ACS

A Role for a Single-Stranded Junction in RNA Binding and Specificity by the Tetrahymena Group I Ribozyme - Journal of the American Chemical Society. Analogues and Derivatives of Oncrasin-1, a Novel Inhibitor of the C-Terminal Domain of RNA Polymerase II and Their Antitumor Activities - Journal of Medicinal Chemistry. †Department of Thoracic and Cardiovascular Surgery and ‡Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China J. Med. Chem., 2011, 54 (8), pp 2668–2679 DOI: 10.1021/jm101417n Publication Date (Web): March 28, 2011 Copyright © 2011 American Chemical Society Section: Abstract To optimize the antitumor activity of oncrasin-1, a small molecule RNA polymerase II inhibitor, we evaluated 69 oncrasin-1 analogues for their cytotoxic activity against normal human epithelial cells and K-Ras mutant tumor cells.

Citing Articles View all 11 citing articles Citation data is made available by participants in CrossRef's Cited-by Linking service. This article has been cited by 1 ACS Journal articles (1 most recent appear below). Microwave-Assisted Synthesis of 3-Nitroindoles from N-Aryl Enamines via Intramolecular Arene–Alkene CouplingHuy H. Asphalt, Water, and the Prebiotic Synthesis of Ribose, Ribonucleosides, and RNA - Accounts of Chemical Research. Foundation for Applied Molecular Evolution, Gainesville, Florida 32604, United States Acc. Chem. Res., 2012, 45 (12), pp 2025–2034 DOI: 10.1021/ar200332w Publication Date (Web): March 28, 2012 Copyright © 2012 American Chemical Society Dedication Dedicated to the memory of Robert Shapiro.

Biography Steven Benner is Distinguished Fellow and Founder of the Westheimer Institute for Science and Technology at the Foundation for Applied Molecular Evolution. Hyo-Joong Kim received his B.S. in chemistry education and M.S. in chemistry from the Seoul National University. Matthew Carrigan received his Ph.D. from the University of Florida and joined the Foundation in 2005.

Section: Abstract RNA has been called a “prebiotic chemist’s nightmare” because of its combination of large size, carbohydrate building blocks, bonds that are thermodynamically unstable in water, and overall intrinsic instability. Citing Articles View all 11 citing articles. Before and after Endosomal Escape: Roles of Stimuli-Converting siRNA/Polymer Interactions in Determining Gene Silencing Efficiency - Accounts of Chemical Research. Department of Pharmaceutical Sciences, Department of Chemical Engineering and Materials Science, Department of Biomedical Engineering, and Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States Acc. Chem. Res., 2012, 45 (7), pp 1077–1088 DOI: 10.1021/ar200241v Publication Date (Web): November 21, 2011 Copyright © 2011 American Chemical Society *To whom correspondence should be addressed. Biography Young Jik Kwon is an associate professor of Pharmaceutical Sciences, Chemical Engineering & Materials Science, Biomedical Engineering, and Molecular Biology and Biochemistry at University of California, Irvine.

Section: Abstract Silencing the expression of a target gene by RNA interference (RNAi) shows promise as a potentially revolutionizing strategy for manipulating biological (pathological) pathways at the translational level. Citing Articles View all 20 citing articles. Catalyzed and Spontaneous Reactions on Ribozyme Ribose - Journal of the American Chemical Society. Cellular Dynamics of RNA Modification - Accounts of Chemical Research. Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States Acc.

Chem. Res., 2011, 44 (12), pp 1380–1388 DOI: 10.1021/ar200057m Publication Date (Web): May 26, 2011 Copyright © 2011 American Chemical Society Biography Chengqi Yi received his Ph.D. from the Department of Chemistry with Professor Chuan He at the University of Chicago. Tao Pan received his Ph.D. from Yale University with Professor Joseph Coleman. Section: Abstract Five decades of research have identified more than 100 ribonucleosides that are post-transcriptionally modified.

Many RNA modifications are not essential for life, which parallels the observation that many well-characterized protein and DNA modifications are not essential for life. We discuss four specific examples of RNA modification in detail here. We then consider two recent technical advances that have stimulated the study of the cellular dynamics in modified ribonucleosides.

