Journal of Nucleic Acids Using Chemical Approaches to Understand RNA Structure and Function in Biology Guest Editors: Dmitry A. Stetsenko, and Arthur van Aerschot Using Chemical Approaches to Understand RNA Structure and Function in Biology Journal of Nucleic Acids Using Chemical Approaches to Understand RNA Structure and Function in Biology Guest Editors: Dmitry A. Stetsenko and Arthur van Aerschot Copyright © 2012 Hindawi Publishing Corporation. All rights reserved. This is a special issue published in “Journal of Nucleic Acids.” All articles are open access articles distributed under the Creative Com- mons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Editorial Board Luigi A. Agrofoglio, France Ramon´ Eritja, Spain P. E. Nielsen, Germany Hiroyuki Asanuma, Japan Marina Gottikh, Russia Satoshi Obika, Japan Ashis K. Basu, USA John A. Hartley, UK Tatiana S. Oretskaya, Russia Ben Berkhout, The Netherlands Roland K. Hartmann, Germany Tobias Restle, Germany AnnL.Beyer,USA Tapas K Hazra, USA Mitsuo Sekine, Japan Christiane Branlant, France Hyouta Himeno, Japan Jacek Stawinski, Sweden Emery H. Bresnick, USA Robert Hudson, Canada Dmitry A. Stetsenko, UK Tom Brow n, UK Shigenori Iwai, Japan Hiroshi Sugiyama, Japan Janusz M. Bujnicki, Poland B. H. Kim, Republic of Korea Zucai Suo, USA Jyoti Chattopadhyaya, Sweden Jørgen Kjems, Denmark Akio Takenaka, Japan G. L. Dianov, UAE Xingguo Liang, Japan Yitzhak Tor, USA Aidan Doherty, UK Luis A. Marky, USA Dmitry Veprintsev, UK Joachim Engels, Germany Atsushi Maruyama, Japan Birte Vester, Denmark Contents Using Chemical Approaches to Understand RNA Structure and Function in Biology, Dmitry A. Stetsenko and Arthur van Aerschot Volume 2012, Article ID 972575, 2 pages Chemical Approaches for Structure and Function of RNA in Postgenomic Era,TaeSukRo-Choi and Yong Chun Choi Volume 2012, Article ID 369058, 40 pages Site-Selective Artificial Ribonucleases: Oligonucleotide Conjugates Containing Multiple Imidazole Residues in the Catalytic Domain, Natalia G. Beloglazova, Martin M. Fabani, Nikolai N. Polushin, Vladimir V. Sil’nikov, Valentin V. Vlassov, Elena V. Bichenkova, and Marina A. Zenkova Volume 2011, Article ID 748632, 17 pages A Potential of microRNAs for High-Content Screening, Andrius Serva, Christoph Claas, and Vytaute Starkuviene Volume 2011, Article ID 870903, 15 pages Molecular Beacons: Powerful Tools for Imaging RNA in Living Cells, Ricardo Monroy-Contreras and Luis Vaca Volume 2011, Article ID 741723, 15 pages Resveratrol, MicroRNAs, Inflammation, and Cancer, Esmerina Tili and Jean-Jacques Michaille Volume 2011, Article ID 102431, 9 pages Synthetic Pre-miRNA-Based shRNA as Potent RNAi Triggers, Kazuya Terasawa, Kazuharu Shimizu, and Gozoh Tsujimoto Volume 2011, Article ID 131579, 6 pages Conformational-Dependent and Independent RNA Binding to the Fragile X Mental Retardation Protein, Xin Yan and Robert B. Denman Volume 2011, Article ID 246127, 14 pages Use of Specific Chemical Reagents for Detection of Modified Nucleotides in RNA, Isabelle Behm-Ansmant, Mark Helm, and Yuri Motorin Volume 2011, Article ID 408053, 17 pages Branched RNA: A New Architecture for RNA Interference, Anna Avin˜o,´ Sandra M. Ocampo, Jose´ Carlos Perales, and Ramon Eritja Volume 2011, Article ID 586935, 7 pages tRNA/mRNA Mimicry by tmRNA and SmpB in Trans-Translation,DaisukeKurita,AkiraMuto, and Hyouta Himeno Volume 2011, Article ID 130581, 9 pages Hindawi Publishing Corporation Journal of Nucleic Acids Volume 2012, Article ID 972575, 2 pages doi:10.1155/2012/972575 Editorial Using Chemical Approaches to Understand RNA Structure and Function in Biology Dmitry A. Stetsenko1 and Arthur van Aerschot2 1 Department of Bioengineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK 2 Department of Pharmaceutical Sciences, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium CorrespondenceshouldbeaddressedtoDmitryA.Stetsenko,[email protected] Received 10 August 2011; Accepted 10 August 2011 Copyright © 2012 D. A. Stetsenko and A. van Aerschot. