| | Molecular Biology Proteomic screen defines the hepatocyte nuclear factor 1α-binding partners and identifies HMGB1 as a new cofactor of HNF1α Miao Yu, Jian Wang, Wei Li, Yan Zhi Yuan, Chang Yan Li, Xiao Hong Qian, Wang Xiang Xu, Yi Qun Zhan, and Xiao Ming Yang PMCID: PMC2275099 Chromatinized templates reveal the requirement for the LEDGF/p75 PWWP domain during HIV-1 integration in vitro Yaïr Botbol, Nidhanapati K. Raghavendra, Shaila Rahman, Alan Engelman, and Marc Lavigne PMCID: PMC2275106 Inhibition of DNA replication fork progression and mutagenic potential of 1, N6-ethenoadenine and 8-oxoguanine in human cell extracts Joel H. Tolentino, Tom J. Burke, Suparna Mukhopadhyay, W. Glenn McGregor, and Ashis K. Basu PMCID: PMC2275085 Saccharomyces cerevisiae HMO1 interacts with TFIID and participates in start site selection by RNA polymerase II Koji Kasahara, Sewon Ki, Kayo Aoyama, Hiroyuki Takahashi, and Tetsuro Kokubo PMCID: PMC2275077 Target genes and structure of the direct repeats in the DNA-binding sequences of the response regulator PhoP in Streptomyces coelicolor Alberto Sola-Landa, Antonio Rodríguez-García, Alexander Kristian Apel, and Juan F. Martín PMCID: PMC2275107 Longevity and resistance to stress correlate with DNA repair capacity in Caenorhabditis elegans Moonjung Hyun, Jihyun Lee, Kyungjin Lee, Alfred May, Vilhelm A. Bohr, and Byungchan Ahn PMCID: PMC2275101 RNA The cucumovirus 2b gene drives selection of inter-viral recombinants affecting the crossover site, the acceptor RNA and the rate of selection Bu-Jun Shi, Robert H. Symons, and Peter Palukaitis PMCID: PMC2275080 Kluyveromyces lactis γ-toxin, a ribonuclease that recognizes the anticodon stem loop of tRNA Jian Lu, Anders Esberg, Bo Huang, and Anders S. Byström PMCID: PMC2275089 Knockdown of TNFR1 by the sense strand of an ICAM-1 siRNA: dissection of an off-target effect Paul R. Clark, Jordan S. Pober, and Martin S. Kluger PMCID: PMC2275081 Comprehensive features of natural and in vitro selected GNRA tetraloop-binding receptors Cody Geary, Stéphanie Baudrey, and Luc Jaeger PMCID: PMC2275092 Antagonism of microRNA-122 in mice by systemically administered LNA-antimiR leads to up-regulation of a large set of predicted target mRNAs in the liver Joacim Elmén, Morten Lindow, Asli Silahtaroglu, Mads Bak, Mette Christensen, Allan Lind-Thomsen, Maj Hedtjärn, Jens Bo Hansen, Henrik Frydenlund Hansen, Ellen Marie Straarup, Keith McCullagh, Phil Kearney, and Sakari Kauppinen PMCID: PMC2275095 Characterization of a ribonuclease III-like protein required for cleavage of the pre-rRNA in the 3′ETS in Arabidopsis P. Comella, F. Pontvianne, S. Lahmy, F. Vignols, N. Barbezier, A. DeBures, E. Jobet, E. Brugidou, M. Echeverria, and J. Sáez-Vásquez PMCID: PMC2275086 A conserved U-rich RNA region implicated in regulation of translation in Plasmodium female gametocytes Joanna A. M. Braks, Gunnar R. Mair, Blandine Franke-Fayard, Chris J. Janse, and Andrew P. Waters PMCID: PMC2275103 Phytohormone abscisic acid control RNA-dependent RNA polymerase 6 gene expression and post-transcriptional gene silencing in rice cells Ji Hyun Yang, Hyun Hee Seo, So Jung Han, Eun Kyung Yoon, Moon Sik Yang, and Woo Sung Lee PMCID: PMC2275079 DNA mimicry by a high-affinity anti-NF-κB RNA aptamer Nicholas J. Reiter, L. James Maher, III, and Samuel E. Butcher PMCID: PMC2275087 The third RNA recognition motif of Drosophila ELAV protein has a role in multimerization Gakuta Toba and Kalpana White PMCID: PMC2275111 Structural Biology Loop dependence of the stability and dynamics of nucleic acid hairpins Serguei V. Kuznetsov, Cha-Chi Ren, Sarah A. Woodson, and Anjum Ansari PMCID: PMC2275088 Assembly and structural analysis of a covalently closed nano-scale DNA cage Felicie F. Andersen, Bjarne Knudsen, Cristiano Luis Pinto Oliveira, Rikke F. Frøhlich, Dinna