Infrared and Raman studies show that poly(dA).cntdot.poly(dT) and d(AAAAATTTTT)2 exhibit a heteronomous conformation in films at 75% relative humidity and a B-type conformation at high humidities and in solution

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Abstract
The decadeoxynucleotide d(AAAAATTTTT)2 in duplex form and the double-helical polynucleotide poly(dA).cntdot.poly(dT) have been studied by Raman and infrared (IR) spectroscopy under a variety of environmental conditions. The IR spectra have been taken of cast films and compared to the IR spectra of the alternating poly(dA-dT), which shows clear B-genus vibrational spectra under conditions of high (> 92%) and low (75%) relative humidity (RH). From the IR data, it is shown that d(AAAAATTTTT)2 and poly(dT) adopt a B-genus conformation in films with high water content. When the relative humidity of the film is decreased, the IR spectra reflect a gradual evolution of the geometry of both d(AAAAATTTTT)2 and poly(dA).cntdot.poly(dT) into a form intermediate between the B genus and A genus, but the IR spectrum of a pure A genus has not been obtained. In these DNAs at 75% RH, the IR bands of adenosine have the same frequencies as those found in poly(dA-dT) at 75% RH where the local furanose conformation is C3'' endo/anti, but the thymidine frequencies do not resemble those of poly(dA-dT) at 75% RH but rather those of poly(dA-dT) at high humidities. It is conluded that both poly(dA).cntdot.poly(dT) and d(AAAAATTTTT)2 adopt a fully heteronomous duplex geometry in cast films at low humidity. For studies in aqueous solution the Raman effect was employed. As a model for the heteronomous conformation in solution, the duplex poly(rA).cntdot.poly(dT) was used. Two methods were devised to estimate the amount of heteronomous conformation for d(AAAAATTTTT)2 and poly(dA).cntdot.poly(dT) in solution from the intensities of a sugar-phosphate band and an adenine band obtained by a fit of the Raman spectrum to a sum of Lorentzians bands. These measurements indicate that about 30% of the adenine residues were attached to furanose rings with the C3''-endo/anti conformation on the time scale of the Raman effect. This would mean that no more than about 15% of the furanose rings in the duplex are in this conformation. If the conformation of poly(dA).cntdot.poly(dT) is fluctuating rapidly in solution, this small amount of C3''-endo ring pucker might be difficult to detect by other techniques such as NMR.