Like DNA, most biologically active RNAs, including mRNA, tRNA, rRNA, snRNAs and other non-coding RNAs, contain self-complementary sequences that allow parts of the RNA to fold and pair with itself to form double helices. Structural analysis of these RNAs has revealed that they are highly structured, having the abilty to fold into three dimensional shapes. Unlike DNA, their structures do not consist of long double helices but rather collections of short helices packed together into structures akin to proteins. In this fashion, RNAs can achieve chemical catalysis, like enzymes. For instance, determination of the structure of the ribosome—an enzyme that catalyzes peptide bond formation, revealed that the active site is composed entirely of RNA.
Each nucleotide in RNA contains a ribose sugar, with carbons numbered 1’ through 5’. A base is attached to the 1’ position, generally purines adenine (A) and cytosine ©, as well as pyrimidines guanine (G) or uracil (U). A phosphate group is attached to the 3’ position of one ribose and the 5’ position of the next. The phosphate groups have a negative charge each at physiological pH, making RNA a charged molecule (polyanion). The bases may form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil. However other interactions are possible, such as a group of adenine bases binding to each other in a bulge, or the GNRA tetraloop that has a guanine–adenine base-pair.
Chemical structure of RNA
An important structural feature of RNA that distinguishes it from DNA is the presence of a hydroxyl group at the 2’ position of the ribose sugar. The presence of this functional group causes the helix to adopt the A-form (a more compact geometry) rather than the B-form most commonly observed in DNA. This results in a very deep and narrow major groove and a shallow and wide minor groove. A second consequence of the presence of the 2’-hydroxyl group is that in conformationally flexible regions of an RNA molecule (that is, not involved in formation of a double helix), it can chemically attack the adjacent phosphodiester (phosphorus-ribose) bond to cleave the backbone.
