Soumya Shraddhya Paul, Amity University, Noida
The DNA structure, twist, and properties depend on the external stimuli. The common structure of the DNA is helical, and it tends to maintain this helicity in order to remain in its stable form. But through recent studies scientists are trying to show how helicity can be influenced or changed by the external ion concentration. Conformational changes that happen in the DNA are very vital for the biological processes to take place. It has been noted due to external factors like ion concentration and temperature, DNA bend, twists and stretches bringing a global change in its three-dimensional structure. With thorough study, if we can characterize these changes that happen and how exactly they happen, it can utilize this in various Biotechnology applications. Therefore, to understand these changes scientists decided to study more about DNA in various ionic concentrations.
The Study:
As we know that salt concentrations affect the DNA structure, as well as cations also work to provide screening to the negatively charged phosphate groups present on the DNA. It was noticed that since cations are attached to the backbone of the DNA it can affect stability. Hence ion type was also taken into consideration. In this study, the main focus was the salt concentration, valency, ions concentration and ions type. To perform this study and to fill all the gaps Magnetic tweezers were used. Through this instrument, one can determine how salt concentration can affect the DNA twist. Through this instrument global conformational changes can be easily observed, as this uses precisely calculated magnetic forces to visualize the structure or changes. For this experiment, 7.9-kbp DNA- a construct- is prepared.
Results from the study:
Through this study, it was found that the DNA twist increases with an increase in ion concentration. When it comes to salt concentration, the type of cation present affects the DNA twist. Metal ions like Li+ or Ca2+ (high charge density) are more efficient in overwinding and twisting. Whereas, metal ions with intermediate charge density like Na+ or Ba2+ reduces twisting and winding. An accurate force field is needed for the prediction of twists due to divalent cations.
Significance of the study:
Through this study, we managed to resolve how alkaline earth metal and alkali influence the helical twist of the DNA using a combination of all-atom molecular dynamics and simulations of single-molecule magnetic tweezers experiments. Hofmeister series was used to find the activity at 100 mM, DNA twist increases as: Ba2+ < Na+ < K+ < Rb+ < Li+ ≈ Cs+ < Sr2+ < Mg2+ < Ca2+. In the end, through this study, we can use these results to find how DNA can be used in various fields under different conditions.
Some relevant Fun Facts:
- Any nucleic acid (DNA or RNA) is negatively charged due to the phosphate group attached to it.
- DNA is long, it can stretch through the Earth and the Sun 600 times.
- The differences that we see in each other are due to the 0.1% uniqueness that our DNA has.
- The human genome has 3 billion base pairs of DNA.
- Due to our evolutionary history DNA can link us to different places we have never been before.
Reference:
- Cruz-León, S., Vanderlinden, W., Müller, P., Forster, T., Staudt, G., Lin, Y.-Y., Lipfert, J., & Schwierz, N. (2021). Twisting DNA by salt [Preprint]. Biophysics. https://doi.org/10.1101/2021.07.14.452306
Author info:
Soumya Shraddhya Paul is an undergrad biotechnology student who worked in building 3D prosthetics in Base Hospital Delhi Cantt, and holds a key interest in nutraceuticals and enzymology.
Publications:
- https://bioxone.in/news/worldnews/understanding-b-cell-genomics-to-fight-against-covid-19/
- https://bioxone.in/news/worldnews/the-current-ebola-epidemic-comes-to-an-end/
- https://bioxone.in/news/worldnews/epigenetic-changes-can-cause-permanent-changes-to-offsprings/
- https://bioxone.in/news/worldnews/crispr-act-3-0-a-revolution-in-plant-gene-technology/
Social Media Info: www.linkedin.com/in/soumya-shraddhya-paul-858229203
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