NOE-type Experiments for nucleic acids

The nomenclature used for describe through-space interactions in nuclic acids is  d_x(l;r) where l corresponds to the proton in the 5'-nucleotide unit,  r to the proton in the 3'-nucleotide unit, and x is the type of interaction. Thus,  several types of through-space interactions can be detected in polynucleotides by NMR:

• Intranucleotide interactions giving information about sugar puckering and glycosidic torsion angle.
• Internuclotide sequential interactions giving information about base stacking.
• Internucleotide cross-stand interactions giving information about base pair formation.

The internuclear distance can be derived from the cross-peak intensities in NOESY-type experiments recorded in D₂O and/or H₂O (for exhangeable protons). Thus, in general we can distinguish:

• Intense cross-peak for short distances between 1.8-3.0 A.
• Medium cross-peak for distances between 3.0-4.0 A.
• Weak cross-peak for distances between 4.0-5.0 A
• Absence of cross-peak for distance larger than 5 A.

Three-dimensional structures of oligonucleotides are usually generated by distance geometry and molecular dynamics calculations using distance and torsion angle constraints derived from NMR experiments. Relaxation matrix analysis (RMA) has been used to enhance the accuracy of NOE-derived distance constraints by considering multispin effects ( 99MRC564 ).