Open AccessSequence‐dependent structural variation in single‐helical DNA Proton NMR studies of d(T‐A‐T‐A) and d(A‐T‐A‐T) in aqueous solution
Author(s) -
MELLEMA JanRemt,
PIETERS Jane M. L.,
MAREL Gijs A.,
BOOM Jacques H.,
HAASNOOT Cornelis A. G.,
ALTONA Cornelis
Publication year - 1984
Publication title -
european journal of biochemistry
Language(s) - English
Resource type - Journals
eISSN - 1432-1033
pISSN - 0014-2956
DOI - 10.1111/j.1432-1033.1984.tb08371.x
Subject(s) - conformational isomerism , chemistry , nuclear overhauser effect , crystallography , aqueous solution , proton , nuclear magnetic resonance spectroscopy , spectroscopy , two dimensional nuclear magnetic resonance spectroscopy , dna , spectral line , stereochemistry , pyrimidine , sequence (biology) , molecule , physics , organic chemistry , quantum mechanics , biochemistry , astronomy
The two deoxyribotetranucleoside triphosphates d(T‐A‐T‐A) and d(A‐T‐A‐T) were investigated in aqueous solution by one‐ and two‐dimensional proton NMR at 300 and 500 MHz. It is demonstrated that both compounds occur predominantly in the single‐helical form. Accurate coupling constants are obtained by computer simulation of several 500‐MHz spectra. The data are interpreted in terms of N and S pseudorotational ranges. The geometry of the major S‐type conformers displays a clear sequence dependence, as expressed by variation of the endocyclic backbone angle δ (C5′‐C4′‐C3′‐O3′). A simple sum rule is proposed to predict δ variation in single‐helical DNA fragments. Comparisons are made with other sequence‐dependent geometries as observed in a double‐helical B‐DNA fragment in the crystalline state. Furthermore, one‐ and two‐dimensional nuclear Overhauser effect (NOE) spectroscopy was carried out on d(T‐A‐T‐A). An inventory is made of the observed intra‐ and inter‐residue NOEs. The NOE data confirm the presence of a highly stacked single‐helical conformation of d(T‐A‐T‐A) in solution. No indications are found for the formation of a bulge‐out structure as observed for analogous alternating purine‐pyrimidine oligoribonucleotides.