DNA Gene's Basic Structure as a Nonperturbative Circuit Quantum Electrodynamics: Is RNA Polymerase II the Quantum Bus of Transcription?

Previously, we described that Adenine, Thymine, Cytosine, and Guanine nucleobases were superconductors in a quantum superposition of phases on each side of the central hydrogen bond acting as a Josephson Junction. Genomic DNA has two strands wrapped helically around one another, but during transcription, they are separated by the RNA polymerase II to form a molecular condensate called the transcription bubble. Successive steps involve the bubble translocation along the gene body. This work aims to modulate DNA as a combination of n-nonperturbative circuits quantum electrodynamics with nine Radio-Frequency Superconducting Quantum Interference Devices (SQUIDs) inside. A bus can be coupled capacitively to a single-mode microwave resonator. The cavity mode and the bus can mediate long-range, fast interaction between neighboring and distant DNA SQUID qubits. RNA polymerase II produces decoherence during transcription. This enzyme is a multifunctional biomolecular machine working like an artificially engineered device. Phosphorylation catalyzed by protein kinases constitutes the driving force. The coupling between n-phosphorylation pulses and any particular SQUID qubit can be obtained selectively via frequency matching.