Functional Nucleic Acids for DNA Nanotechnology - DNA Nanotechnology: From Structure to Function - page 12

Fig. 2.3 ( a ) The distance of two thrombin aptamers precisely controlled by the 5-helix-bundle
structure to influence the binding affinity to thrombin (Reprinted by permission from Macmillan
Publishers Ltd.: Ref. [ 72 ]. Copyright 2008). ( b ) The cascade biocatalytic reaction of GOx and HRP
activated upon the assembly of nanostructure by addition of cocaine (Reprinted with the permission
from Ref. [ 65 ]. Copyright 2009 American Chemical Society)
The space distribution of multiple ligands on one biological regime is closely
related to its biological function. The protein arrays based on DNA nanostructures
with different aptamers are a good model to study this kind of reaction with high
spatial resolution. Yan's group [ 72 ] studied the distance effect on the multivalent
binding proteins on DNA nanostructures by aptamers with precise nanoscale control
over the spatial resolution. Two thrombin aptamers against two different binding
sites are introduced into the assembly system. By varying the distance between
aptamers on the rigid structure of the DNA assembly, an optimal distance could be
achieved where two aptamers cooperatively bound thrombin with enhanced affinity
than one each. As shown in Fig. 2.3 a, the distance has been controlled over 2, 3.5,
5.3, and 6.9 nm on five-helix-bundle structure. The gel-mobility shift assays proved
the optimal distance was 5.3 nm for bivalent binding of thrombin with 10- to 50-fold