| | Survey and Summary AU-rich elements and associated factors: are there unifying principles? Carine Barreau, Luc Paillard, and H. Beverley Osborne PMCID: PMC1325018 Articles Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI–DNA complexes Robert K. Neely, Dalia Daujotyte, Saulius Grazulis, Steven W. Magennis, David T. F. Dryden, Saulius Klimašauskas, and Anita C. Jones PMCID: PMC1310896 Solution structure of ψ32-modified anticodon stem–loop of Escherichia coli tRNAPhe Javier Cabello-Villegas and Edward P. Nikonowicz PMCID: PMC1322268 The leucine rich region of DNA-PKcs contributes to its innate DNA affinity Shikha Gupta and Katheryn Meek PMCID: PMC1310895 Coupling DNA-binding and ATP hydrolysis in Escherichia coli RecQ: role of a highly conserved aromatic-rich sequence Morgan C. Zittel and James L. Keck PMCID: PMC1310897 Identification of a 14mer RNA that recognizes and binds flavin mononucleotide with high affinity Peter C. Anderson and Sandro Mecozzi PMCID: PMC1322272 Oligomerization of HEXIM1 via 7SK snRNA and coiled-coil region directs the inhibition of P-TEFb Dalibor Blazek, Matjaz Barboric, Jiri Kohoutek, Irena Oven, and B. Matija Peterlin PMCID: PMC1322273 Role of the N- and C-terminal extensions on the activity of mammalian mitochondrial translational initiation factor 3 Kalpana Bhargava and Linda L. Spremulli PMCID: PMC1310894 Synthesis and hybridization studies of oligonucleotides containing 1-(2-deoxy-2-α-C-hydroxymethyl-β-d-ribofuranosyl)thymine (2′-α-hm-dT) Chang Geng Peng and Masad J. Damha PMCID: PMC1322267 Structure and energy of a DNA dodecamer under tensile load Stefano Piana PMCID: PMC1316112 Developing a programmed restriction endonuclease for highly specific DNA cleavage Kristin Eisenschmidt, Thomas Lanio, András Simoncsits, Albert Jeltsch, Vera Pingoud, Wolfgang Wende, and Alfred Pingoud PMCID: PMC1316111 Molecular flexibility in ab initio drug docking to DNA: binding-site and binding-mode transitions in all-atom Monte Carlo simulations Remo Rohs, Itai Bloch, Heinz Sklenar, and Zippora Shakked PMCID: PMC1312361 Gene expression studies in isolated mitochondria: Solanum tuberosum rps10 is recognized by cognate potato but not by the transcription, splicing and editing machinery of wheat mitochondria David Choury, Jean-Claude Farré, Xavier Jordana, and Alejandro Araya PMCID: PMC1312363 Genomic blueprint of Hahella chejuensis, a marine microbe producing an algicidal agent Haeyoung Jeong, Joung Han Yim, Choonghwan Lee, Sang-Haeng Choi, Yon Kyoung Park, Sung Ho Yoon, Cheol-Goo Hur, Ho-Young Kang, Dockyu Kim, Hyun Hee Lee, Kyun Hyang Park, Seung-Hwan Park, Hong-Seog Park, Hong Kum Lee, Tae Kwang Oh, and Jihyun F. Kim PMCID: PMC1312362 The autoregulatory translational control element of poly(A)-binding protein mRNA forms a heteromeric ribonucleoprotein complex Gopal P. Patel, Shuhua Ma, and Jnanankur Bag PMCID: PMC1316114 Mycobacterium tuberculosis NAD+-dependent DNA ligase is selectively inhibited by glycosylamines compared with human DNA ligase I Sandeep Kumar Srivastava, Divya Dube, Neetu Tewari, Namrata Dwivedi, Rama Pati Tripathi, and Ravishankar Ramachandran PMCID: PMC1316110 Dynamic regulation of replication independent deposition of histone H3 in fission yeast Eun Shik Choi, Jin A Shin, Hyun Soo Kim, and Yeun Kyu Jang PMCID: PMC1316113 DNA base flipping by a base pair-mimic nucleoside Shu-ichi Nakano, Yuuki