Is Quantum Information Approach Suitable For Modelling Genetic Code?

• Applicant: Professorin Dr. Elena Fimmel
• Subject Area: Electronic Semiconductors, Components and Circuits, Integrated Systems, Sensor Technology, Theoretical Electrical Engineering ; Bioinformatics and Theoretical Biology
• Term: from 2020 to 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 453234620

• Final Report Year: 2022

Final Report Abstract

In the course of the project, some rules of the stochastic organisation of genomes found in recent years were empirically verified and supplemented by new observations. The new findings could be obtained in particular as a result of quantum-informatic modelling of the genetic data. On this basis, considerations about a form of representation of genetic data that respects the rules of the stochastic organisation of genomes were deepened. One result of these considerations is the concept of the general method of vector-metric identification of genes. The main idea is the assignment of a unique genomic vector-metric ID to each ’n-plet’ (e.g. codon) within a certain community of ’n-plets’ (e.g. within a chromosome). Complementary to a form of representation that respects the stochastic organisation of genomes, a methodology of noise-resistant compression of genetic information was considered, taking into account the universal rules of the stochastic organisation of genomes. The idea has as its starting point the recent decline in the cost and time of sequencing and assembling complete genomes, which has led to an increased need for data storage. As a result, the importance of efficient strategies for compressing acquired biological data grew. A suitable approach was found to be the so-called arithmetic coding, which is already known as a compression method for biological data. However, until now, its implementation did not take into account the specific rules of the stochastic organisation of genomes and compressed the DNA sequences like an arbitrary text, which leads to severe limitations in its application. Another important issue that has been researched during the project is the application of the errordetecting genetic codes to the design of synthetic proteins modelled as the so-called Hecht-proteins. It is expected that this will have the potential to reduce costs and increase the robustness of the proteins. In this context, the nucleotide environment of the stop codons UAG, UGA and UAA was investigated in particular. Among other things, the question was pursued as to why only UAA is a ’correct’ stop codon, while UAG and UGA can also be interpreted in some organisms under special conditions as each coding for an amino acid.

Publications

• Computational Analysis of Genetic Code Variations Optimized for the Robustness against Point Mutations with Wobble-like Effects. Life, 11(12), 1338.
  Fimmel, Elena; Gumbel, Markus; Starman, Martin & Strüngmann, Lutz