Phosphodiester angles

J-Resolved Constant Time r Experiment for the Determination of the Phosphodiester Backbone Angles a and f 172... 

As an example of the measurement of cross-correlated relaxation between CSA and dipolar couplings, we choose the J-resolved constant time experiment [30] (Fig. 7.26 a) that measures the cross-correlated relaxation of 1H,13C-dipolar coupling and 31P-chemical shift anisotropy to determine the phosphodiester backbone angles a and in RNA. Since 31P is not bound to NMR-active nuclei, NOE information for the backbone of RNA is sparse, and vicinal scalar coupling constants cannot be exploited. The cross-correlated relaxation rates can be obtained from the relative scaling (shown schematically in Fig. 7.19d) of the two submultiplet intensities derived from an H-coupled constant time spectrum of 13C,31P double- and zero-quantum coherence [DQC (double-quantum coherence) and ZQC (zero-quantum coherence), respectively]. These traces are shown in Fig. 7.26c. The desired cross-correlated relaxation rate can be extracted from the intensities of the cross peaks according to ... 

The above potential energy approach of building double helical polynucleotides is illustrated below for some hypothetical B-family poly(dA) poly(dT) chains. For simplicity, the helices are generated as a function of the phosphodiester angles < and u> only. 

Figure 3. Contour diagram of the base stacking potential energy Kg of sequential adenine bases and the hydrogen bonding potential energy VHB of the complementary A T base pairs as a function of the phosphodiester rotation angles

Figure 6. Contour diagram of the distances d and d between successive Cl atoms in a DNA duplex as a function of the phosphodiester angles. The (X) denotes the conformation of the ideal theoretical helix of Figure 3 with d = d = 4.8 A. The shaded area on the diagram describes the local motions that preserve base stacking in a flexible duplex. See text for further explanation.

The effect of counterion on the synthetic DNA conformation has been probed by comparing the NMR parameters in high salt sodium and tetramethylammonium solutions. We observe a specific change at one of the two glycosidic torsion angles and at one of the two phosphodiester linkages for poly(dA-dT) on proceeding from Na+ to TMA+ solutions. 

Nucleic acids have a phosphodiester backbone that includes a ribose or deoxyri-bose group that is bound to a base (G, A, C, U, or T). The furanose sugar can adopt different conformations, and the link of the sugar to the base may have various torsion angles. 

At the level of primary structure, several recent experiments have shown the effect of base sequence on the local structure of DNA. A dramatic example is the crystal structure of d(CpG) as determined by Rich and coworkers ( ). This molecule crystallizes in a left-handed double helical form called Z-DNA, which is radically different in its structural properties from the familiar right-handed B-DNA structure. Dickerson and Drew (10) showed in the crystal structure of the dodecanucleotide d(CGCGAATTCGCG) that the local twist angle of a DNA double helix varies with sequence. Deoxyribonuclease I cuts the phosphodiester backbone of the dodecanucleotide preferentially at sites of high twist angle (l 1). From these and other (12,13) experiments we see that the structure of DNA varies with base sequence, and that enzymes are sensitive to these details of structure. 

Figure 1.61 Conformational freedom is heavily restricted in nucleic acids owing to lack of free rotation about 0 —P and P—0 bonds, (a) Nucleic acid equivalent of the Ramachandran plot illustrating the theoretically allowed angles of C and a. (b) Free rotation is primarily damped owing to the gauche effect in which lone-pair-o- orbital overlaps in phosphodiester links generate double bond character in 0—P bonds that restrict free rotation (adapted from Govil, 1976 [Wiley]).

Figure 1.62 Newman projections of to show the dihedral angles subtended about the 0 —P and P—0 bonds (C and a respectively) in order to demonstrate how highly regular dihedral angles set up a highly extended phosphodiester backbone conformation. Bonds are colour coded in the same way as Figs. 1.60 1.61.

Fig. 4 From left to right are shown the molecular conformations for 3(1-> 3) glucan, a(1- 5) glucan and phosphodiester link between ribose units with the labelled dihedral angles.

The Karplus-like relationship between HCOP and CCOP dihedral angles and and three-bond coupling constants, respectively, has been used to determine the conformation about the ribose-phosphate backbone of nucleic acids in solution. Torsional angles about both the C3 -03 and C5 -05 bonds in 3, 5 -phosphodiester linkages have been determined from the coupled and P NMR spectra. 

It is interesting to add that simple modifications of the glycosidic angle x. which fixes the base plane with respect to the phosphodiester backbone, are also a powerful way of provoking important conformational transitions. This was demonstrated in early modeling by Olson which lead to unusual ribbon-like structures of DNA. More recently, it has been shown that such deformations are related to certain protein induced DNA deformations, leading to the so-call TA-DNA conformation and to the conformations created by extreme stretching of the double helix (see Section 3.5 and Protein-Nucleic Acid Interactions). 

---