Comparison of Cationic and Amphipathic Cell Penetrating Peptides for siRNA Delivery and Efficacy - Molecular Pharmaceutics. Department of Pharmacology and Pharmaceutical Sciences, University of Southern California School of Pharmacy, Los Angeles, California 90033, United States Mol. Pharmaceutics, 2012, 9 (2), pp 299–309 DOI: 10.1021/mp200481g Publication Date (Web): December 15, 2011 Copyright © 2011 American Chemical Society *University of Southern California School of Pharmacy, 1985 Zonal Avenue, PSC 404B, Los Angeles, CA 90033, United States. Section: Abstract Cell penetrating peptides (CPPs) are short strands of arginine- and/or lysine-rich peptides (<30 amino acids) that use their cationic nature for efficient intracellular accumulation. Citing Articles View all 15 citing articles Citation data is made available by participants in CrossRef's Cited-by Linking service. This article has been cited by 4 ACS Journal articles (4 most recent appear below).

Efficient Delivery of Sticky siRNA and Potent Gene Silencing in a Prostate Cancer Model Using a Generation 5 Triethanolamine-Core PAMAM Dendrimer - Molecular Pharmaceutics. † Département de Chimie, Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, Aix-Marseille Université, 163 avenue de Luminy, 13288 Marseille, France # State Key Laboratory of Virology, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China ‡ Centre de Recherche en Cancérologie de Marseille, UMR1068 Inserm, Institut Paoli-Calmettes, Aix-Marseille Université, France § Molecular Simulation Engineering (MOSE) Laboratory, Department of Industrial Engineering and Information Technology (DI3), University of Trieste, Via Valerio 10, 34127 Trieste, Italy Mol. DOI: 10.1021/mp2006104 Publication Date (Web): December 30, 2011 Copyright © 2011 American Chemical Society *Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, Département de Chimie, 163 avenue de Luminy, 13288 Marseille cedex 09, France.

Section: Abstract Citing Articles View all 31 citing articles. Enhanced Extravasation, Stability and in Vivo Cardiac Gene Silencing via in Situ siRNA–Albumin Conjugation - Molecular Pharmaceutics. Error. Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States Acc. Chem. Res., 2011, 44 (12), pp 1270–1279 DOI: 10.1021/ar2000452 Publication Date (Web): July 6, 2011 Copyright © 2011 American Chemical Society To whom correspondence should be addressed.

Biography Jennifer L. Amarpreet Ahluwalia is an undergraduate student pursuing a B.S. in biochemistry and molecular biology at The Pennsylvania State University in the Schreyer Honors College. Philip C. Section: Abstract Catalysis in living cells is carried out by both proteins and RNA. The charged amino acids make critical contributions to the mechanisms of nearly all protein enzymes. We examine advances in measuring and analyzing perturbed pKa values in RNA. Citing Articles View all 16 citing articles Citation data is made available by participants in CrossRef's Cited-by Linking service.

This article has been cited by 10 ACS Journal articles (5 most recent appear below). Error. Department of Chemistry and Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States J. Am. Chem. Soc., 2012, 134 (1), pp 256–262 DOI: 10.1021/ja206455t Publication Date (Web): November 9, 2011 Copyright © 2011 American Chemical Society Section: Abstract The function of RNA depends on its ability to adopt complex and dynamic structures, and the incorporation of site-specific cross-linking probes is a powerful method for providing distance constraints that are valuable in RNA structural biology. 8 Å of a phosphorothioate-bound Pt(II) metal center. Citing Articles View all 2 citing articles Citation data is made available by participants in CrossRef's Cited-by Linking service.

Exploring RNA Structural Codes with SHAPE Chemistry - Accounts of Chemical Research. Department of Chemistry, University of North Carolina Chapel Hill, North Carolina 27599-3290, United States Acc. Chem. Res., 2011, 44 (12), pp 1280–1291 DOI: 10.1021/ar200051h Publication Date (Web): May 26, 2011 Copyright © 2011 American Chemical Society Biography Kevin M. David M. Section: Abstract RNA is the central conduit for gene expression. The core innovation derives from our discovery that the nucleophilic reactivity of the ribose 2'-hydroxyl in RNA is gated by local nucleotide flexibility. SHAPE reactivities are largely independent of nucleotide identity but correlate closely with model-free measurements of molecular order. SHAPE chemistry is based on very simple reactive carbonyl centers that can be varied to yield slow- and fast-reacting reagents.

