DNA methylation is a biological process by which methyl groups are added to the DNA molecule. The DNA methylation profile on a promoter region of adenomatous polyposis coli (APC) gene plays a critical role in the epigenetic change that may trigger the onset of various cancers. The detection of DNA methylation on the promoter of the APC gene has become a promising candidate for early cancer diagnosis. Colorimetric sensor based on the assembly of gold nanoparticles (AuNPs)demonstrates rapid sensing and low-cost approach which can be further developed as point-of-care diagnostic tools. To gain molecular-level insights into the signature interactions between methylated DNA and AuNPs, molecular dynamics (MD) simulation was used to investigate: (i) the conformation of methylated DNA in aqueous solution; (ii) the physicochemical property of methylated DNA; (iii) physisorption of methylated DNA in the stabilization of cysteamine-capped AuNPs (Cyst/AuNPs); (iv) mechanism of DNA methylation detection <i>via</i> assemblies of Cyst/AuNPs. Our simulations illustrated different conformation of DNA with different methylation profile in the aqueous solution. The methylated DNA shows higher aggregation once compared with the unmethylated DNA. In the presence of Cys/AuNPs,  large aggregation of methylated DNA can prevent AuNPs from the agglomeration due to the steric hindrance. The backbone of oligonucleotides played a remarkable role in the adsorption of the DNA onto the gold surface. The oxygen, nitrogen, and methyl group in methylated DNA demonstrated non-covalent interaction between DNA and gold surface. The elucidation of adsorption of methylated DNA onto the gold surface paves the way for a novel designing of colorimetric AuNP-based biosensor for DNA methylation detection and it can be utilized as a universal cancer screening

<i>In silico</i> study of molecular mechanism of universal cancer screening based on unique interactions between APC gene and gold nanoparticles

ACS Spring Meeting 2021

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In silico study of molecular mechanism of universal cancer screening based on unique interactions between APC gene and gold nanoparticles