Krüger, Jörg Bungert, Mavis Agbandje-McKenna, Robert McKenna, Sissel Juul, Christopher Veigaard, Jørn Koch, John L. Rubinstein, Bernt Guldbrandtsen, Marianne S. Hede, Göran Karlsson, Anni H. Andersen, Jan Skov Pedersen, and Birgitta R. Knudsen PMCID: PMC2275108 Kinking the double helix by bending deformation Quan Du, Alexander Kotlyar, and Alexander Vologodskii PMCID: PMC2275110 Biochemical and structural characterization of Cren7, a novel chromatin protein conserved among Crenarchaea Li Guo, Yingang Feng, Zhenfeng Zhang, Hongwei Yao, Yuanming Luo, Jinfeng Wang, and Li Huang PMCID: PMC2275093 Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation Yuhei Araiso, Sotiria Palioura, Ryuichiro Ishitani, R. Lynn Sherrer, Patrick O’Donoghue, Jing Yuan, Hiroyuki Oshikane, Naoshi Domae, Julian DeFranco, Dieter Söll, and Osamu Nureki PMCID: PMC2275076 G-quadruplex preferentially forms at the very 3′ end of vertebrate telomeric DNA Jun Tang, Zhong-yuan Kan, Yuan Yao, Quan Wang, Yu-hua Hao, and Zheng Tan PMCID: PMC2275102 Thermodynamic characterization of specific interactions between the human Lon protease and G-quartet DNA Si-Han Chen, Carolyn K. Suzuki, and Shih-Hsiung Wu PMCID: PMC2275097 Catalytic mechanism of the tryptophan activation reaction revealed by crystal structures of human tryptophanyl-tRNA synthetase in different enzymatic states Ning Shen, Minyu Zhou, Bei Yang, Yadong Yu, Xianchi Dong, and Jianping Ding PMCID: PMC2275098 Genomics Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes Johanna Eddy and Nancy Maizels PMCID: PMC2275096 Microarray analysis using disiloxyl 70mer oligonucleotides Marcus Gry Björklund, Christian Natanaelsson, Amelie Eriksson Karlström, Yong Hao, and Joakim Lundeberg PMCID: PMC2275082 Methods Online Measuring the dynamic surface accessibility of RNA with the small paramagnetic molecule TEMPOL Vincenzo Venditti, Neri Niccolai, and Samuel E. Butcher PMCID: PMC2275091 Improved genome-wide localization by ChIP-chip using double-round T7 RNA polymerase-based amplification Harm van Bakel, Folkert J. van Werven, Marijana Radonjic, Mariel O. Brok, Dik van Leenen, Frank C. P. Holstege, and H. T. Marc Timmers PMCID: PMC2275083 Meta-prediction of phosphorylation sites with weighted voting and restricted grid search parameter selection Ji Wan, Shuli Kang, Chuanning Tang, Jianhua Yan, Yongliang Ren, Jie Liu, Xiaolian Gao, Arindam Banerjee, Lynda B. M. Ellis, and Tongbin Li PMCID: PMC2275094 Detection of a circadian enhancer in the mDbp promoter using prokaryotic transposon vector-based strategy Yota B. Kiyohara, Keigo Nishii, Maki Ukai-Tadenuma, Hiroki R. Ueda, Yasuo Uchiyama, and Kazuhiro Yagita PMCID: PMC2275109 Cell-free cloning of highly expanded CTG repeats by amplification of dimerized expanded repeats Robert J. Osborne and Charles A. Thornton PMCID: PMC2275075 A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis Gerardo Turcatti, Anthony Romieu, Milan Fedurco, and Ana-Paula Tairi PMCID: PMC2275100 Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies Daniel Shriner, Tesfaye M. Baye, Miguel A. Padilla, Shiju Zhang, Laura K. Vaughan, and Ann E. Loraine PMCID: PMC2275105 Nucleic Acid Enzymes Characterization and evolutionary history of an archaeal kinase involved in selenocysteinyl-tRNA formation R. Lynn Sherrer, Patrick O’Donoghue, and Dieter Söll PMCID: PMC2275090 Multiple DNA-binding sites in Tetrahymena telomerase Sharon N. Finger and Tracy M. Bryan PMCID: PMC2275084 Coupling of DNA binding and helicase activity is mediated by a conserved loop in the MCM protein Nozomi Sakakibara, Rajesh Kasiviswanathan, Eugene Melamud, Mimi Han, Frederick P. Schwarz, and Zvi Kelman PMCID: PMC2275104 EXOG, a novel paralog of Endonuclease G in higher eukaryotes Iwona A. Cymerman, Inn Chung, Benedikt M. Beckmann, Janusz M. Bujnicki, and Gregor Meiss PMCID: PMC2275078 |
