Investigating the dynamics of surface-immobilized DNA nanomachines

TY - JOUR

T1 - Investigating the dynamics of surface-immobilized DNA nanomachines

AU - Dunn, Katherine Elizabeth

AU - Trefzer, Martin Albrecht

AU - Johnson, Steven David

AU - Tyrrell, Andrew Martin

N1 - © 2016, The Authors.

PY - 2016/7/8

Y1 - 2016/7/8

N2 - Surface-immobilization of molecules can have a profound influence on their structure, function and dynamics. Toehold-mediated strand displacement is often used in solution to drive synthetic nanomachines made from DNA, but the effects of surface-immobilization on the mechanism and kinetics of this reaction have not yet been fully elucidated. Here we show that the kinetics of strand displacement in surface-immobilized nanomachines are significantly different to those of the solution phase reaction, and we attribute this to the effects of intermolecular interactions within the DNA layer. We demonstrate that the dynamics of strand displacement can be manipulated by changing strand length, concentration and G/C content. By inserting mismatched bases it is also possible to tune the rates of the constituent displacement processes (toehold-binding and branch migration) independently, and information can be encoded in the time-dependence of the overall reaction. Our findings will facilitate the rational design of surface-immobilized dynamic DNA nanomachines, including computing devices and track-based motors.

AB - Surface-immobilization of molecules can have a profound influence on their structure, function and dynamics. Toehold-mediated strand displacement is often used in solution to drive synthetic nanomachines made from DNA, but the effects of surface-immobilization on the mechanism and kinetics of this reaction have not yet been fully elucidated. Here we show that the kinetics of strand displacement in surface-immobilized nanomachines are significantly different to those of the solution phase reaction, and we attribute this to the effects of intermolecular interactions within the DNA layer. We demonstrate that the dynamics of strand displacement can be manipulated by changing strand length, concentration and G/C content. By inserting mismatched bases it is also possible to tune the rates of the constituent displacement processes (toehold-binding and branch migration) independently, and information can be encoded in the time-dependence of the overall reaction. Our findings will facilitate the rational design of surface-immobilized dynamic DNA nanomachines, including computing devices and track-based motors.

KW - Biophysical Phenomena

KW - DNA/chemistry

KW - Immobilized Nucleic Acids/chemistry

KW - Kinetics

KW - Nanostructures

UR - http://www.scopus.com/inward/record.url?scp=84978160583&partnerID=8YFLogxK

U2 - 10.1038/srep29581

DO - 10.1038/srep29581

M3 - Article

C2 - 27387252

SN - 2045-2322

VL - 6

JO - Scientific Reports

JF - Scientific Reports

M1 - 29581

ER -