Highlights / Data
Last modified on 30 January 2007.
- Secondary Structure - two or more consecutive, antiparallel, and nested base pairs.
- Tertiary Structure - all non-canonical (A:C, C:A, G:G, A:A, A:G, G:A, U:U, C:C, C:U, and U:U) base-base interactions plus interactions not classified as a secondary base pair. These include:
- lone (or single) pair - a single base pair not associated with a secondary structure helix.
- pseudoknots - non-nested base pairs.
- base triples - a third, unpaired base interaction with a base pair.
- Color Codes for Figures:
- cyan - secondary structure
- orange - tertiary: non-canonical
- green - tertiary: canonical (lone)
- pink - tertiary base triples (the underlying base pair is colored as a separate unit)
- purple - tertiary: pseudoknots
- blue - tertiary: parallel
- Hairpin Loop (H) - nucleotides capping the end of a single helix.
- Internal Loop (I) - nucleotides flanked by two helices.
- Multi-Stem Loop (M) - nucleotides flanked by three or more helices.
Examples of Base Pair and Unpaired Structural Motifs:
This set of figures shows these motifs using the color and letter codes defined above. Unpaired nucleotides are designated in red with the single-letter codes H, I, or M.
Selecting an image will download a PostScript version of that image.
Our definition of secondary structure base pairs includes the condition that those interactions must be nested. The topological arrangement of nested and pseudoknotted interactions are displayed in the following two figures. The standard view of the secondary structure of tRNA (PostScript) is available for comparison.