Probes of RNA structure

Volume 468. Biophysical, Chemical, and Functional Probes of RNA Structure, Interactions and Folding Part A Edited by Daniel Herschlag... 

AP photophysics is determined by its environment, which makes 2AP a useful probe of RNA structure and dynamics but because its properties depend on its environment, the incorporation of 2AP into an RNA must be done cautiously, preferably with prior knowledge of the site—duplex or single strand, tight turn or floppy loop, etc. With that caveat in mind, 2AP has been used in several ways to provide unique information on the folding and dynamics of both small and large RJSIAs. 

Eamshaw DJ, Gait MJ. Modified oligoribonucleotides as site-specific probes of RNA structure and function. Biopolymers 1998 48 39-55. 

CiesioUca, J. Metal ion-induced cleavages in probing of RNA structure. RNA Biochemistry and Biotechnology, NATO Science Series, 3-70 High Technology, 1999, pp.111-121. 

Kostenko E, Dobrikov M, Phshnyi D, Petyuk V (2001) 5 -Bis-pyrenylated oligonucleotides displaying excimer fluorescence provide sensitive probes of RNA sequence and structure. Nucleic Acids Res 29 3611-3620... 

CONTENTS Preface, C. Allen Bush. Thermodynamic Solvent Isotope Effects and Molecular Hydrophobicity, Terrence G. Oas and Eric J. Toone. Membrane Interactions of Hemolytic and Antibacterial Peptides, Karl Lohner and Richard M. Epand. Spin-Labeled Metabolite Analogs as Probes of Enzyme Structure, Chakravarthy Narasimhan and Henry M. Miziorko. Current Perspectives on the Mechanism of Catalysis by the Enzyme Enolase, John M. Brewer and Lukasz Leb-ioda. Protein-DNA Interactions The Papillomavirus E2 Proteins as a Model System, Rashmi S. Hedge. NMR-Based Structure Determination for Unlabeled RNA and DNA, Philip N. Borer, Lucia Pappalardo, Deborah J. Kenwood, and Istvan Pelczer. Evolution of Mononuclear to Binuclear CuA An EPR Study, William E. Antholine. Index. 

A similar base-catalyzed reaction sequence can be used to displace N -methylguanine and to cleave the pol5mucleotide. Ethylnitrosourea, in its reaction with purines, is useful as a structural probe of RNA. 

R95 E. C. Thiel, Y. Ke, Z. Gdaniec and H. Sierzputowska-Gracz, The IRE Model for Families of RNA Structures Selective Recognition by Binding Proteins (IRPs), NMR Spectroscopy and Probing with Metal Coordination Complexes , p. 241 vol. 74, 2000... 

NMR has developed as a powerful probe of the structure and dynamics of nucleic acids in solution. With the development of synthetic schemes in which defined RNA and DNA fragments can be routinely produced in multi-milligram quantities and the concomitant development of sequence-specific 2D H/ H and NMR methodologies (1-9) for assignment of individual P signals, analysis of the P NMR spectra of modest size oligonucleotides (12-20 base pairs) is now... 

Hikida Y, Kimoto M, Yokoyama S, Hirao I (2010) Site-specific fluorescent probing of RNA molecules by unnatural base-pair transcription for local structural conformation analysis. Nat Protoc 5(7) 1312-1323. doi 10.1038/nprot.2010.77... 

To modify the unique chemical groups on nucleic acids, novel methods have been developed that allow derivatization through discrete sites on the available bases, sugars, or phosphate groups (see Chapter 1, Section 3 for a discussion of RNA and DNA structure). These chemical methods can be used to add a functional group or a label to an individual nucleotide or to one or more sites in oligonucleotide probes or full-sized DNA or RNA polymers. 

NMR is a powerful and versatile tool for structural studies of biological RNAs and complexes they form with other nucleic acids, proteins, and small molecules. The goal of these studies is to determine the role that structure and dynamics play in biological function. NMR has the capacity to determine high-resolution structures, as well as to map RNAiligand interfaces at low resolution. Most structures of RNA and RNA-ligand complexes are under 20 KDa in size however, recent advances allow for determination of solution structures of complexes up to 40 kDa. NMR can also probe dynamic motions in RNA on micro- to millisecond time scales. A number of biologically relevant internal motions such as... 

A number of microorganisms produce free nucleosides which, although structurally similar to the nucleosides of primary biosynthesis, are not normally utilized for nucleic acid synthesis. These have emerged as useful probes for the elucidation of the biochemistry of RNA, DNA... 

The work, summarized by Brown and Todd (424), clearly indicated the 3, 5 linkage in RNA, the occurrence of 2 3 -cyclic phosphates as intermediates in the cleavage of RNA, and the high proportion of pyrimidines on the 3 side of the bond cleaved. Subsequent investigations have probed more deeply into the problem of specificity, investigating different parts of the nucleotide structure. 

Mechanistic studies of RNA enzymes (ribozymes) and ribonucleoprotein (RNP) complexes such as the ribosome and telomerase, often seek to characterize RNA structural features, either dynamic or static, and relate these properties to specific catalytic functions. Many experimental techniques that probe RNA structure-function relationships rely upon site-specific incorporation of chemically modified ribonucleotides into the RNA of interest, often in the form of chemical cross-linkers to probe for sites of protein-RNA interaction or small organic fluorophores to measure dynamic structural properties of RNAs. The ability to arbitrarily modify any RNA molecule has been greatly enabled by modern RNA synthesis techniques however, there remains a practical size... 

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