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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN"><!--Converted with LaTeX2HTML 98.1p1 release (March 2nd, 1998)originally by Nikos Drakos (nikos@cbl.leeds.ac.uk), CBLU, University of Leeds* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan* with significant contributions from: Jens Lippmann, Marek Rouchal, Martin Wilck and others --><HTML><HEAD><TITLE>Introduction</TITLE><META NAME="description" CONTENT="Introduction"><META NAME="keywords" CONTENT="FEBS98-html"><META NAME="resource-type" CONTENT="document"><META NAME="distribution" CONTENT="global"><META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1"><LINK REL="STYLESHEET" HREF="FEBS98-html.css"><LINK REL="next" HREF="node4.html"><LINK REL="previous" HREF="node2.html"><LINK REL="up" HREF="FEBS98-html.html"><LINK REL="next" HREF="node4.html"></HEAD><BODY BGCOLOR=#FFDEAD TEXT=#202020 LINK=#800000 ALINK=#ffff00 VLINK=#353976><!--Navigation Panel--><A NAME="tex2html91" HREF="node4.html"><IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="img/next_motif.gif"></A> <A NAME="tex2html88" HREF="FEBS98-html.html"><IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="img/up_motif.gif"></A> <A NAME="tex2html82" HREF="node2.html"><IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="img/previous_motif.gif"></A> <A NAME="tex2html90" HREF="node1.html"><IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents" SRC="img/contents_motif.gif"></A> <BR><B> Next:</B> <A NAME="tex2html92" HREF="node4.html">Software platforms and environment</A><B> Up:</B> <A NAME="tex2html89" HREF="FEBS98-html.html">Algorithms and Thermodynamics for</A><B> Previous:</B> <A NAME="tex2html83" HREF="node2.html">Abstract</A><BR><BR><!--End of Navigation Panel--><H1><A NAME="SECTION00030000000000000000">Introduction</A></H1><P>RNA is ubiquitous in the cell and is important for many processes. Theactivity of RNA is determined by its structure, the way it is foldedback on itself. Secondary structure modeling of RNA predicts, orotherwise determines, the pattern of Watson-Crick (WC), wobble andother, non-canonical pairings that occur when the RNA is folded. Forthe purposes of this article, a non-canonical base pair is defined asnon Watson-Crick (non W-C) and non-wobble (not GU or UG). There aremany different kinds of RNA. Ribosomal RNA (rRNA) is a crucial partof the ribosome which is found in all living cells and in organellessuch as mitochondria and chloroplasts. Small nuclear RNAs (snRNA) forma vital part of sliceosomes that process mRNAs in eukaryotes. Theseare 2 examples of <EM>structural</EM> RNAs.<P>Messenger RNAs (mRNA) do more than just carry information. Secondarystructures can be used in part to explain translational controls inmRNA [<A HREF="node19.html#MACP9001">1</A>,<A HREF="node19.html#SMIM9001">2</A>], and replication controls insingle-stranded RNA viruses [<A HREF="node19.html#MILD9001">3</A>]. Although the vastmajority of known mRNAs code for proteins or structural RNAs, some donot [<A HREF="node19.html#BRAC9001">4</A>,<A HREF="node19.html#BROC9101">5</A>]; and it is likely that the secondarystructures of these transcripts play an important role in theirregulatory function in the cell. It is to be expected that many moresuch functional RNAs will be discovered in the future.<P>RNA is not just a passive structural element or a regulator. It isalso an active component in many situations. Thus RNA acting alone isable to catalyze RNA processing [<A HREF="node19.html#CECT8601">6</A>,<A HREF="node19.html#CECT9001">7</A>]. In aprotein-RNA complex, the RNA component of ribonuclease P is an activecomponent of tRNA processing [<A HREF="node19.html#DARS9201">8</A>]. <P>The function of an RNA can only be understood in terms of itssecondary or tertiary structure. For the understanding of catalyticactivity, knowledge of secondary structure alone is insufficient.However, few large structures have been determined by crystallography[<A HREF="node19.html#KIMS7401">9</A>,<A HREF="node19.html#ROBJ7401">10</A>,<A HREF="node19.html#PLEH9401">11</A>] and the need formodeling is great. Secondary structure modeling can reasonably beviewed as a first step towards three dimensional modeling. Forexample, in small and large subunit rRNA, all tertiary interactions,including base triples, involve only 3% and 2% of the nucleotides,respectively [<A HREF="node19.html#GUTR9501">12</A>]. In contrast, nucleotides in secondarystructure comprise 60% and 58% of these rRNAs.<P>Secondary structure modeling is therefore a significant firststep to the far more difficult process of three dimensionalatomic resolution modeling. Knowledge of secondary structure, togetherwith additional information on structural constraints or tertiaryinteractions, can be used to construct atomic resolution structuralmodels [<A HREF="node19.html#MICF9001">13</A>,<A HREF="node19.html#MAJF9101">14</A>,<A HREF="node19.html#MAJF9301">15</A>].<P><HR><!--Navigation Panel--><A NAME="tex2html91" HREF="node4.html"><IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="img/next_motif.gif"></A> <A NAME="tex2html88" HREF="FEBS98-html.html"><IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="img/up_motif.gif"></A> <A NAME="tex2html82" HREF="node2.html"><IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="img/previous_motif.gif"></A> <A NAME="tex2html90" HREF="node1.html"><IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents" SRC="img/contents_motif.gif"></A> <BR><B> Next:</B> <A NAME="tex2html92" HREF="node4.html">Software platforms and environment</A><B> Up:</B> <A NAME="tex2html89" HREF="FEBS98-html.html">Algorithms and Thermodynamics for</A><B> Previous:</B> <A NAME="tex2html83" HREF="node2.html">Abstract</A><!--End of Navigation Panel--><ADDRESS><TABLE><TR><TD><IMG SRC=img/shield16.gif HSPACE=20></TD><TD><I>Michael Zuker <BR>Institute for Biomedical Computing<BR>Washington University in St. Louis<BR>1998-12-05</I></TD></TR></TABLE></ADDRESS></BODY></HTML>⌨️ 快捷键说明
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