The application of SHAPE to challenging problems in biology has revealed surprises in well-studied systems. Citing Articles View all 34 citing articles Citation data is made available by participants in CrossRef's Cited-by Linking service. Hyperbranched Polymeric “Star Vectors” for Effective DNA or siRNA Delivery - Accounts of Chemical Research. Division of Medical Engineering and Materials, National Cerebral and Cardiovascular Center Research Institute Acc. Chem. Res., 2012, 45 (7), pp 994–1004 DOI: 10.1021/ar200220t Publication Date (Web): February 21, 2012 Copyright © 2012 American Chemical Society *Mailing address: Division of Medical Engineering and Materials National Cerebral and Cardiovascular Center Research Institute, 5-7-1 Fujishiro-dai, Suita, Osaka 565-8565, Japan.

Biography Yasuhide Nakayama received his Ph.D. degree from Osaka University in 1991. Section: Abstract Although gene therapy offers an attractive strategy for treating inherited disorders, current techniques using viral and nonviral delivery systems have not yielded many successful results in clinical trials. Cationic polymers, such as polyethylenimine (PEI) and poly(N,N-dimethylaminopropyl acrylamide) (PDMAPAAm), can generate nanoparticles through the formation of polyion complexes, “polyplexes” with DNA. Citing Articles View all 15 citing articles. In Vitro Selection and Characterization of a Novel Zn(II)-Dependent Phosphorothiolate Thiolesterase Ribozyme - Biochemistry.

†Department of Medicinal and Applied Chemistry and ‡Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan § Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan Biochemistry, 2012, 51 (1), pp 496–510 DOI: 10.1021/bi201585d Publication Date (Web): December 16, 2011 Copyright © 2011 American Chemical Society *Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 80708, Taiwan. Funding Statement This work was supported by the National Science Council of Taiwan (Grants NSC95-2113-M-037-007/008, NSC96-2113-M-037-004-MY2, and NSC99-2113-M-037-008 to T.

Section: Abstract Here we present the in vitro selection of a novel ribozyme specific for Zn2+-dependent catalysis on hydrolysis of a phosphorothiolate thiolester bond. Citing Articles View all 2 citing articles. Incorporation of Positively Charged Linkages into DNA and RNA Backbones: A Novel Strategy for Antigene and Antisense Agents - Chemical Reviews. Insights from Crystal Structures into the Opposite Effects on RNA Affinity Caused by the S- and R-6′-Methyl Backbone Modifications of 3′-Fluoro Hexitol Nucleic Acid - Biochemistry.

Mapping the Landscape of RNA Dynamics with NMR Spectroscopy - Accounts of Chemical Research. Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main, Germany Acc. Chem. Res., 2011, 44 (12), pp 1292–1301 DOI: 10.1021/ar200137d Publication Date (Web): September 6, 2011 Copyright © 2011 American Chemical Society Biography Harald Schwalbe studied chemistry at Goethe-University of Frankfurt and received his Ph.D. with Prof. Jörg Rinnenthal received his diploma in biochemistry from the Goethe-University in Frankfurt and completed his Ph.D. in the group of Harald Schwalbe in 2010. Janina Buck received her diploma in chemistry from the Goethe-University in Frankfurt and completed her Ph.D. in the group of Harald Schwalbe in 2010.

Jan Ferner received his diploma in chemistry from the Goethe-University in Frankfurt and completed his Ph.D. in the group of Harald Schwalbe in 2009. Section: Abstract Citing Articles View all 16 citing articles. Molecular Mechanisms of RNA-Triggered Gene Silencing Machineries - Accounts of Chemical Research. Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States Acc. Chem. Res., 2012, 45 (7), pp 1122–1131 DOI: 10.1021/ar200253u Publication Date (Web): February 3, 2012 Copyright © 2012 American Chemical Society Biography Zhonghan Li received his B.S. in Biological Sciences in 2005 from Fudan University, China.

