500-MHz proton NMR study of poly(dG).cntdot.poly(dC) in solution using one-dimensional nuclear Overhauser effect

Abstract

Secondary structures of poly(dG).poly(dC) and poly(dG).poly(dm5C) in solution are determined by nuclear Overhauser effect (NOE) measurements on GH8-deuterated and -nondeuterated DNAs with low presaturation pulse lengths (10-25 ms) and low-power and prolonged accumulations in the range of 50,000-72,000 scans. Under these conditions, the NOE difference spectra were free from diffusion. Primary NOEs between base protons GH8/CH6 and sugar protons H1', H2'/H2'', and H3' suggest that in poly(dG).poly(dC) both guanine and cytosine nucleotides adopt a C3'-endo, low anti X = 200-220 degrees conformation. Computer modeling of the NOE data enable identification for the first time, in terms of the geometry of the nucleotide repeat, handedness, and helix geometry, of the structure of poly(dG).poly(dC) to be the A form, and the derived structure for the polymer duplex is very close to the single crystal structure of the double-helical d-GGGGCCCC [McCall, M., Brown, T., & Kennard, O. (1985) J. Mol. Biol. 183, 385-396]. Similar nuclear Overhauser effect data on poly(dG).poly(dm5C) revealed that G and m5C adopt a C2'endo, anti X = 240-260 degrees conformation, which indicates that this DNA exhibits the B form in solution. In summary, the results presented in this paper demonstrate that methylation of cytosines in poly(dG).poly(dC) causes A----B transition in the molecule.

An A-DNA triplet code: thermodynamic rules for predicting A- and B-DNA.

“…2C) (33). More recent CD and NMR studies have established that it is A-DNA in aqueous solution (34), and this has been confirmed with chiral probes (35). In addition, linear dichroism studies in neutral aqueous buffer show that the bases of poly(dG)-poly(dC) are more dramatically inclined than observed for B-DNA, and this is characteristic of A-DNA (36).…”

The Complex of Poly(dG) · Poly(dC) with Arginine: Stabilization of the B Form and Transition to Multistranded Structures

“…al. (3) have recently found that this polymer maintains the A form even in water solution, which is the first instance in which this form of DNA has been reported to be stable in solution. On the other hand, studies carried out in our laboratory (4,5) have shown that the transition to the A form is never found in DNA when it is neutralized by arginine and related peptides.…”

DNA in dormant spores of Bacillus species is in an A‐like conformation

“…On the other hand, the presence of some regions of A-iike DNA in vivo might be expected, because G-rich oligodeoxyribonucleotides often crystallize in an A-like helical form, and may be on the borderline of the B->A transition in solution (Heinemann etai., 1989;McCall etai., 1985). Indeed, there is significant evidence that the conformation of poly(dG) poly(dC) in solution is A-like (Arnott and Seising, 1974;Nishimara etai., 1985;Sarma et al, 1986). It has been suggested that small regions of DNA are in an A-like conformation in vivo thus facilitating interaction with specific proteins, but this suggestion has never been substantiated (Reynolds et ai., 1985;Rhodes and Klug, 1986).…”

“…They bind avidly to poly(dG)-poly(dG), followed by poly(dG-dC) poly(dG-dC), random sequence DNA such as chromosomal or plasmid DNA, and then poly(dA-dT)-poly(dA-dT); poly(dA)-poly(dT) is not bound (Setlow et ai., 1992). The preference of a/ptype SASP for these different DNAs is notable, because the conformation of poly(dG)-poly(dC) in solution may well be A-like (Arnott and Seising, 1974;Nishimara etai., 1985;Sarma etai., 1986). Poly(dG-dC)-poly(dG-dC) and poly(dA-dT)-poly(dA-dT) can assume an A-like conformation as their hydration level is lowered, but the A-form of poly(dA-dT)-poly(dA-dT) is metastable while that of poly(dG-dC)-poly(dG-dC) is stable (Saenger, 1984).…”