A solution using regular expressions and substitution, as already shown, is probably best but just to show another way -

knoppix@Microknoppix:~$ perl -E '
> $_ = q{3851 A A G G T T};
> say;
> @e = split m{( )};
> $_ = join q{}, @e[ grep { ( $_ + 1 ) % 4 } 0 .. $#e ];
> say;'
3851 A A G G T T
3851 AA GG TT
knoppix@Microknoppix:~$
[download]

I hope this is of interest.