Computational design of single-stranded DNA hairpin aptamers immobilized on a biosensor substrate

Abstract

Aptamer interactions with a surface of attachment are central to the design and performance of aptamer-based biosensors. We have developed a computational modeling approach to study different system designs-including different aptamer-attachment ends, aptamer surface densities, aptamer orientations, and solvent solutions-and applied it to an anti MUC1 aptamer tethered to a silica biosensor substrate. Amongst all the system designs explored, we found that attaching the anti MUC1 aptamer through the 5' terminal end, in a high surface density configuration, and solvated in a 0.8 M NaCl solution provided the best exposure of the aptamer MUC1 binding regions and resulted in the least amount of aptamer backbone fluctuations. Many of the other designs led to non-functional systems, with the aptamer collapsing onto the surface. The computational approach we have developed and the resulting analysis techniques can be employed for the rational design of aptamer-based biosensors and provide a valuable tool for improving biosensor performance and repeatability.

Figure 1

Cartoon of the chemical structure of epoxide-amine linker and epoxide monolayer attachment.(Top) Epoxide monolayer molecule attached to SiO₂ surface (Bottom) Epoxide-amine linker molecule attached to SiO₂ surface and 5′ terminal of the aptamer.

Figure 2

Anti MUC1 aptamer tethered to SiO₂ biosensor substrate in configuration 1 (5′ end attachment, parallel to surface, low density). (A) Side view of simulation cell (B) Top view with periodic display. Water and ion molecules are not displayed.

Figure 3

Anti MUC1 aptamer tethered to SiO₂ biosensor substrate in configuration 2 (5′ end attachment, perpendicular to surface, low density). (A) Side view of simulation cell (B) Top view with periodic display. Water and ion molecules are not displayed.

Figure 4

Two anti MUC1 aptamers tethered to SiO₂ biosensor substrate in configuration 3 (5′ end attachment, perpendicular to surface, high density). (A) Side view of simulation cell (B) Top view with periodic display. Water and ion molecules are not displayed.

Figure 5

Anti MUC1 aptamer tethered to SiO₂ biosensor substrate in configuration 4 (3′ end attachment, perpendicular to surface, low density) (A) Side view of simulation cell (B) Top view with periodic display. Water and ion molecules are not displayed.

Figure 6

Two anti MUC1 aptamers tethered to SiO₂ biosensor substrate in configuration 5 (3′ end attachment, perpendicular to surface, high density) (A) Side view of periodic cell (B) Top view with periodic display. Water and ion molecules are not displayed.

Figure 7

Representative starting configurations for different ion concentrations. (A) Configuration 5a corresponds to the neutralized system and (B) Configuration 5b corresponds a 0.8 M solution after neutralization. Water atoms are not displayed. Sodium ions are shown in yellow (A, B) and Chloride ions are shown in cyan (B).

Figure 8

Snapshots of the MD simulation of the anti MUC1 aptamer tethered to the SiO₂ biosensor substrate in configuration 1 (5′ end attachment, parallel to surface, low density) neutralized (top) and in 0.8 M (bottom) solution concentrations at 0 ns, 0.5 ns, 1 ns, 5 ns, and 10 ns. The MUC1 binding residues (thymine residues 11 and 13) are displayed in purple.

Figure 9

Snapshots of the MD simulation of the anti MUC1 aptamer tethered to the SiO₂ biosensor substrate in configuration 2 (5′ end attachment, perpendicular to surface, low density) neutralized (top) and in 0.8 M (bottom) solution concentrations at 0 ns, 0.5 ns, 1 ns, 5 ns, and 10 ns. The MUC1 binding residues (thymine residues 11 and 13) are displayed in purple.

Figure 10

Snapshots of the MD simulation of two anti MUC1 aptamer tethered to the SiO₂ biosensor substrate in configuration 3 (5′ end attachment, perpendicular to surface, high density) neutralized (top) and in 0.8 M (bottom) solution concentrations at 0 ns, 0.5 ns, 1 ns, 5 ns, and 10 ns. The MUC1 binding residues (thymine residues 11 and 13) are displayed in purple. In each image, aptamer strand 1 is shown on the left and strand 2 is shown on the right.

Figure 11

Snapshots of the MD simulation of the anti MUC1 aptamer tethered to the SiO₂ biosensor substrate in configuration 4 (3′ end attachment, perpendicular to surface, low density) neutralized (top) and in 0.8 M (bottom) solution concentrations at 0 ns, 0.5 ns, 1 ns, 5 ns, and 10 ns. The MUC1 binding residues (thymine residues 11 and 13) are displayed in purple.

Figure 12

Snapshots of the MD simulation of the anti MUC1 aptamer tethered to the SiO₂ biosensor substrate in configuration 5 (3′ end attachment, perpendicular to surface, high density) neutralized (top) and in 0.8 M (bottom) solution concentrations at 0 ns, 0.5 ns, 1 ns, 5 ns, and 10 ns. The MUC1 binding residues (thymine residues 11 and 13) are displayed in purple. In each image, aptamer strand 1 is shown on the left and aptamer strand 2 is shown on the right.