This question is, in my opinion, based on an incorrect premise but nevertheless throws up a number of points about protein folding and protein structure that can be addressed, albeit briefly.
The False Premise
“it is a generally accepted idea that protein folding is completely determined
by the sequence of amino acids”
What is ...
I don't know precisely what you mean by "analyze", which could be anything from simply "view" or "measure distances", to evaluating an energy function on a crystal structure or molecular dynamics simulation, to prediction of binding sites de novo. The tools are different for each case, though some can do several things.
For simply viewing, measuring ...
You seem to be under the impression that there are a set number mutations per cell, which is not true. The number of mutations is roughly proportional to the number of bases — this is because mutations typically happen as a result of errors during DNA replication .1 Consequently, more DNA will not protect the coding portions of the genome from mutation.
I'm not an expert but a start could be PyMOL https://pymol.org/2/
Unfortunately, you need a license to use the latest version
An earlier (free) version can be found here:https://sourceforge.net/projects/pymol/files/latest/download
A tutorial can be found here:https://pymolwiki.org/index.php/Practical_Pymol_for_Beginners
Hope that helps to start!
Transcription of DNA is ultimately controlled by "various transcription factors, small nuclear RNAs and so on" in the cell.
The molecules which make up the "various transcription factors", etc. are already present in the cell when a new transcription begins. As you note, most all of these molecules are themselves dependent on the transcription of DNA, but ...
In terms of structure: both are composed of amino acids.
A peptide is when at least two amino acid are linked together.
A protein is composed of multiple amino acids and have a secondary, tertiary and even quaternary structure.
In terms of function: larger molecules have more complex functions.
Peptides can act as a intracellular or extracellular ligands ...
In general, "apo" is used to indicate an apoenzyme — that is the protein part of an enzyme without essential cofactor(s).
This is actually defined in the Experimental section of the paper:
Cas9/Cpf1 without gRNA (ApoCas9/Cpf1)
So, in this case ApoCas9 is Cas9 endonuclease that is not bound to a guide RNA.