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Structural disruption of an adenosine-binding DNA aptamer on graphene: implications for aptasensor design

Version 2 2024-06-03, 17:43
Version 1 2022-10-26, 04:30
journal contribution
posted on 2024-06-03, 17:43 authored by Zak E Hughes, Tiffany WalshTiffany Walsh
We report on the predicted structural disruption of an adenosine-binding DNA aptamer adsorbed via noncovalent interactions on aqueous graphene. The use of surface-adsorbed biorecognition elements on device substrates is needed for integration in nanofluidic sensing platforms. Upon analyte binding, the conformational change in the adsorbed aptamer may perturb the surface properties, which is essential for the signal generation mechanism in the sensor. However, at present, these graphene-adsorbed aptamer structure(s) are unknown, and are challenging to experimentally elucidate. Here we use molecular dynamics simulations to investigate the structure and analyte-binding properties of this aptamer, in the presence and absence of adenosine, both free in solution and adsorbed at the aqueous graphene interface. We predict this aptamer to support a variety of stable binding modes, with direct base-graphene contact arising from regions located in the terminal bases, the centrally located binding pockets, and the distal loop region. Considerable retention of the in-solution aptamer structure in the adsorbed state indicates that strong intra-aptamer interactions compete with the graphene-aptamer interactions. However, in some adsorbed configurations the analyte adenosines detach from the binding pockets, facilitated by strong adenosine-graphene interactions.

History

Journal

ACS sensors

Volume

2

Pagination

1602-1611

Location

Washington, D.C.

eISSN

2379-3694

Language

eng

Publication classification

C1 Refereed article in a scholarly journal

Copyright notice

2017, American Chemical Society

Issue

11

Publisher

American Chemical Society