Investigation of the Stability of D5SIC-DNAM-Incorporated DNA duplex in Taq Polymerase Binary system: A Systematic Classical MD Approach

25 October 2023, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

DNA polymerases are fundamental enzymes that play a crucial role in processing DNA with high fidelity and accuracy ensuring the faithful transmission of genetic information. The recognition of unnatural base pairs (UBPs) by polymerases, enabling their replication, represents a significant and groundbreaking discovery with profound implications for genetic expansion. Romesberg et al. examined the impact of DNA containing 2,6-dimethyl-2H-isoquiniline-1-thione: D5SIC (DS) and 2-methoxy-3-methylnaphthalene: DNAM (DN) UBPs bound to T. aquaticus DNA polymerase (Taq) through crystal structure analysis. Here, we have used polarizable and nonpolarizable classical molecular dynamics (MD) simulations to investigate the structural aspects and stability of Taq in complex with a DNA duplex including a DS-DN pair in the terminal templating and priming positions. Our results suggest that the flexibility of UBP-incorporated DNA in the terminal position is arrested by the polymerase, thus preventing fraying and mispairing. Our investigation also reveals that the UBP remains in an intercalated conformation inside the active site, exhibiting two distinct orientations in agreement with experimental findings. Our analysis pinpoints particular residues responsible for favorable interactions with the UBP, with some relying on van der Waals interactions while others on Coulombic forces.

Keywords

Taq polymerase
Unnatural Base pair
non-Watson-Crick-Franklin Base Pair
Classical MD simulations
AMBER Forcefields
Polarizable Forcefields (AMOEBA)

Supplementary materials

Title
Description
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MD and EDA data
Description
RMSD, delRMSF, geometrical parameters and EDA data of the systems
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Coordinates and Parameters
Description
Coordinates and parameters of all the conformers used in AMBER and AMOEBA mediated simulations
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Normal mode analysis
Description
Most contributing normal modes of all the conformers
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