Vacuum UV CD spectra of homopolymer duplexes and triplexes containing A.T or A.U base pairs.

Vacuum UV circular dichroism (CD) spectra were measured down to 174 nm for five homopolymers, five duplexes, and four triplexes containing adenine, uracil, and thymine. Near 190 nm, the CD bands of polyd(A)] and polyr(A)] were larger than the CD bands of the polypyrimidines, polyd(T)], polyd(U)], and polyr(U)]. Little change was observed in the 190 nm region upon formation of the duplexes (polyd(A).d(T)], polyd(A).d(U)], polyr(A).d(T)], polyr(A).d(U)], and polyr(A).r(U)]) or upon formation of two of the triplexes (polyd(T).d(A).d(T)] and polyd(U).d(A).d(U)]). This showed that the purine strand had the same or a similar structure in these duplexes and triplexes as when free in solution. Both A.U and A.T base pairing induced positive bands at 177 and 202 nm. For three triplexes containing polyd(A)], the formation of a triplex from a duplex and a free pyrimidine strand induced a negative band centered between 210 and 215 nm. The induction of a band between 210 and 215 nm indicated that these triplexes had aspects of the A conformation.