| Abstract: | Procedures are developed which make a first neighbor frequency analysis possible from a CD spectrum of homopyrimidine: homopurine DNA's. The contribution to the CD spectrum from the various first neighbor frequencies present in homopyrimidine: homopurine-type DNA's has been determined, and hence the CD spectrum for any DNA of this type with known first neighbor frequencies can easily be calculated. An identical analysis is presented for the determination of extinction coefficients. It is further shown that unlike the more usual heteropurine–pyrimidine DNA's a random sequence does not lead to a simplified formalism. Finally, it is concluded that the homopyrimidine: homopurine DNA's have a structure that is different from that of the more usual heterobase DNA's. A procedure capable of determining first neighbor frequencies from a CD spectrum for heterobase and/or homopurine: homopyrimidine DNA's is described. This procedure is used to determine that there is only minimal interference between these two types of DNA in the first neighbor analysis. |
