DNA Damage-Repair Mechanisms

and π-electron delocalization for the neutral and redox forms of purine when proceeding from the gas phase (DFT) to water (PCM). *J. Mol. Model.*, 2013, 19,

*DNA - Damages and Repair Mechanisms*

[91] Brovarets', O.O., Hovorun, D.M. A novel conception for spontaneous transversions caused by homopyrimidine DNA mismatches: A QM/ QTAIM highlight. *Phys. Chem. Chem.*

[92] Brovarets', O.O., Hovorun, D.M. Prototropic tautomerism and basic molecular principles of hypoxanthine mutagenicity: An exhaustive quantumchemical analysis. J. Biomol. Struct.

*Phys.*, 2015, 17, 21381–21388.

Dynam., 2013, 31, 913–936.

[93] Berman, H.M., Olson, W.K., Beveridge, D.L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.H., Srinivasan, A.R., Schneider, B. The Nucleic Acid Database: A comprehensive relational

database of three-dimensional

1992, 63, 751–759.

Res., 2014, 42, D114–22.

structures of nucleic acids. Biophys. J.,

[94] Narayanan, B.C., Westbrook, J., Ghosh, S., Petrov, A.I., Sweeney, B., Zirbel, C.L., Leontis, N.B., Berman, H. M. The Nucleic Acid Database: New features and capabilities. Nucleic Acids

[85] Brovarets', O.O., Hovorun, D.M. Renaissance of the tautomeric hypothesis of the spontaneous point mutations in DNA: New ideas and computational approaches.

Mitochondrial DNA - New Insights / Ed. by Herve Seligmann, London, United Kingdom: IntechOpen, 2018. ISBN 978–

[86] Brovarets', O.O., Hovorun, D.M. Physicochemical mechanism of the wobble DNA base pairs Gua�Thy and Ade�Cyt transition into the mismatched base pairs Gua\*�Thy and Ade�Cyt\* formed by the mutagenic tautomers. *Ukr. Bioorg. Acta*, 2009, 8, 12–18.

[87] Brovarets', O.O., Hovorun, D.M. Tautomeric transition between wobble А�С DNA base mispair and Watson-

[88] Brovarets', O.O., Hovorun, D.M. How many tautomerisation pathways connect Watson-Crick-like G\*�T DNA base mispair and wobble mismatches? *J. Biomol. Struct. Dynam.*, 2015, 33, 2297–

[89] Brovarets', O.O., Hovorun, D.M. Wobble\$Watson-Crick tautomeric transitions in the homo-purine DNA mismatches: A key to the intimate mechanisms of the spontaneous

transversions. *J. Biomol. Struct. Dynam.*,

[90] Brovarets', O.O., Hovorun, D.M. Novel physico-chemical mechanism of the mutagenic tautomerisation of the Watson–Crick-like A�G and C�T DNA base mispairs: A quantum-chemical picture. *RSC Adv.*, 2015, 5, 66318–66333.

2015, 33, 2710–2715.

Crick-like A�C\* mismatch: Microstructural mechanism and biological significance. *Phys. Chem. Chem. Phys.*, 2015, 17, 15103–15110.

2315.

**18**

3947–3960.

953–51-6167-7.

**21**

**Chapter 2**

World

**Abstract**

organisms.

**1. Introduction**

polymerase to replicate RNA [4].

Origin of DNA Repair in the RNA

The early history of life on Earth likely included a stage in which life existed as self-replicating protocells with single-stranded RNA (ssRNA) genomes. In this RNA world, genome damage from a variety of sources (spontaneous hydrolysis, UV, etc.) would have been a problem for survival. Selection pressure for dealing with genome damage would have led to adaptive strategies for mitigating the damage. In today's world, RNA viruses with ssRNA genomes are common, and these viruses similarly need to cope with genome damage. Thus ssRNA viruses can serve as models for understanding the early evolution of genome repair. As the ssRNA protocells in the early RNA world evolved, the RNA genome likely gave rise, through a series of evolutionary stages, to the double-stranded DNA (dsDNA) genome. In ssRNA to dsDNA evolution, genome repair processes also likely evolved to accommodate this transition. Some of the basic features of ssRNA genome repair appear to have been retained in descendants with dsDNA genomes. In particular, a type of strandswitching recombination occurs when ssRNA replication is blocked by a damage in the template strand. Elements of this process appear to have a central role in recombinational repair processes during meiosis and mitosis of descendant dsDNA

**Keywords:** RNA world, RNA virus, recombination repair, copy-choice, synthesisdependent strand annealing (SDSA), DNA repair, archaea, genome damage,

Protocellular organisms may have come into existence 2.5 to 3.5 billion years ago [1, 2]. Woese [3] proposed that the genomes of the early protocellular forms of life were individual strands of RNA rather than DNA, and that these RNA strands were present as separate genome segments, rather than being linked together end-to-end as is generally the case for genes in DNA. The idea that, during an early period in the evolution of life, genetic information was stored and transmitted solely by RNA molecules has come to be known as the "RNA world hypothesis." This hypothesis is currently being tested by many investigators. Of particular significance, Horning and Joyce [4] have demonstrated that the replication of genetic information and its conversion into functional molecules can be accomplished with RNA in the complete absence of protein. RNA molecules with catalytic activity are called ribozymes. An RNA ribozyme developed by Horning and Joyce can act as an RNA

strand-switching, self-replication, single-stranded RNA

*Harris Bernstein and Carol Bernstein*
