Python Programming for Biology: Bioinformatics and Beyond

RNA structure

Unlike  its  DNA  cousin,  RNA  doesn’t  form  long,  continuous  double-helical  structures.

RNA, once it is synthesised from a DNA template during transcription, is a single strand

of  nucleotide  polymer  which  may  then  fold  into  a  three-dimensional  structure.  Any

structure might not be of much importance if the RNA is only acting as a messenger for

protein  synthesis.  However,  for  RNA  molecules  that  are  not  translated,  and  have  other

roles in biology, their three-dimensional conformation is often essential for their function,

just  as  it  is  for  proteins.  Unlike  proteins,  however,  which  form  globules  due  to  the

presence  of  hydrophobic  residues,  RNA  structures  tend  to  form  initially  because  of  the

hydrogen bonding that occurs between pairs of bases, i.e. the same kind of complementary

interaction  that  occurs  between  DNA  strands.  Such  base  pairing  describes  the  secondary

structure of the RNA. In this way an RNA can fold back on itself, or interact with another

RNA molecule, to form a small region of double-stranded duplex. A common feature seen

in  RNA  structures  is  stem-loops,  where  the  strand  is  pinched  together  because  there  are

two relatively close complementary sections (the stem), leaving a loop at the end. The full

conformation  (tertiary  structure)  is  a  three-dimensional  arrangement  of  the  loops  and

duplex  regions  relative  to  one  another.  Because  RNA  has  only  a  few,  chemically  similar

kinds of residue its structural diversity is somewhat limited compared to that of proteins.

Nonetheless, there are some RNAs that are complex enough to form biological catalysts,

just like protein enzymes; these are called ribozymes.