| | Molecular Biology Twin gradients in APOBEC3 edited HIV-1 DNA reflect the dynamics of lentiviral replication Rodolphe Suspène, Christophe Rusniok, Jean-Pierre Vartanian, and Simon Wain-Hobson PMCID: PMC1635257 CK2-mediated stimulation of Pol I transcription by stabilization of UBF–SL1 interaction Chih-Yin Lin, Sonia Navarro, Sita Reddy, and Lucio Comai PMCID: PMC1635259 Identification of a plastid response element that acts as an enhancer within the Chlamydomonas HSP70A promoter Erika D. von Gromoff, Michael Schroda, Ulrike Oster, and Christoph F. Beck PMCID: PMC1635268 Zfp206 regulates ES cell gene expression and differentiation Wen Zhang, Emily Walker, Owen J. Tamplin, Janet Rossant, William L. Stanford, and Timothy R. Hughes PMCID: PMC1635278 Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells Daniela Schmitter, Jody Filkowski, Alain Sewer, Ramesh S. Pillai, Edward J. Oakeley, Mihaela Zavolan, Petr Svoboda, and Witold Filipowicz PMCID: PMC1635286 A novel archaeal regulatory protein, Sta1, activates transcription from viral promoters Alexandra Kessler, Guennadi Sezonov, J. Iñaki Guijarro, Nicole Desnoues, Thierry Rose, Muriel Delepierre, Stephen D. Bell, and David Prangishvili PMCID: PMC1635249 Isolation and characterization of the TIGA genes, whose transcripts are induced by growth arrest Norikazu Yabuta, Hiroaki Onda, Masafumi Watanabe, Naohisa Yoshioka, Ippei Nagamori, Tomoyuki Funatsu, Shingo Toji, Katsuyuki Tamai, and Hiroshi Nojima PMCID: PMC1635288 Identification of a structural and functional domain in xNAP1 involved in protein–protein interactions Christine Friedeberg, Garry Scarlett, John McGeeghan, Anita Abu-daya, Matthew Guille, and Geoff Kneale PMCID: PMC1635243 A peptide with alternating lysines can act as a highly specific Z-DNA binding domain Yang-Gyun Kim, Hyun-Ju Park, Kyeong Kyu Kim, Ky Lowenhaupt, and Alexander Rich PMCID: PMC1635270 XE7: A novel splicing factor that interacts with ASF/SF2 and ZNF265 A. Helena Mangs, Helen J.L. Speirs, Christine Goy, David J. Adams, M. Andrea Markus, and Brian J. Morris PMCID: PMC1635291 CTD kinase I is required for the integrity of the rDNA tandem array Sabrina Grenetier, Céline Bouchoux, and Valérie Goguel PMCID: PMC1635248 RNA Exportin-5 orthologues are functionally divergent among species Satoshi Shibata, Mitsuho Sasaki, Takashi Miki, Akira Shimamoto, Yasuhiro Furuichi, Jun Katahira, and Yoshihiro Yoneda PMCID: PMC1635293 Amino acid residues critical for RNA-binding in the N-terminal domain of the nucleocapsid protein are essential determinants for the infectivity of coronavirus in cultured cells Yong Wah Tan, Shouguo Fang, Hui Fan, Julien Lescar, and D.X. Liu PMCID: PMC1635287 Controlling activation of the RNA-dependent protein kinase by siRNAs using site-specific chemical modification Sujiet Puthenveetil, Landon Whitby, Jin Ren, Kevin Kelnar, Joseph F. Krebs, and Peter A. Beal PMCID: PMC1635244 A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation Zhi John Lu, Douglas H. Turner, and David H. Mathews PMCID: PMC1635246 Examination of the structural and functional versatility of glmS ribozymes by using in vitro selection Kristian H. Link, Lixia Guo, and Ronald R. Breaker PMCID: PMC1635283 Binding of human SLBP on the 3′-UTR of histone precursor H4-12 mRNA induces structural rearrangements that enable U7 snRNA anchoring Sophie Jaeger, Franck Martin, Joëlle Rudinger-Thirion, Richard Giegé, and Gilbert Eriani PMCID: PMC1635294 Structural Biology Site-directed spin labeling measurements of nanometer distances in nucleic acids using a sequence-independent nitroxide probe Qi Cai, Ana Karin Kusnetzow, Wayne L. Hubbell, Ian S. Haworth, Gian Paola C. Gacho, Ned Van Eps, Kálmán Hideg, Eric J. Chambers, and Peter Z. Qin PMCID: PMC1635252 DNA bending by bHLH charge variants Robert J. McDonald, Jason D. Kahn, and L. James Maher, III PMCID: PMC1635255 Survey and Summary Spatial organization of transcription by RNA polymerase III Rebecca A. Haeusler and David R. Engelke PMCID: PMC1635290 Sequence-specific binding of single-stranded RNA: is there a code for recognition? Sigrid D. Auweter, Florian C. Oberstrass, and Frédéric H.