The interaction between bases on different strands of DNA molecules depends somewhat on the identities of neighboring bases. For example, the melting temperature of an oligonucleotide with the sequence GGGGGAAAAA is different than that of GAGAGAGAGA even though both contain the exact same number of G-C and A-T base pairs. (The melting temperature is the temperature at which half of the base pairs are broken between the oligonucleotide and its complementary sequence). Therefore, instead of treating a DNA helix as a string of interactions between base pairs, many thermodynamic algorithms that calculate DNA melting temperatures use the nearest-neighbor model, which treats a DNA helix as a string of interactions between ‘neighboring’ base pairs. Thus the sequence GGCTGC consists of the nearest neighbors GG, GC, CT, TG and GC. The nearest-neighbor frequencies of a certain double stranded DNA molecule are: AG, 0.15; GT, 0.03; CC, 0.08, and TT, 0.10. In each case the nearest neighbor is written in the 5′?3′ direction. What would be the nearest neighbor frequencies of CT, AC, GG and AA?
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