Rna secondary structure prediction

The study of RNA structure calls for a distinct set of computational tools designed expressly for RNA applications. Recall there are three major categories of RNA, messenger RNA (mRNA), transfer RNA (tRNA) and ribosomal RNA (rRNA). Ribosomal RNA and ribozymes have catalytic functions, like proteins, while messenger RNA has an information storage function, like DNA. A good resource for reviewing the major types of RNA and their functions can be found in the online RNA Structure Primer , available at the RNABase RNA Structure Database website RNABase The RNA Structure Database,

RNA is usually thought of as a single stranded linear molecule, however, in a biological system this is not the case. Frequently, different regions of the same RNA strand will fold together via base pair interactions to make intricate secondary and tertiary structures that are essential for correct biological function. Common secondary structure motifs include hairpin loops, stems, and bulges. Diagrams of these motifs can be viewed on the IMB JENA Nucleic Acid Nomenclature and Structure web page, under section 8 of the Table of Contents, secondary structural elements. To observe tertiary structure in an RNA molecule, view the structure of phenylalanine tRNA from the yeast crystal structure , available from the Nucleic Acid Database (NDB) Project, Rutgers.

Though RNA is usually single stranded, in some RNA virus genomes it will form a double stranded helix. However, unlike DNA, RNA forms an A-form double helix. The RNA double helix differs from that of the DNA double helix because of the presence of ribose, rather than deoxyribose, in the sugar phosphate backbone of the molecule. The addition of a hydroxyl group at the C2 postion in the ribose sugar is responsible for the A-form geometry in double stranded RNA. The A-form makes a right-handed helix, like the B-form double helix, but is a shorter, wider helix than the B-form, and the major groove is deep, but narrow, making it virtually inaccessible to proteins. It is in the major groove that the chemical groups are sequence-specific and dependent on base identity, and therefore, this is where proteins tend to bind a DNA double helix. Because the RNA A-form double helix contains a major groove that is too narrow and deep for proteins to access, the minor groove becomes more important for protein interactions with RNA helices. Also, proteins that interact with specific RNA sequences commonly bind single-stranded RNA segments. For an example of an RNA/protein complex, view the NDB entry for the Protein/Hepatitis Delta Virus Ribozyme Complex . When a strand of DNA forms a double helix with a strand of RNA, this will also result in an A-form helix. An example of a DNA/RNA complex can be found by viewing the NDB entry for the RNA-DNA complex formed by the 10-23 DNA enzyme .

RNA molecules sometimes contain the unusual nucleotides ribothymidine, dihydrouridine, pseudouridine and inosine. In addition, RNA somewhat commonly forms a G-U wobble base pair, and makes other non-canonical base pairs, a listing of which can be found on the George Fox group's Non-Canonical Base Pair Database web page, University of Houston.