Python Programming for Biology: Bioinformatics and Beyond

Figure 15.3.  The sequence, secondary structure and folded, three-dimensional

structure of an RNA molecule. The illustrated RNA sequence is from a tRNA molecule,

which forms a particular three-dimensional structure to perform its biological role

(transferring a particular amino acid to the ribosome particle during transcription). The

RNA molecule contains short internal regions of complementary base pairs and folds by

looping to form hydrogen bonds within itself, as illustrated by the secondary structure.

Nuclear  magnetic  resonance  (NMR)  is  the  second  most  common  form  of

macromolecular  structure  determination.  Although  overall  many  more  structures  have

been determined by crystallography, NMR is particularly common for smaller structures,

where it works best; indeed there is generally a limit to the size of the molecule that can be

studied  this  way.  NMR  typically  uses  a  concentrated  solution  of  the  subject  (although

solid-state  samples  are  becoming  more  common),  which  is  then  placed  in  an  extremely

powerful electromagnet. In such a strong magnetic field some of the atomic nuclei, those

that  have  spin-active  isotopes,  will  align  with  the  magnetic  field.  While  the  spin-active

hydrogen-1  and  phosphorus-31  isotopes  are  very  abundant  in  nature,  the  carbon-13  and

nitrogen-15 isotopes are rare and thus biological samples are usually artificially enriched

with  these.  The  magnetic  alignments  of  spin-active  atomic  nuclei  are  then  detected  by

passing  a  pulse  of  radio  waves  though  the  sample,  so  that  they  resonate.  Because  the

resonance frequencies of the atoms depend on their chemical and structural environment,

individual atoms often have distinct resonant frequencies. By the use of specially designed

radio  pulses  the  magnetisation  can  be  moved  from  one  atom  to  another,  selectively  to

covalently  bound  atoms  or  those  that  are  close  in  space.  Such  experiments  correlate  the

observed resonances so that, often after a lengthy analysis, they can be connected together

to  identify  which  resonance  goes  with  which  atom  and  then  how  the  resonances  are

arranged in space, thus yielding a three-dimensional structure.