Acronyms and Definitions
Bulge: unpaired nucleotides on only one strand
cUNCGg: example of notation for closing base pair and loop; the lowercase font denotes the closing base pair, and the uppercase the loop
Internal loop: unpaired nucleotides on both strands
M: either A or C
N: any of the four bases (A, G, C, or U) is tolerated
Optical melting: technique using the temperature dependence of spectroscopic parameters to determine the thermodynamic parameters of a folding process
R: a purine, either A or G
Riboswitches: RNA molecules that bind substrates (often small molecules) tightly and specifically and alter gene expression
Ribozyme: catalytic RNA molecules; smaller ribozymes (

30–80 nt) include the hepatitis delta virus, whereas larger ribozymes (

200–400 nt) include the
Tetrahymena ribozyme
RNA defects/imperfections: secondary structural elements other than Watson-Crick base pairing, including bulges and internal loops
RNP: RNA-protein complex
RNA folding problem: understanding and predicting how RNA folds from a random coil into its native structure
Tetraloop: a hairpin loop consisting of four non-Watson-Crick paired nucleotides
TGGE: temperature gradient gel electrophoresis
Y: a pyrimidine, either C or U