Cyclic constraint on the protein-RNA/DNA interaction

The engagement of protein and ribonucleic acid (RNA)/deoxyribonucleic acid (DNA) is examined in three varied conformations of protein molecules and two different configurations of RNA/DNA, namely finite and cyclic. This analysis emphasizes density of states (DOS) and band structures by making use of a tight-binding Hamiltonian in combination with Green's function techniques. At a steady temperature and a defined quantity of building blocks in the RNA and DNA strands, the spectral diagrams show flat energy curves for both RNA and DNA molecules, showcasing characteristics akin to those found in semiconductors. The key distinctions between the cyclic configuration and the finite case lie in the peak height and the arrangement of the peaks in the DOS, as well as the shifts in band positions. The coupling of protein molecules with the RNA and DNA models yields a reduction of the energy gap in the protein-RNA system and a progression from semiconductor properties to metallic ones in the protein-DNA structure. Furthermore, the role of temperature in determining the DOS leads to changes in the peak levels and their respective positions. It is expected that the coupling of protein and RNA/DNA will directly exert a straightforward influence on the electronic attributes of RNA/DNA, which differ among diverse protein structures, thus creating opportunities for newly conducted research with significant biological implications.