Thumbnail Image
Publication

Structural Disruption of an Adenosine-Binding DNA Aptamer on Graphene: Implications for Aptasensor Design

; 
Walsh, T.R.
Publication Date
2017-11-24
End of Embargo
Supervisor
Keywords
DNA aptamers, Molecular dynamics, Graphene, Bio-nanotechnology
Rights
(c) 2017 American Chemical Society. This is an Open Access article distributed under the ACS AuthorChoice License (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html), which permits copying and distribution of the article or any adaptations for non-commercial purposes.
cb
Peer-Reviewed
Yes
Open Access status
openAccess
Accepted for publication
2017-10-24
Institution
Department
Awarded
Embargo end date
Collections
Life Sciences Publications
Show all metadata
Files
Thumbnail Image
hughes_walsh_2017.pdf
Adobe PDF, 6.92 MB
Additional title
Abstract
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.
URI
http://hdl.handle.net/10454/15727
Version
Published version
Citation
Hughes ZE and Walsh TR (2017) Structural Disruption of an Adenosine-Binding DNA Aptamer on Graphene: Implications for Aptasensor Design. ACS Sensors. 2(11): 1602-1611.
Link to publisher’s version
Link to published version
Link to Version of Record
https://doi.org/10.1021/acssensors.7b00435
Type
Article
Qualification name
Notes