Physical studies on synthetic DANs containing 5-methylcytosine

Abstract

In synthetic DNAs in which cytosine or 5-methylcytosine is base-paired with guanine or hypoxanthine, the physical properties depend both on base composition and base sequence. The absorption spectra of poly(dI) · poly(m 5dC) and poly(dI-m 5dC) · poly(dI-m 5dC) closely resemble the spectra of an equimolar mixture of nucleotides; the maxima near 250 nm corresponds to dIMP absorption and the shoulder at 278 nm corresponds to 5-methyldeoxyCMP absorption. In contrast, when dIMP is replaced by dGMP, the maxima remain near 250 nm, but there is no shoulder; the pyrimidine absorption appears to be blue-shifted by approx. 28 nm. The fluorescence of 5-methyldeoxyCMP is unperturbed when incorporated into randomcoil poly(m 5dC) and is blue-shifted by approx. 8 nm when incorporated into poly(dI-m 5dC) · poly(dI-m 5dC). Incorporation of 5-methyldeoxyCMP into poly(dG-m 5dC) · poly(dG-m 5dC) reduces the fluorescence yield several-fold and blue-shifts the emission by approx. 50 nm. Methylation of pyrimidines raises the melting temperature of both poly(dR-dY) · poly(dR-dY) and Poly(dR) · poly(dY) and reverses the order of melting: methylation (and also bromination) gives the homopolymer pair a higher melting temperature than the alternating copolymer. Methylation also invariably reduces the buoyant density of the synthetic DNAs in neutral and alkaline CsCl, but the decrement is not constant. Methylation of poly(dI-dC) also recudes its buoyant density in neutral and alkaline Cs 2SO 4. Methylation of poly(dG-dC) increases its buoyant density in neutral Cs 2SO 4 and reduces it in alkaline Cs 2SO 4.