J vs Beta Angle

Phosphodiester backbone torsion angles are normally found in one od the three staggered conformation: gauche+, gauche-, or trans. The beta torsion angle can be derived from the 3JP5'-H5'3JP5'-H5'' and 3JP5'-C4' coupling constants and has been used for many years in the conformational analysis of the phosphodiester linkages in nucleotides. Karplus equation has been parametrizated in: 95TL1949 , 94NAR2658. In particular, for the beta angle, this three rotamers have unique J values:
  • Trans conformation: Both 3JP-H5' are small and 3JP5'-C4' is large.
  • If is not trans, either 3JP-H5' is large and 3JP5'-C4' is small. and stereospecific H5' assignment is required.
  • Some methods to measure them are: