Effect of distortions in the deoxyribose phosphate backbone conformation of duplex oligodeoxyribonucleotide dodecamers containing GT, GG, GA, AC, and GU base-pair mismatches on phosphorus-31 NMR spectra

Abstract

We have previously suggested that variations in the 31P chemical shifts of individual phosphates in duplex oligonucleotides are attributable to torsional angle changes in the deoxyribose phosphate backbone. This hypothesis is not directly supported by analysis of the 1H/31P two-dimensional J-resolved spectra of a number of mismatch dodecamer oligonucleotide duplexes including the following sequences: d-(CGTGAATTCGCG), d(CGUGAATTCGCG), d(CGGGAATTCGCG), d(CGAGAATTCGCG), and d(CGCGAATTCACG). The 31P NMR signals of the dodecamer mismatch duplexes were assigned by 2D 1H/31P pure absorption phase constant time (PAC) heteronuclear correlation spectra. From the assigned H3' and H4' signals, the 31P signals of the base-pair mismatch dodecamers were identified. JH3'-P coupling constants for each of the phosphates of the dodecamers were obtained from 1H/31P J-resolved selective proton flip 2D spectra. By use of a modified Karplus relationship, the C4'-C3'-O3'-P torsional angles (epsilon) were obtained. JH3'-P coupling constants were measured for many of the oligonucleotides as a function of temperature. There exists a good linear correlation between 31P chemical shifts and the epsilon torsional angle. This correlation can be further extended to the C3'-O3'-P-O5' torsional angle (zeta) by using a linear relationship between epsilon and zeta obtained from crystal structure studies. The 31P chemical shifts follow the general observation that the more internally the phosphate is located within the oligonucleotide sequence, the more upfield the 31P resonance occurs. In addition, 31P chemical shifts show sequence- and site-specific variations. Analysis of the backbone torsional angle variations from the coupling constant analysis has provided additional information regarding the origin of these variations in 31P chemical shifts.

Thermodynamic stability and solution conformation of tandem G · A mismatches in RNA and RNA · DNA hybrid duplexes

“…In addition, there is a second stable conformation in DNA with t(g-), [(t) called B,, (Fratini et al, 1982). The latter conformation is associated with a large downfield shift of the phosphate resonance, as observed in tandem mismatches in the context YGAR (Roongta et al, 1990;Chou et al, 1992;Lane et al, 1992), and in DNA with intercalated drugs (Searle and Lane, 1992). The lack of characteristic downfield-shifted phosphate resonances is consistent with all phosphodiester conformations being in the e(t), <(g-) range.…”

Properties of multiple G · A mismatches in stable oligonucleotide duplexes

“…Concentrations of single strands ( C, ) were determined spectrophotometrically at a temperature well above the T, (melting temperature; maximum point on the first derivative of the ultraviolet melting curve) and absorption coefficients were calculated (Puglisi and Tinoco, 1989). Thermodynamic parameters were calculated using the following equations (SantaLucia et al, 1991;Marky and Breslauer, 1987):…”

“…"P-NMR analysis (Roongta et al, 1990). The phosphate peaks were assigned using a P-H heteronuclear-correlation experiment (Fig.…”

TWo-Dimensional1H and31P NMR Spectra and Restrained Molecular Dynamics Structure of an Oligodeoxyribonucleotide Duplex Refined via a Hybrid Relaxation Matrix Procedure

“…A "crankshaft" motion interconverts BI and BII conformations with only a modest movement of the phosphate. It is largely this variation in ε and ζ (as well as 8,3,36,39,62,68) that allows the sugar phosphate backbone to "stretch" or "contract" to allow for variations in the local structure of B-DNA.…”

“…The 31 P signal of the random coil state is shifted downfield relative to that of the duplex DNA (37,38). The 31 P chemical shift difference between the two g -, g -and t, g -conformational states is estimated to be 1.5-1.6 ppm (33,39).…”