-T. Allain PMCID: PMC1635273 Genomics Organization of chromosome ends in the rice blast fungus, Magnaporthe oryzae Cathryn Rehmeyer, Weixi Li, Motoaki Kusaba, Yun-Sik Kim, Doug Brown, Chuck Staben, Ralph Dean, and Mark Farman PMCID: PMC1635262 Transcriptome response to heavy metal stress in Drosophila reveals a new zinc transporter that confers resistance to zinc Hasmik Yepiskoposyan, Dieter Egli, Tim Fergestad, Anand Selvaraj, Carina Treiber, Gerd Multhaup, Oleg Georgiev, and Walter Schaffner PMCID: PMC1635269 Chemistry Dynamic assembly of primers on nucleic acid templates Nicole A. Leal, Makoto Sukeda, and Steven A. Benner PMCID: PMC1635275 Methods Online Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection Dylan Chivian and David Baker PMCID: PMC1635247 A simple DNA stretching method for fluorescence imaging of single DNA molecules Ting-Fung Chan, Connie Ha, Angie Phong, Dongmei Cai, Eunice Wan, Lucinda Leung, Pui-Yan Kwok, and Ming Xiao PMCID: PMC1635263 A spreadable, non-integrative and high copy number shuttle vector for Sulfolobus solfataricus based on the genetic element pSSVx from Sulfolobus islandicus Tiziana Aucelli, Patrizia Contursi, Michele Girfoglio, Mosè Rossi, and Raffaele Cannio PMCID: PMC1635272 Mouse microRNA profiles determined with a new and sensitive cloning method Shuji Takada, Eugene Berezikov, Yoshihiro Yamashita, Mariana Lagos-Quintana, Wigard P. Kloosterman, Munehiro Enomoto, Hisashi Hatanaka, Shin-ichiro Fujiwara, Hideki Watanabe, Manabu Soda, Young Lim Choi, Ronald H. A. Plasterk, Edwin Cuppen, and Hiroyuki Mano PMCID: PMC1635289 AccuTyping: new algorithms for automated analysis of data from high-throughput genotyping with oligonucleotide microarrays Guohong Hu, Hui-Yun Wang, Danielle M. Greenawalt, Marco A. Azaro, Minjie Luo, Irina V. Tereshchenko, Xiangfeng Cui, Qifeng Yang, Richeng Gao, Li Shen, and Honghua Li PMCID: PMC1635267 Using RNA secondary structures to guide sequence motif finding towards single-stranded regions Michael Hiller, Rainer Pudimat, Anke Busch, and Rolf Backofen PMCID: PMC1903381 Computational Biology PLPD: reliable protein localization prediction from imbalanced and overlapped datasets KiYoung Lee, Dae-Won Kim, DoKyun Na, Kwang H. Lee, and Doheon Lee PMCID: PMC1636404 Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues Xueping Yu, Jimmy Lin, Donald J. Zack, and Jiang Qian PMCID: PMC1635265 Genetic regulation of fluxes: iron homeostasis of Escherichia coli Szabolcs Semsey, Anna M. C. Andersson, Sandeep Krishna, Mogens Høgh Jensen, Eric Massé, and Kim Sneppen PMCID: PMC1635276 Nucleic Acid Enzymes A strand-passage conformation of DNA gyrase is required to allow the bacterial toxin, CcdB, to access its binding site Andrew B. Smith and Anthony Maxwell PMCID: PMC1635281 The fidelity of DNA synthesis by yeast DNA polymerase zeta alone and with accessory proteins Xuejun Zhong, Parie Garg, Carrie M. Stith, Stephanie A. Nick McElhinny, Grace E. Kissling, Peter M. J. Burgers, and Thomas A. Kunkel PMCID: PMC1635245 Biochemical analysis of the substrate specificity and sequence preference of endonuclease IV from bacteriophage T4, a dC-specific endonuclease implicated in restriction of dC-substituted T4 DNA synthesis Nobutaka Hirano, Hiroyuki Ohshima, and Hideo Takahashi PMCID: PMC1635256 Homing endonuclease I-CreI derivatives with novel DNA target specificities Laura E. Rosen, Holly A. Morrison, Selma Masri, Michael J. Brown, Brendan Springstubb, Django Sussman, Barry L. Stoddard, and Lenny M. Seligman PMCID: PMC1635285 Human replication protein A unfolds telomeric G-quadruplexes Tonatiuh Romero Salas, Irina Petruseva, Olga Lavrik, Anne Bourdoncle, Jean-Louis Mergny, Alain Favre, and Carole Saintomé PMCID: PMC1635258 |
