The newer Cisco switches only support
dot1Q encapsulation. You do not need to do anything because it is already configured that way. Older Cisco switches could support
switchport trunk encapsulation isl or
switchport trunk encapsulation dot1Q, but newer switches do not need the
switchport trunk encapsulation command because they only support the 802.1Q trunking.
You should really be moving away from VTP and DTP. The current best practices are to set VTP to transparent mode and manually configure VLANs allowed across the trunk. VTP can inadvertently crash your whole network. Another best practice is to only allow a VLAN to be on a single access switch. This greatly reduces the chances of a broadcast storm. An access switch can have multiple VLANs, but those VLANs on that access switch should not extend to any other access switches. Modern networking is layer-3, and it is very rare to need devices on the same layer-2 network.
DTP is a vulnerable protocol that can be misused by end-users. If you have a trunk, you should nail it up and use the
switchport nonegotiate command on the interface to disable DTP. You do not want the trunk to switch to access mode if someone plugs in a non-trunking device, nor do you want an end-user to be able to connect a device running DTP and get access to all your VLANs.