1. Qubits for transcription factors and other regulators
Genetics is consistent with the hypothesis that genes correspond to those tqc moduli whose outputs determine whether genes are expressed or not. The naive first guess would be that the value of single qubit determines whether the gene is expressed or not. Next guess replaces " is " with " can be".
Indeed, gene expression involves promoters, enhancers and silencers (see this). Promoters are portions of the genome near genes and recognized by proteins known as transcription factors. Transcription factors bind to the promoter and recruit RNA polymerase, an enzyme that synthesizes RNA. In prokaryotes RNA polymerase itself acts as the transcription factor. For eukaryotes situation is more complex: at least seven transcription factors are involved with the recruitment of the RNA polymerase II catalyzing the transcription of the messenger RNA. There are also transcription factors for transcription factors and transcription factor for the transcription factor itself.
The implication is that several qubits must have value "Yes" for the actual expression to occur since several transcription factors are involved with the expression of the gene in general. In the simplest situation this would mean that the computation halts to a measurement of single qubit for subset of genes including at least those coding for transcription factors and other regulators of gene expression.
2. Intron-exon qubit
Genes would have very many final states since each nucleotide is expected to correspond to at least single qubit. Without further measurements that state of nucleotides would remain highly entangled for each gene. Also these other qubits are expected to become increasingly important during evolution.
For instance, eukaryotic gene expression involves a transcription of RNA and splicing out of pieces of RNA which are not translated to amino-acids (introns). Also the notion of gene is known to become increasingly dynamical during the evolution of eukaryotes so that the expressive power of genome increases. A single qubit associated with each codon telling whether it is spliced out or not would allow maximal flexibility. Tqc would define what genes are and the expressive power of genes would be due to the evolution of tqc programs: very much like in the case of ordinary computers. Stopping sign codon and starting codon would automatically tell where the gene begins and ends if the corresponding qubit is "Yes". In this picture the old fashioned static genes of prokaryotes without splicings would correspond to tqc programs for which the portions of genome with a given value of splicing qubit are connected.
3. What about braids between DNA, RNA, tRNA and aminoacids
This simplified picture might have created the impression that aminoacids are quantum outsiders obeying classical bio-chemistry. For instance, transcription factors would in this picture end up to the promoter by a random process and "Print" would only increase the density of the transcription factor. If DNA is able to perform tqc, it would however seem very strange if it would be happy with this rather dull realization of other central functions of the genetic apparatus.
One can indeed consider besides dark braids connecting DNA and its conjugate - crucial for the success of replication - also braids connecting DNA to mRNA and other forms of RNA, mRNA to tRNA, and tRNA to aminoacids. These braids would provide the topological realization of the genetic code and would increase dramatically the precision and effectiveness of the transcription and translation if these processes correspond to quantum transitions at the level of dark matter leading more or less deterministically to the desired outcome at the level of visible matter be it formation of DNA doublet strand, of DNA-mRNA association, of mRNA-tRNA association or tRNA-aminoacid association.
For instance, a temporary reduction of the value of Planck constant for these braids would contract these to such a small size that these associations would result with a high probability. The increase of Planck constant for braids could in turn induce the transfer of mRNA from the nucleus, the opening of DNA double strand during transcription and mitosis.
Also DNA-aminoacid braids might be possible in some special cases. The braiding between regions of DNA at which proteins bind could be a completely general phenomenon. In particular, the promoter region of gene could be connected by braids to the transcription factors of the gene and the halting of tqc computation to printing command could induce the reduction of Planck constant for these braids inducing the binding of the transcription factor binds to the promoter region. In a similar manner, the region of DNA at which RNA polymerase binds could be connected by braid strands to the RNA polymerase.
For details see the new chapter DNA as Topological Quantum Computer of "Genes and Memes".