Please consider to setsockopt(IPV6_USE_MIN_MTU) to IPv6 UDP socket as per draft-andrews-dnsext-udp-fragmentation. Almost all DNS servers (BIND, Unbound, NSD, ... ) set this option.

PMTUD on DNS/UDP is actually harmful because it makes many timeouts and resends if there is small MTU link (e.g. v6 over v4 tunnel) between server and clients.