Measurement of anomalously high hydration of (dA)_n · (dT)_n double helices in dilute solution

Abstract

DIFFERENT DNA sequences have different physical properties, which seem to be important for their biological function^1-3. In particular, (dA)_n · (dT)_n has many unusual features^1,4, which include resistance to conformational changes in a variable chemical environment⁵, an unusual thermodynamics of interaction with ligands⁶, and the inability to reassociate into nucleosomes⁷. Short A · T base-pair runs also play a critical role in DNA bending⁸. It is believed that hydration of DNA is an important factor in determining the physical chemical and biological properties of different regions of DNA¹. Until now, however, it has not been possible to study the details of the hydration of DNA in dilute solution with sufficient sensitivity and precision. Moreover, it was not known if different base sequences differ in the extent of their hydration. Indirect evidence that (d A)_n · (dT)_n can be hydrated to a greater extent than other DNA sequences may be inferred from a recent study of the binding of drugs to polynucleotides⁶. Here we used a novel high-precision technique measuring ultrasonic velocity⁹ to obtain direct estimates of the extent of hydration of various oligo- and polynucleotides in dilute solution. We report that different DNA sequences differ in their hydration, and that (dA)_n · (dT)_n in particular has an anomalously high level of hydration.