RNAs structure

Double heliees ean be formed between one DNA and one RNA polynucleotide. Helices of this kind are of great importanee in biology and occur, for example, in transcription and in antisense oligonucleotides (Chapter 11.6). 

All RNA molecules represent copies of genes on the cellular DNA, but there are some important differences in structure between DNA and RNA. 

The features of RNA structure that distinguish it from DNA follow  

Most types of cellular RNA are involved in various steps in protein synthesis or gene expression. 

The function of the ribosome, including its main catalytic activity, depends on several forms of ribosomal RNA (rRNA). 

Ribosomes are large nucleoprotein machines composed of large and small subunits that carry out protein synthesis. 

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Although experimental studies of DNA and RNA structure have revealed the significant structural diversity of oligonucleotides, there are limitations to these approaches. X-ray crystallographic structures are limited to relatively small DNA duplexes, and the crystal lattice can impact the three-dimensional conformation [4]. NMR-based structural studies allow for the determination of structures in solution however, the limited amount of nuclear overhauser effect (NOE) data between nonadjacent stacked basepairs makes the determination of the overall structure of DNA difficult [5]. In addition, nanotechnology-based experiments, such as the use of optical tweezers and atomic force microscopy [6], have revealed that the forces required to distort DNA are relatively small, consistent with the structural heterogeneity observed in both DNA and RNA. 

Computational studies of nucleic acids offer the possibility to enliance and extend the infonnation available from experimental work. Computational approaches can facilitate the experimental detennination of DNA and RNA structures. Dynamic information. 

RNA structures, compared to the helical motifs that dominate DNA, are quite diverse, assuming various loop conformations in addition to helical structures. This diversity allows RNA molecules to assume a wide variety of tertiary structures with many biological functions beyond the storage and propagation of the genetic code. Examples include transfer RNA, which is involved in the translation of mRNA into proteins, the RNA components of ribosomes, the translation machinery, and catalytic RNA molecules. In addition, it is now known that secondary and tertiary elements of mRNA can act to regulate the translation of its own primary sequence. Such diversity makes RNA a prime area for the study of structure-function relationships to which computational approaches can make a significant contribution. 

Abstract Protoberberine alkaloids and related compounds represent an important class of molecules and have attracted recent attention for their various pharmacological activities. This chapter deals with the physicochemical properties of several isoquinoline alkaloids (berberine, palmatine and coralyne) and many of their derivatives under various environmental conditions. The interaction of these compounds with polymorphic DNA structures (B-form, Z-form, H -form, protonated form, triple helical form and quadruplex form) and polymorphic RNA structures (A-form, protonated form, triple helical form and quadruplex form) reported by several research groups, employing various analytical techniques such as spectrophotometry, spectrofluorimetry, circular dichro-ism, NMR spectroscopy, viscometry as well as molecular modelling and thermodynamic analysis to elucidate their mode and mechanism of action for structure-activity relationships, are also presented. 

The assumption was that, at a later phase of development, amino acids would attach themselves to the RNA structures, which would reach the approximate length of today s tRNA molecules. The structures could be stabilized, for example, by Ca2+ ions in the space between the strands (with their negatively charged phosphate... 

The RNA structures and protein folds mentioned in Section 4.11 are limited in number and most of the basic varieties, but not all, are maintained throughout evolution (see Sections 7.8 and 8.10). 

Mg2+ Glycolytic pathway (enolase) All kinases and NTP reactions" Signalling (transcription factors) DNA/RNA structures Light capture... 

W. Wintermeyer, J. M. Robertson, H. Weidman, and H. G. Zauchau, in Transfer RNA Structure, Properties and Recognition (P. R. Schimmel, D. Soil, and J. N. Abelson, eds.), 445 157, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York (1979). 

Determination of the three-dimensional RNA structure within the ribosome is still in its infancy. Nonetheless, it is expected that by combin-... 

R. Giege M. Frugier, Transfert RNA Structure and Identity. In Translation Mechanisms J. Lapointe, L. Brakier-Gingras, Eds. Eurekah.com/Landes Bioscience Georgetown TX, 2003 pp 1-24. 

In mid-1997 an international conference took place in Santa Cruz, USA, in which, for the first time, the exclusive topic was structural aspects of RNA molecules. A report covering this meeting contains an impressive graphic which shows the RNA structures, RNA/DNA complexes, and RNA/protein complexes contained in the brookhaven database as a function of the year of their publication [29]. Between 1988 and 1993 there were just 20. However, in 1996 alone no less than 41 structures appeared. These new dimensions were headed by the crystal structural elucidation of the first larger RNA molecule since the first crystal structure of tRNA in 1973 [30], the 48 nucleotide long hammerhead ribo-zyme (HHR) [31-33]. This landmark achievement was followed by a crystal structure analysis of the P4-P6-domain of a group I intron [34-36] and, more recently, a crystal structure of the hepatitis delta virus ribozyme [37]. 

All these studies established that the folding of RNA molecules is organized in a hierarchical manner. The assembly of complex RNA structures occurs in discrete transitions which build upon the folding of sub-systems that can then self-organize to even bigger and more complex structures [38-40]. 

A landmark achievement in RNA structure determination was the solution of the crystal structure of the 160 nucleotide long P4-P6 domain of the Tetrahyme-na group I intron [19,34,35,39]. The P4-P6-domain folds into a compact structure with a sharp turn that is stabilized by tight packing of the heHces. This newly discovered structural element was designated as the ribose-zipper because of the hydrogen bonds between ribose residues of the helices that participate in the structure. In addition, stabiHzation of RNA folds in P4-P6 occurs mainly via... 

Abstract The last few years have seen a considerable increase in our understanding of catalysis by naturally occurring RNA molecules, called ribozymes. The biological functions of RNA molecules depend upon their adoption of appropriate three-dimensional structures. The structure of RNA has a very important electrostatic component, which results from the presence of charged phosphodiester bonds. Metal ions are usually required to stabilize the folded structures and/or catalysis. Some ribozymes utilize metal ions as catalysts while others use the metal ions to maintain appropriate three-dimensional structures. In the latter case, the correct folding of the RNA structures can perturb the pKa values of the nucleo-tide(s) within a catalytic pocket such that they act as general acid/base catalysts. The various types of ribozyme exploit different cleavage mechanisms, which depend upon the architecture of the individual ribozyme. 

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