DB<104> $a="3851 A A G G T T"
 
  DB<105> $a=~s/([ACGT]) ([ACGT])/$1$2/g
 
  DB<106> p $a
3851 AA GG TT
[download]

PS:

> The colleague who knows python only suggested a long difficult method of writing out each combination (ie 1+2, 3+4, etc.)...

This pretty much reflects the impression I have when reading in python boards... :)