Russian researchers find new way for DNA repair. Lead researcher says discovery has opened up new perspective for researchers in terms of DNA damage and repair, but it will take time to develop new drugs and neurological treatments.

DNA Repair

A team of researchers, led by Professor Vasily M. Studitsky from the Lomonosov Moscow State University, has discovered a previously unknown mechanism by which DNA repairs itself. These findings, published in AAAS’ first open access online-only journal Science Advances, could help establish new perspectives for treating and preventing neurodegenerative disorders.

Understanding Structure And Susceptibility To Damage

Deoxyribonucleic acid (DNA) is chemically unstable. This feature causes various kinds of lesions to form in its structure, leading to mutations and abnormalities. Hence, the need for a mechanism that identifies and regulates DNA damage, signaling and repair is significantly required by our body.

Lead researcher Vasily M. Studitsky, who is also the head of the Laboratory of Regulation of Transcription and Replication at the Biological Faculty of the Lomonosov Moscow State University, explained that in higher organisms, DNA is bound with proteins called histones to form a complex structure known collectively as the nucleosome. This formation resembles a ‘beaded necklace’. Approximately 200 base pairs make up one nucleosome – eight histone proteins around which double helix of DNA is wound, forming supercoiled loops. The portion of the helix that interacts with the histones is hidden.

The entire two meter-long genome is compactly packaged as described by Studitsky, so much so as to fit inside a microscopic nucleus. However, there are specific areas from which genetic information is read, and this compactness makes it difficult for repair enzymes to access these areas. In case of any damage left unrepaired, severe genetic mutations and cell death can occur.

Role Of RNA Polymerase

The research team focused on the mechanism that detects lesions and breaks in single-stranded DNA – regions where the association between histones and nucleotides in a single strand is lost. A lot is already known about the mechanisms of transcription (formation of complementary single-stranded mRNA from a single strand of DNA), translation (formation of protein from the mRNA template) and DNA replication. It is known that DNA must unwound and temporarily dissociate with histones in order to form mRNA and daughter DNA strands.

During transcription, the enzyme RNA polymerase ‘rides’ on a single DNA strand, stopping if it comes across a lesion or a break. This enzyme acts as a ‘proof-reader’, initiating a cascade of reactions that trigger repair enzymes to correct the damage in that particular strand only.

Research Hypothesis And Experimentation

“We have shown, not yet in the cell, but in vitro, that the repair of breaks in the other DNA chain, which is “hidden” in the nucleosome, is still possible,” Studitsky claimed. The research team hypothesized that this might be possible due to the formation of unique DNA loops in the nucleosome. These loops form in regions where DNA coils back on nucleosomes along with polymerase. The latter can then crawl along these loops just as it would on histone-free DNA strands, and wherever a break is encountered, it initiates a cascade of repair enzymes.

To test their hypothesis, researchers inserted ‘special sites’ into precise locations on DNA in vitro – sites where single-stranded breaks could be introduced via enzymes. They then studied the effect of these breaks on the progress of RNA ploymearse. It was seen that when the break was present in one strand, the enzyme stopped only in nucleosomes and not in the histone-free DNA of the other strand. Surprisingly, the enzyme stopped right after the break and not before it.

“It was difficult enough to understand the mechanism that allows it to notice the damage at the “back” of RNA polymerase, as if it had “eyes on the back of the head”,” commented the lead researcher.

Analysis And Conclusion

A comprehensive study of the breaks in various positions revealed that the stopping of RNA polymerase was caused by the introduced loops, which blocked the movement of the enzyme.

“We have shown that the formation of loops, which stop the polymerase, depends on its contacts with histones. If you make them more robust, it will increase the efficiency of the formation of loops and the probability of repair, which in turn will reduce the risk of disease. If these contacts are destabilized, then by using special methods of drug delivery you can program the death of the affected cells,” Studitsky concluded, adding that this discovery has opened up a new perspective for researchers in terms of DNA damage and repair, however developing new drugs and neurological treatments will take time.