sears and Mark D. Szczelkun PMCID: PMC1192831 Interaction of Staufen1 with the 5′ end of mRNA facilitates translation of these RNAs Samuel Dugré-Brisson, George Elvira, Karine Boulay, Laurent Chatel-Chaix, Andrew J. Mouland, and Luc DesGroseillers PMCID: PMC1193567 Involvement of KSRP in the post-transcriptional regulation of human iNOS expression–complex interplay of KSRP with TTP and HuR Katrin Linker, Andrea Pautz, Marcel Fechir, Thomas Hubrich, Jobst Greeve, and Hartmut Kleinert PMCID: PMC1192834 Identifying cooperative transcriptional regulations using protein–protein interactions Nobuyoshi Nagamine, Yuji Kawada, and Yasubumi Sakakibara PMCID: PMC1192832 Molecular details of quinolone–DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it Karsten Siegmund, Shruti Maheshwary, Sukunath Narayanan, William Connors, Matthias Riedrich, Michael Printz, and Clemens Richert PMCID: PMC1192833 NEIL1 excises 3′ end proximal oxidative DNA lesions resistant to cleavage by NTH1 and OGG1 Jason L. Parsons, Dmitry O. Zharkov, and Grigory L. Dianov PMCID: PMC1196207 dSAP18 and dHDAC1 contribute to the functional regulation of the Drosophila Fab-7 element Silvia Canudas, Silvia Pérez, Laura Fanti, Sergio Pimpinelli, Navjot Singh, Steven D. Hanes, Fernando Azorín, and M. Lluïsa Espinás PMCID: PMC1196206 Nucleotide modification at the γ-phosphate leads to the improved fidelity of HIV-1 reverse transcriptase Brent A. Mulder, Steve Anaya, Peilin Yu, Keun Woo Lee, Anvy Nguyen, Jason Murphy, Richard Willson, James M. Briggs, Xiaolian Gao, and Susan H. Hardin PMCID: PMC1197130 Human vault-associated non-coding RNAs bind to mitoxantrone, a chemotherapeutic compound Subash C. B. Gopinath, Akimasa Matsugami, Masato Katahira, and Penmetcha K. R. Kumar PMCID: PMC1201340 Biased exon/intron distribution of cryptic and de novo 3′ splice sites Jana Královičová, Mikkel B. Christensen, and Igor Vořechovský PMCID: PMC1197134 Limitations and potentials of current motif discovery algorithms Jianjun Hu, Bin Li, and Daisuke Kihara PMCID: PMC1199555 Coordinate control of cell cycle regulatory genes in zebrafish development tested by cyclin D1 knockdown with morpholino phosphorodiamidates and hydroxyprolyl-phosphono peptide nucleic acids Kevin T. Duffy, Mary Frances McAleer, William R. Davidson, Laszlo Kari, Csaba Kari, Chang-Gong Liu, Steven A. Farber, Keith C. Cheng, Jason R. Mest, Eric Wickstrom, Adam P. Dicker, and Ulrich Rodeck PMCID: PMC1199556 Efficient isothermal expansion of human telomeric and minisatellite repeats by Thermococcus litoralis DNA polymerase Jörg S. Hartig and Eric T. Kool PMCID: PMC1199558 Reduction of nucleosome assembly during new DNA synthesis impairs both major pathways of double-strand break repair L. Kevin Lewis, G. Karthikeyan, Jared Cassiano, and Michael A. Resnick PMCID: PMC1197131 Interactions between the archaeal Cdc6 and MCM proteins modulate their biochemical properties Rajesh Kasiviswanathan, Jae-Ho Shin, and Zvi Kelman PMCID: PMC1201339 Thermodynamically based DNA strand design Dan Tulpan, Mirela Andronescu, Seo Bong Chang, Michael R. Shortreed, Anne Condon, Holger H. Hoos, and Lloyd M. Smith PMCID: PMC1199561 A thermodynamic approach to designing structure-free combinatorial DNA word sets Michael R. Shortreed, Seo Bong Chang, DongGee Hong, Maggie Phillips, Bridget Campion, Dan C. Tulpan, Mirela Andronescu, Anne Condon, Holger H. Hoos, and Lloyd M. Smith PMCID: PMC1199559 Quenched autoligation probes allow discrimination of live bacterial species by single nucleotide differences in rRNA Adam P. Silverman and Eric T. Kool PMCID: PMC1199560 The Gumbel pre-factor k for gapped local alignment can be estimated from simulations of global alignment Sergey Sheetlin, Yonil Park, and John L. Spouge PMCID: PMC1199557 An evolutionary intra-molecular shift in the preferred U3 snoRNA binding site on pre-ribosomal RNA Anton V. Borovjagin and Susan A. Gerbi PMCID: PMC1199564 Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility Gali Golan, Dmitry O. Zharkov, Hadar Feinberg, Andrea S. Fernandes, Elena I. Zaika, Jadwiga H. Kycia, Arthur P. Grollman, and Gil Shoham PMCID: PMC1199562 Methods Online Site-specific biotinylation of RNA molecules by transcription using unnatural base pairs Kei Moriyama, Michiko Kimoto, Tsuneo Mitsui, Shigeyuki Yokoyama, and Ichiro Hirao PMCID: PMC1188086 Rapid generation of long synthetic tandem repeats and its application for analysis in human artificial chromosome formation Tom Ebersole, Yasuhide Okamoto, Vladimir N. Noskov, Natalay Kouprina, Jung-Hyun Kim, Sun-Hee Leem, J. Carl Barrett, Hiroshi Masumoto, and Vladimir Larionov PMCID: PMC1197135 Single small-interfering RNA expression vector for silencing multiple transforming growth factor-β pathway components Amarsanaa Jazag, Fumihiko Kanai, Hideaki Ijichi, Keisuke Tateishi, Tsuneo Ikenoue, Yasuo Tanaka, Miki Ohta, Jun Imamura, Bayasi Guleng, Yoshinari Asaoka, Takao Kawabe, Makoto Miyagishi, Kazunari Taira, and Masao Omata PMCID: PMC1188087 Direct isolation of specific RNA-interacting proteins using a novel affinity medium Ding-Gan Liu and Li Sun PMCID: PMC1192835 Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation (BATI) Guo-Hua Zhou, Mari Gotou, Tomoharu Kajiyama, and Hideki Kambara PMCID: PMC1197137 Scoring schemes of palindrome clusters for more sensitive prediction of replication origins in herpesviruses David S. H. Chew, Kwok Pui Choi, and Ming-Ying Leung PMCID: PMC1197138 Detecting seeded motifs in DNA sequences Cinzia Pizzi, Stefania Bortoluzzi, Andrea Bisognin, Alessandro Coppe, and Gian Antonio Danieli PMCID: PMC1197136 Corrigendum I-ApeI, a novel intron-encoded LAGLIDADG homing endonuclease from the archaeon, Aeropyrum pernix K1 Norimichi Nomura, Yayoi Morinaga, Nobuaki Shirai, and Yoshihiko Sako PMCID: PMC1199563 Corrects: Norimichi Nomura, et al. I-ApeI: a novel intron-encoded LAGLIDADG homing endonuclease from the archaeon, Aeropyrum pernix K1. Nucleic Acids Res. 2005; 33(13): e116. |
