Official stable downloadable version of sci-biology/primer3 is 2.3.4. The ebuild of version 2.3.1 can be used without changes as far as I see, compiled fine on my amd64 machine.
+*primer3-2.3.4 (12 Dec 2012) + + 12 Dec 2012; Justin Lecher <jlec@gentoo.org> -primer3-1.1.4-r2.ebuild, + +primer3-2.3.4.ebuild, +files/primer3-2.3.4-buildsystem.patch: + Version Bump, #446982; cleaned old +