DNA repair pathway

A good recent review of plant DNA repair is Raina et al Frontiers in Genetics 22 June 2021 or here. Brief list of terminology:

• Deoxyribonucleotide = molecule composed of an aromatic base connected to a sugar which is connected to a phosphate group (base-sugar-phosphate)
• Base = one of the four aromatic heterocyclic groups of a deoxyribonucleotide: A, G, C, {Thymine|T]]
• strand = chain of nucleotides with sugar phosphate links via phosphodiester bonds(sugar-phosphate-sugar-phosphate-sugar)
• DNA = Double strand of deoxyribonucleotides kept together by base pairs and pi-pi interactions between neighboring bases in each strand
• Base pair = noncovalent inter-strand attraction between A and T or G and C of a DNA

DNA Repair in plants

Types of errors

• mismatch - where the base pairing is wrong, like A opposite another A
• alkylation - where an alkyl group is chemically added onto a base
• UV damage - where energy from UV causes chemical changes to a base
• intercalation - where a polyaromatic hydrocarbon (common in cigarette smoke) inserts between bases of DNA and sticks via hydrophobic and pi-pi interactions
• apurination - where a base falls off a nucleotide in DNA, leaving behind the sugar-phosphate backbone strand
• single strand break - where one of the strands in a DNA has a break in the sugar-phosphate backbone, leaving the rest of the DNA intact
• double strand break - where both strands in a DNA have a break in the sugar-phosphate backbone at the same position, but the DNA is kept together via pi-pi interactions between neighboring bases in each strand
• interstrand crosslink - where a chemical bond is formed between nucleotides in opposite strands
• intrastrand crosslink - where a chemical bond is formed between nucleotides in the same strand

All of these errors will change the normal function of DNA, leading to serious, often fatal damage to a cell or organism if not repaired quickly.

Repair mechanisms

1. Direct Reversal Repair
2. Mismatch Repair
3. Excision repair
4. Homologous Recombination Repair
5. Non-homologous End-Joining

Introduction

Genomic DNA is the blue print of life. This DNA is under constant attacks by various sources, and as a result, the DNA can be damaged. If the DNA is damaged for whatever reason, mutations can occur, and if the damage is not repaired in a timely manner, there can be permanent damage to the organism. For example, cancers in humans come from damaged DNA. What are the sources of DNA damage? Some happen during cell replication, however the largest source is environmental, such as UV radiation and toxins. DNA in plants experience the worst environmental attacks, as plants cannot move away from damaging UV rays or toxic substances in soils. Remarkably, plants can grow and propagate without much ill effects from such external attacks on their DNA. How is this possible? Because plants have the best DNA repair mechanisms among all life forms. The same error can be fixed by more than one path, almost guaranteeing that any damage to the DNA is repaired as quickly as possible.