Tariq M. Section: Abstract Gene silencing by RNA triggers is an ancient, evolutionarily conserved, and widespread phenomenon. In this Account, we focus on our current understanding of the structure and function of various classes of RNAi triggers and how this knowledge has contributed to our understanding of the biogenesis and catalytic functions of siRNA and microRNA in mammalian cells. Citing Articles View all 16 citing articles Citation data is made available by participants in CrossRef's Cited-by Linking service. This article has been cited by 4 ACS Journal articles (4 most recent appear below). Multifunctional Nanogels for siRNA Delivery - Accounts of Chemical Research.

School of Chemistry and Biochemistry and the Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States Acc. Chem. Res., 2012, 45 (7), pp 985–993 DOI: 10.1021/ar200216f Publication Date (Web): December 19, 2011 Copyright © 2011 American Chemical Society Biography L. Michael H. Section: Abstract The application of RNA interference to treat disease is an important yet challenging concept in modern medicine. Over the last several years, our research group has investigated hydrogel nanoparticles (nanogels) as candidate delivery vehicles for therapeutics, including siRNA.

Through the layering of multiple, orthogonal chemistries in a nanogel structure, we can impart multiple functions to the materials. Proof-of-principle experiments have demonstrated the utility of multifunctional nanogels. Citing Articles View all 23 citing articles Citation data is made available by participants in CrossRef's Cited-by Linking service.

New Sensor For Cell Metabolites | March 12, 2012 Issue - Vol. 90 Issue 11. Novel Modifications in RNA - ACS Chemical Biology. Department of Chemistry, University of California, Davis, California 95616, United States ACS Chem. Biol., 2012, 7 (1), pp 100–109 DOI: 10.1021/cb200422t Publication Date (Web): December 8, 2011 Copyright © 2011 American Chemical Society Section: Abstract The past several years have seen numerous reports of new chemical modifications for use in RNA. Citing Articles View all 24 citing articles Citation data is made available by participants in CrossRef's Cited-by Linking service. This article has been cited by 7 ACS Journal articles (5 most recent appear below). On The Origin Of Sugars. Photoinduced RNA Interference - Accounts of Chemical Research. Polymers for siRNA Delivery: Inspired by Viruses to be Targeted, Dynamic, and Precise - Accounts of Chemical Research.

Probing the Metal-Ion-Binding Strength of the Hydroxyl Group - Chemical Reviews. Product and Mechanistic Analysis of the Reactivity of a C6-Pyrimidine Radical in RNA - Journal of the American Chemical Society. Recent Advances in Developing Small Molecules Targeting RNA - ACS Chemical Biology. Recognition of Double-Stranded RNA by Guanidine-Modified Peptide Nucleic Acids - Biochemistry. Riboswitches: Discovery of Drugs That Target Bacterial Gene-Regulatory RNAs - Accounts of Chemical Research. RNA Folding Pathways and the Self-Assembly of Ribosomes - Accounts of Chemical Research. RNA Folding Pathways and the Self-Assembly of Ribosomes - Accounts of Chemical Research. RNA-Binding and Viral Reverse Transcriptase Inhibitory Activity of a Novel Cationic Diamino Acid-Based Peptide - Journal of Medicinal Chemistry. Roche RNAi Assets Go To Arrowhead | Latest News | Chemical & Engineering News.

RTRACS: A Modularized RNA-Dependent RNA Transcription System with High Programmability - Accounts of Chemical Research. Small-Interfering RNA (siRNA)-Based Functional Micro- and Nanostructures for Efficient and Selective Gene Silencing - Accounts of Chemical Research. SPANosomes as Delivery Vehicles for Small Interfering RNA (siRNA) - Molecular Pharmaceutics. Synthesis, Properties, and Applications of Oligonucleotides Containing an RNA Dinucleotide Phosphorothiolate Linkage - Accounts of Chemical Research. The Molecular Interactions That Stabilize RNA Tertiary Structure: RNA Motifs, Patterns, and Networks - Accounts of Chemical Research. Thermodynamics of Ligand Binding to a Heterogeneous RNA Population in the Malachite Green Aptamer - Biochemistry. Ultrasensitive DNA Microarray Biosensing via in Situ RNA Transcription-Based Amplification and Nanoparticle-Enhanced SPR Imaging - Journal of the American Chemical Society.