Uotani, Kazuya Uenishi, Masayuki Fujii, and Naoki Sugimoto PMCID: PMC1316115 Automatic assessment of alignment quality Timo Lassmann and Erik L. L. Sonnhammer PMCID: PMC1316116 Easily denaturing nucleic acids derived from intercalating nucleic acids: thermal stability studies, dual duplex invasion and inhibition of transcription start Vyacheslav V. Filichev, Birte Vester, Lykke H. Hansen, and Erik B. Pedersen PMCID: PMC1322271 Structural polymorphism of the HIV-1 leader region explored by computational methods Wojciech Kasprzak, Eckart Bindewald, and Bruce A. Shapiro PMCID: PMC1322270 Characterization of a catalytically efficient acidic RNA-cleaving deoxyribozyme Srinivas A. Kandadai and Yingfu Li PMCID: PMC1325019 Methods Online New approaches to the analysis of palindromic sequences from the human genome: evolution and polymorphism of an intronic site at the NF1 locus Susanna M. Lewis, Shuang Chen, Jeffrey N. Strathern, and Alison J. Rattray PMCID: PMC1310899 Use of a mixed tissue RNA design for performance assessments on multiple microarray formats Karol L. Thompson, Barry A. Rosenzweig, P. Scott Pine, Jacques Retief, Yaron Turpaz, Cynthia A. Afshari, Hisham K. Hamadeh, Michael A. Damore, Michael Boedigheimer, Eric Blomme, Rita Ciurlionis, Jeffrey F. Waring, James C. Fuscoe, Richard Paules, Charles J. Tucker, Thomas Fare, Ernest M. Coffey, Yudong He, Patrick J. Collins, Kurt Jarnagin, Susan Fujimoto, Brigitte Ganter, Gretchen Kiser, Tamma Kaysser-Kranich, Joseph Sina, and Frank D. Sistare PMCID: PMC1322274 Rapid and quantitative detection of homologous and non-homologous recombination events using three oligonucleotide MLPA Petra Langerak, Anders O. H. Nygren, Jan P. Schouten, and Heinz Jacobs PMCID: PMC1310898 Iterative in vivo assembly of large and complex transgenes by combining the activities of ![[var phi]](corehtml/pmc/pmcents/x03C6.gif) C31 integrase and Cre recombinase Felix Dafhnis-Calas, Zhengyao Xu, Steve Haines, Sunir K. Malla, Margaret C. M. Smith, and William R. A. Brown PMCID: PMC1316120 Quantum dots to monitor RNAi delivery and improve gene silencing Alice A. Chen, Austin M. Derfus, Salman R. Khetani, and Sangeeta N. Bhatia PMCID: PMC1312364 Distortion of quantitative genomic and expression hybridization by Cot-1 DNA: mitigation of this effect Heather L. Newkirk, Joan H.M. Knoll, and Peter K. Rogan PMCID: PMC1316118 Human and mouse oligonucleotide-based array CGH Paul van den IJssel, Marianne Tijssen, Suet-Feung Chin, Paul Eijk, Beatriz Carvalho, Erik Hopmans, Henne Holstege, Dhinoth Kumar Bangarusamy, Jos Jonkers, Gerrit A. Meijer, Carlos Caldas, and Bauke Ylstra PMCID: PMC1316119 Integrating probe-level expression changes across generations of Affymetrix arrays Laura L. Elo, Leo Lahti, Heli Skottman, Minna Kyläniemi, Riitta Lahesmaa, and Tero Aittokallio PMCID: PMC1316121 A novel experimental approach for systematic identification of box H/ACA snoRNAs from eukaryotes Ai-Di Gu, Hui Zhou, Chun-Hong Yu, and Liang-Hu Qu PMCID: PMC1316117 Corrigendum Correlation between sequence conservation and the genomic context after gene duplication Richard A. Notebaart, Martijn A. Huynen, Bas Teusink, Roland J. Siezen, and Berend Snel PMCID: PMC1322269 Corrects: Richard A. Notebaart, et al. Correlation between sequence conservation and the genomic context after gene duplication. Nucleic Acids Res. 2005; 33(19): 6164–6171. |
