Conformational Isomerizations of the Poly(dA-dT) and Poly(amino²dA-dT) Duplexes Involving the Unusual X-DNA Double Helix: A Fourth Derivative Spectrophotometric Study

Abstract

Fourth derivative spectrophotometry has been applied to monitor conformational isomerizations of polynucleotides for the first time. The transitions studied have been the B-A and A-X isomerizations of poly(dA-dT) and the B-X one of poly(amino2dA-dT). Parameters obtained from the fourth derivative spectra have been used to follow these conformational changes. The A form of poly(dA-dT) has been characterized by a new fourth derivative peak at 293.0 nm which can be associated to interstrand adenine-adenine interactions. Furthermore, some of the fourth derivative peaks in the long wavelength region (270-310 nm) can be related to stacking interactions present in the polynucleotide double helices. The tentative assignment of these peaks, particularly that at 299.0 nm in the derivative spectra of poly(amino2dA-dT), to n----pi electronic transitions is discussed.

An A-form of poly(amino2dA-dT).cntdot.poly(amino2dA-dT) induced by polyamines

“…The addition of 30 µ spermine to the polynucleotide solution induces a conformational change which produces slight hyperchromism in the 290-310-nm region and hypochromism at the absorption maximum located at 262 nm in the absorption spectrum (Figure 1A). Fourth-derivative spectra undergo small but significant changes very similar to those reported in the previous study, where the conformational change was induced by Mg2+ (Garriga et al, 1990). The main changes in the derivative spectrum are the change in the ratio of the two long-wavelength derivative peaks at 287.0 and 299.0 nm, respectively, and the redshift of the 299.0-nm peak to 300.0 nm (Figure IB).…”

“…The binding of spermidine and spermine to poly(amino2-dA-dT)-poly(amino2dA-dT) produces significant changes in the UV absorption and fourth-derivative spectra. The absorption and fourth-derivative spectra of the polynucleotide in the potassium buffer in the absence of polyamines (Figure 1) are the same as previously reported (Garriga et al, 1990).…”

“…The presence of this kind of cross-strand hydrogen bonds would provide a possible mechanism by which spermine elevates the Tm of the DNA duplex. The Tm of poly(amino2-dA-dT)-poly(amino2dA-dT) in phosphate buffer is 47 °C (Garriga et al, 1990). In the presence of spermine and spermidine we have obtained Tm values significantly higher than that obtained when the transition was induced with Mg2+ (Garriga et al, 1990).…”

“…Later, NMR studies were interpreted as reflecting an A conformation (Borah et al, 1985(Borah et al, , 1986. However, this interpretation was questioned by other authors who claimed that, in these conditions, the polynucleotide adopted the novel type of helix called X-DNA (Vorlickova et al, 1988a;Garriga et al, 1990), which could be stabilized with submillimolar concentrations of Mg2+. Nevertheless, + This work was supported in part by Grant PB89-0301 from the Dirección General de Investigación Científica y Técnica.…”

“…We have used absorption and fourth-derivative UV (Garriga et al, 1990), FTIR, and CD spectroscopies to study the effect of spermine and spermidine on the conformational properties of poly(amino2dA-dT)*poly(amino2dA-dT). At low ionic strength and neutral pH a conformational transition is induced with 30 µ spermine.…”