Are molecular machines encoded in the DNA?
Yes.

The "molecular machines" you are referring to are particular proteins.

The specific one you are referring to, kinesin, is involved in movement along microtubules, part of the structure of the skeleton of a cell, but other proteins act as their own kind of machine to do their own tasks: sometimes catalyzing a biochemical reaction, or responding to a type of stimulus, or forming a shape or structure, or combinations of all of the above.

Protein-coding sections of DNA are well-studied, and there are substantial databases of known proteins. If you go to wikipedia you will see a whole list of different kinesins, if you click on one, for example, KIF1A, on the right hand side it shows you it is found on chromosome 2 in a human, starting at 240,713,764 base pairs and ending at 240,820,308 base pairs. Information for the mouse is also located there.

Proteins in DNA-based life are all synthesized by first producing an RNA transcript from the DNA, which is effectively an RNA copy of a short stretch of DNA, which is then translated into protein. Other RNA molecules are involved in this process, too, as the rRNA part of the ribosome (sort of a 'protein factory') as well as tRNA which carries the amino acid components of proteins as they are being built. Transcription and translation are central to understanding biology at the molecular and cellular level.

Not only can all proteins, from kinesin to collagen, evolve, they all have evolved through natural selection and other evolutionary mechanisms, and they continue to evolve today in all living organisms. Without evolution, no biology would exist. RNA-based biology (today, mostly some of the viruses) is also subject to evolutionary mechanisms, so that isn't something unique to DNA, but rather to heredity and biology in general.