Question

What would be the nearest neighbor frequencies of AC, CT, AA and GG?


Q: 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. What would be the nearest neighbor frequencies of AC, CT, AA and GG? (Once again - in each case the nearest neighbor is written in the 5’→3’ direction.)

Hint: there is a special relationship between the nearest neighbor frequencies that are given and the ones that you are being asked to determine. What is that relationship and how does it help you solve the problem?

Answer 1

Another hint: Nearest neighbor frequencies are expressed as the fraction of total dinucleotide sequences contributed by a particular dinucleotide sequence

Example that may help: CGTCGG contains nearest neighbors GG, GC, CT, and TG with nearest neigbor series of GG=0.2, GC = 0.4, CT = 0.2, and TG = 0.2

Is the answer simply
AC = GT = 0.03
CT = AG = 0.15
AA = TT = 0.10
GG = CC = 0.08 ?

Or do all of the frequencies have to have a total equal to 1?