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Interest of the research community in the aspects of chemical and the Fragile X Mental Retardation protein in another biology of RNA has increased vastly over the last twenty paper by X. Yan and R. B. Denman. The one that follows years, primarily due to the discovery of RNAi, our deepened by D. Kurita et al. amply shows how chemical probing has understanding of the role of miRNA in the subtle regulation provided insights into the mechanisms of trans translation of vital cellular processes, and the realization of the fact that and the role played by transfer-messenger RNA (tmRNA). the RNA world—the realm where RNA plays the key parties A Herculean task of the identification of minor nucleotides as a self-replicating molecule and a universal catalyst—is still in RNA and the use of specific chemical reagents for its pretty much with us today as the ribosomal RNA performs accomplishment are reviewed in the contribution from a its catalytic solo in the formation of the peptide bond in the group of French researchers led by Professor Y. Motorin. ribosome. To answer the needs of Biology, Chemistry had, Taking snapshots of RNA in live cells by means of molecular in turn, multiplied and perfected its approaches to study the beacons technology is the subject of a review of R. Monroy- molecular mechanisms underlying RNA functions in living Contreras and L. Vaca. systems. So, the idea behind this special issue is to show Then the issue goes into details of the interplay between our readership a screenshot of what could be, and has been, a single chemical, resveratrol, and miRNAs during inflam- achieved recently by applying chemical methods to solve the matory processes and cancer, reviewed by E. Tili and J.- problems of RNA biology. Ten articles have been carefully J. Michaille. The miRNA theme continues in the review selected out of the bunch of those submitted to provide, we by A. Serva et al. of the application of high-throughput believe, a balanced view of different facets of RNA structure functional analysis for elucidation of the multiple biological and function and, also, of the array of chemical tools to roles of miRNAs. Here we cross the boundary into the second enable us to peek into them. half of our special issue composed from research papers, The issue is a mix of reviews and research papers and and the one that comes next by K. Terazawa et al. opens thus falls into two parts. We have purposefully incorporated the RNA interference section with synthetic short hairpin a number of authoritative overviews to paint a wider RNAs (shRNAs) as potent RNAi inducers. Another article, background of RNA functioning in the first half. It starts commissioned by researchers from the Iberian Peninsula R. with a general treatise on chemical approaches to study Eritja and coworkers, deals with branched RNA architectures RNA structure-function relationships in the postgenomic for RNAi. erabyT.S.Ro-ChoiandY.C.Choi.DependenceofRNA- Finally, a paper of the issue done by M. A. Zenkova et protein interaction on RNA conformation is highlighted by al. focuses on an applied aspect of RNA technology, namely, a medicinally important example of a noncoding RNA BC1 the development of sequence-specific artificial ribonucleases 2 Journal of Nucleic Acids incorporating multiple imidazole residues that perform sim- ilar function to their counterparts in natural RNA-cleaving enzymes. In conclusion, the issue attempts to present a selection of reviews and research papers, which are designed to illustrate how by using various implements and gadgets from the ever-growing arsenal of Chemistry one can hopefully gain a better understanding of what is happening when RNA molecules interact with their manifold targets and perform their plethora of functions. It must be added that this is by no means a comprehensive picture but rather a momentary screenshot of a dynamic process of harnessing the power of Chemistry to serve the ends of Biology. Sapienti sat. Dmitry A. Stetsenko Arthur van Aerschot Hindawi Publishing Corporation Journal of Nucleic Acids Volume 2012, Article ID 369058, 40 pages doi:10.1155/2012/369058 Review Article Chemical Approaches for Structure and Function of RNA in Postgenomic Era Tae Suk Ro-Choi and Yong Chun Choi Departments of Pharmacology and Biochemistry, College of Medicine, Dong-A University, 3-1 Dong Dae Shin Dong, Seo Gu, Busan 602-714, Republic of Korea Correspondence should be addressed to Tae Suk Ro-Choi, [email protected] Received 18 October 2010; Revised 21 June 2011; Accepted 5 July 2011 Academic Editor: Dmitry A. Stetsenko Copyright © 2012 T. S. Ro-Choi and Y. C. Choi. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. In the study of cellular RNA chemistry, a major thrust of research focused upon sequence determinations for decades. Structures of snRNAs (4.5S RNA I (Alu), U1, U2, U3, U4, U5, and U6) were determined at Baylor College of Medicine, Houston, Tex, in an earlier time of pregenomic era. They show novel modifications including base methylation, sugar methylation,