Divalent ion-induced switch in dna cleavage of kpni endonuclease probed through surface-enhanced raman spectroscopy

Nagaraja, V and Narayana, C and Aggarwal, S and Mondal, S and Siddhanta, S and Bharat, E and Nagamalleswari, E (2021) Divalent ion-induced switch in dna cleavage of kpni endonuclease probed through surface-enhanced raman spectroscopy. In: Journal of Physical Chemistry B, 125 (9). pp. 2241-2250.

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Abstract

We demonstrate the remarkable ability of surfaceenhanced Raman spectroscopy (SERS) to track the allosteric changes in restriction endonuclease KpnI (R.KpnI) caused by metal ions. R.KpnI binds and promiscuously cleaves DNA upon activation by Mg2+ ions. However, the divalent ion Ca2+ induces high fidelity cleavage, which can be overcome by higher concentrations of Mg2+ ions. In the absence of any 3D crystal structure, for the first time, we have elucidated the structural underpinnings of such a differential effect of divalent ions on the endonuclease activity. A combined SERS and molecular dynamics (MD) approach showed that Ca2+ ion activates an enzymatic switch in the active site, which is responsible for the high fidelity activity of the enzyme. Thus, SERS in combination with MD simulations provides a powerful tool for probing the link between the structure and activity of enzyme molecules that play vital roles in DNA transactions. © 2021 American Chemical Society.

Item Type:	Journal Article
Publication:	Journal of Physical Chemistry B
Publisher:	American Chemical Society
Additional Information:	The copyright for this article belongs to American Chemical Society.
Keywords:	Bioinformatics; Crystal structure; DNA; Enzyme activity; Light transmission; Metal ions; Metals; Molecular dynamics, Differential effect; Divalent ions; Endonuclease activities; High-fidelity; MD simulation; Restriction endonucleases; Structure and activities; Surface enhanced Raman spectroscopy, Raman spectroscopy, divalent cation; GGTACC-specific type II deoxyribonucleases; ion; type II site specific deoxyribonuclease, DNA cleavage; genetics; Raman spectrometry, Cations, Divalent; Deoxyribonucleases, Type II Site-Specific; DNA Cleavage; Ions; Spectrum Analysis, Raman
Department/Centre:	Division of Biological Sciences > Microbiology & Cell Biology
Date Deposited:	08 Mar 2023 12:48
Last Modified:	08 Mar 2023 12:48
URI:	https://eprints.iisc.ac.in/id/eprint/80852

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