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B. RNA Structure

As a linear nucleic acid polymer, RNA structure has a lot of similarity to DNA structure.

RNA follows the same rules of base-pairing as DNA (with the substitution of Uracil for Thymine), but short single stranded RNA molecules are much freer to take on a variety of 3-dimensional shapes.

This is particularly evident in the structures of tRNA molecules and ribozymes as well as in the phenomenon of self-splicing of mRNA molecules.

The primary structure (the sequence) of the RNA molecule contains all of the information for self-assembly into complex 3-D structures. The RNA sequence must also contain:

• the genetic code specifying the order of amino acids in proteins
  
  
• the information that controls the beginning and ends of protein coding sequences (translation start and stop signals) and the splicing of introns
  
  
• information that determines the stability of the RNA molecule in the cell and its relative transcriptional level

The process of self-assembly of tRNA molecules into their characteristic stem-loop structures is relatively well understood.

A set of rules based on the concept of free energy minimization have been generated from the study of tRNAs which can be applied to any RNA sequence.

From this algorithm Michael Zuker (Methods in Enzymology, 180, 262-288(1989) created the computer program FoldRNA.

This program has been incorporated into the GCG package as a set of RNA secondary structure prediction tools: MFOLD, PLOTFOLD, FOLDRNA, SQUIGGLES, CIRCLES, DOMES, MOUNTAINS, and STEMLOOP.

These tools allow many different views of RNA secondary structures, but do not necessarily predict the single optimal structure for a given sequence.

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Using Computers for Molecular Biology
Stuart M. Brown, Ph.D., RCR, NYU Medical Center

Comments to: browns02@mcrcr.med.nyu.edu