Intramolecular hydrogen bonding in RNA molecules results in the formation of stem and loop structures (also known as hairpin loops).
RNA in the stem of a stem and loop structure forms a double stranded right-handed helix with . However this double helix is not the same as that of DNA. The most obvious difference is in the tilt of the bases, but there are also differences in the diameter and pitch of the helix[1].
The RNA shown is 24 nucleotides long. Nucleotides 1 through 8 and 17 through 24 form the stem and nucleotides 9 through 16 form the loop. Note the in the stem (A: red, C: green, G: orange, U: blue) and the unpaired bases in the loop (white).
(The stem and loop structure shown is part of the RNA in human telomerase. Telomerase protects chromosomes by restoring DNA that is lost from the ends during DNA replication. The RNA is used as a template and the enzyme is thus an internally-templated RNA-dependant DNA polymerase[2].)
