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Volume 14(11);  November 2008
Bioinformatics
The effect of intron length on exon creation ratios during the evolution of mammalian genomes
Meenakshi Roy, Namshin Kim, Yi Xing, and Christopher Lee
RNA. 2008 November; 14(11): 2261–2273. doi: 10.1261/rna.1024908.
PMCID: PMC2578852
Analysis and classification of RNA tertiary structures
Mira Abraham, Oranit Dror, Ruth Nussinov, and Haim J. Wolfson
RNA. 2008 November; 14(11): 2274–2289. doi: 10.1261/rna.853208.
PMCID: PMC2578864
A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions
Chad J. Creighton, Ankur K. Nagaraja, Samir M. Hanash, Martin M. Matzuk, and Preethi H. Gunaratne
RNA. 2008 November; 14(11): 2290–2296. doi: 10.1261/rna.1188208.
PMCID: PMC2578856
Reports
Mutational analysis of vaccinia virus mRNA cap (guanine-N7) methyltransferase reveals essential contributions of the N-terminal peptide that closes over the active site
Sushuang Zheng and Stewart Shuman
RNA. 2008 November; 14(11): 2297–2304. doi: 10.1261/rna.1201308.
PMCID: PMC2578867
Exonucleolysis is required for nuclear mRNA quality control in yeast THO mutants
Jannie Assenholt, John Mouaikel, Kasper R. Andersen, Ditlev E. Brodersen, Domenico Libri, and Torben Heick Jensen
RNA. 2008 November; 14(11): 2305–2313. doi: 10.1261/rna.1108008.
PMCID: PMC2578857
Kinetic and thermodynamic studies of peptidyltransferase in ribosomes from the extreme thermophile Thermus thermophilus
Daniel Rodriguez-Correa and Albert E. Dahlberg
RNA. 2008 November; 14(11): 2314–2318. doi: 10.1261/rna.1146008.
PMCID: PMC2578854
Articles
Two CRM protein subfamilies cooperate in the splicing of group IIB introns in chloroplasts
Yukari Asakura, Omer Ali Bayraktar, and Alice Barkan
RNA. 2008 November; 14(11): 2319–2332. doi: 10.1261/rna.1223708.
PMCID: PMC2578863
Distinct roles for Khd1p in the localization and expression of bud-localized mRNAs in yeast
Yuko Hasegawa, Kenji Irie, and André P. Gerber
RNA. 2008 November; 14(11): 2333–2347. doi: 10.1261/rna.1016508.
PMCID: PMC2578860
MicroRNA miR-21 overexpression in human breast cancer is associated with advanced clinical stage, lymph node metastasis and patient poor prognosis
Li-Xu Yan, Xiu-Fang Huang, Qiong Shao, MA-Yan Huang, Ling Deng, Qiu-Liang Wu, Yi-Xin Zeng, and Jian-Yong Shao
RNA. 2008 November; 14(11): 2348–2360. doi: 10.1261/rna.1034808.
PMCID: PMC2578865
Crystal structure of Escherichia coli PNPase: Central channel residues are involved in processive RNA degradation
Zhonghao Shi, Wei-Zen Yang, Sue Lin-Chao, Kin-Fu Chak, and Hanna S. Yuan
RNA. 2008 November; 14(11): 2361–2371. doi: 10.1261/rna.1244308.
PMCID: PMC2578853
Peptidyl-CCA deacylation on the ribosome promoted by induced fit and the O3′-hydroxyl group of A76 of the unacylated A-site tRNA
Miljan Simonović and Thomas A. Steitz
RNA. 2008 November; 14(11): 2372–2378. doi: 10.1261/rna.1118908.
PMCID: PMC2578858
The 3′ proximal translational enhancer of Turnip crinkle virus binds to 60S ribosomal subunits
Vera A. Stupina, Arturas Meskauskas, John C. McCormack, Yaroslava G. Yingling, Bruce A. Shapiro, Jonathan D. Dinman, and Anne E. Simon
RNA. 2008 November; 14(11): 2379–2393. doi: 10.1261/rna.1227808.
PMCID: PMC2578866
Characterization of the termination–reinitiation strategy employed in the expression of influenza B virus BM2 protein
Michael L. Powell, Sawsan Napthine, Richard J. Jackson, Ian Brierley, and T. David K. Brown
RNA. 2008 November; 14(11): 2394–2406. doi: 10.1261/rna.1231008.
PMCID: PMC2578862
Overexpressed mitochondrial leucyl-tRNA synthetase suppresses the A3243G mutation in the mitochondrial tRNALeu(UUR) gene
Hyejeong Park, Edgar Davidson, and Michael P. King
RNA. 2008 November; 14(11): 2407–2416. doi: 10.1261/rna.1208808.
PMCID: PMC2578859
Polynucleotide phosphorylase hinders mRNA degradation upon ribosomal protein S1 overexpression in Escherichia coli
Federica Briani, Serena Curti, Francesca Rossi, Thomas Carzaniga, Pierluigi Mauri, and Gianni Dehò
RNA. 2008 November; 14(11): 2417–2429. doi: 10.1261/rna.1123908.
PMCID: PMC2578868
Mutational analysis of the U12-dependent branch site consensus sequence
Jay E. Brock, Rosemary C. Dietrich, and Richard A. Padgett
RNA. 2008 November; 14(11): 2430–2439. doi: 10.1261/rna.1189008.
PMCID: PMC2578861
Method
A novel biochemical method to identify target genes of individual microRNAs: Identification of a new Caenorhabditis elegans let-7 target
Yoshiki Andachi
RNA. 2008 November; 14(11): 2440–2451. doi: 10.1261/rna.1139508.
PMCID: PMC2578851
Erratum
Effects of N2,N2-dimethylguanosine on RNA structure and stability: Crystal structure of an RNA duplex with tandem m2 2G:A pairs
Pradeep S. Pallan, Christoph Kreutz, Silvia Bosio, Ronald Micura, and Martin Egli
RNA. 2008 November; 14(11): 2452–2453.
PMCID: PMC2578855
Corrects: Pradeep S. Pallan, et al. Effects of N2,N2-dimethylguanosine on RNA structure and stability: Crystal structure of an RNA duplex with tandem m2 2G:A pairs. RNA. 2008 November; 14(11): 2452–2453.
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