Approximative He Hamiltonian in descriptive multidimensional scaling statistics of RNA contained information with application to SARS-CoV-2 Spike mRNA and 7SLRNA, RN7SL2 and RN7SL3

Abstract

In the present in silico viral genetics study, a mathematical method was developed for the comparison of RNA sequences. The mathematical method used was to explore component similarities and patch them together with a modern geometric statistical projection method called multidimensional scaling (MDS). The comparison looked into similarities between ≈300 nucleotides (NT) of 7SL RNA and size ≈300 NT subequences of SARS-CoV-2 Spike mRNA. RN7SL2 and RN7SL3 were also compared with SARS-CoV-2 Spike mRNA. In the component comparison, use was made of a He Hamiltonian model for the approximation of the density distribution of the outer two electrons. This was considered a basic ingredient of similarity. Improvements can be implemented later on. With MDS it is possible to blend theoretical with experimentally obtained characteristics of components. Furthermore, complementarity was employed to derive a numerical representation of the formation of RNA knots. With the use of crystallographic and electron microscopic coordinate data sets, we aimed to study a more geometric structure of comparing RNA with RNA and RNA with SRP9/14 protein. We found reason to believe that sub-sequences of the S2 SARS-CoV-2 Spike mRNA around position NT = 3620, can possibly behave similar to 7SLRNA. The latter can form “parasitic” Alu DNA. The hypothesis is drawn that under conditions where e.g. broken DNA occurs and RNA dependent DNA polymerase is present these RNA sub-sequences can, because of similar affinity to SRP9/14, be transformed into transposons and become a DNA parasite.