I don't know much, if anything, about molecular biology. I watched the "inner life of the cell" on Youtube which triggered my curiosity about how these molecular machines came to be. My simple understanding is that if these molecular machines are encoded in the DNA, then they are "evolve-able" by mechanisms such as natural selection. Is that case? And if so, can we identify which part in the DNA sequence have the encoding for these molecular machine such as the Kinesin? Do molecular motor machines get synthesized by the RNA as well?
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.
Yes, it's fair to say molecular machines are encoded in the DNA. As you say, kinesin is a molecular machine - a motor protein that moves molecules along microtubules, which are also proteins. Protein enzymes are one of the most common molecular machines in cells - they build and break down molecules, among other things. Membrane channels are proteins, too, and they could be called molecular machines - I'm picturing a drawbridge that lets tall ships pass when it's open and not when it's closed, though channels are more like holes in the cell membrane than like drawbridges.
The sequence of bases [A, G, C and T] in the DNA tells the cell what protein to make. And, yes, mutations occur in the DNA sequences, which results in mutant proteins - or, variant proteins, because there are often several versions of a protein that work fine.
Wikipedia's article - https://en.wikipedia.org/wiki/Kinesin - tells about the family of kinesis proteins, which are coded for by a corresponding family of genes in DNA.
Yes - RNA is important in synthesizing molecular machines. It carries copies of the DNA codes for different proteins in our genes. It has 3 of the same bases ['letters'] as DNA - A, G, and C, but instead of T it has U, which goes in the RNA sequence wherever T would be in DNA. The RNA copies of the genes go to the ribosome, an amazing molecular factory that takes the information in the RNA copies of the genes and uses it to make proteins, which have amino acids instead of the 4 bases of DNA and RNA.