Development of an Oligonucleotide Functionalized Hydrogel Integrated on a High Resolution Interferometric Readout Platform as a Label-Free Macromolecule Sensing Device

Abstract

Development of an oligonucleotide functionalized hydrogel integrated on a high resolution interferometric readout platform capable of determining changes in optical length of the hydrogel with 2 nm resolution is described. The hydrogels were designed with hybridized dioligonucleotides grafted to the polymer network making up a network junction point in addition to the covalent cross-links. The hybridized dioligonucleotide network junctions were made with a 10 basepair complementary region flanked by additional basepairs that could aid in destabilizing the junction points in competitive displacement hybridization by the added probe oligonucleotides. The probe oligonucleotide destabilizing the junction point thus induces swelling of the functionalized hydrogel that is sensitive to the concentration of the probe, the sequence, and matching length between the probe and sensing oligonucleotide. This design yields a molecular amplification of the change in the optical length of the gel at least 5-fold compared to a hydrogel where sensing functionality is based on hybridization with a grafted oligonucleotide that is not a part of a network junction. Concentration sensitivity applied for specific label-free detection of oligonucleotide is estimated to be in the nanomolar region. Applications of the resulting oligonucleotide imprinted hydrogel for label-free sensing of probe oligonucleotide sequences or taking advantage of the oligonucleotide sequences designed with aptamer functionalities for determination of other types of molecules are discussed.

Visual optical biosensors based on DNA-functionalized polyacrylamide hydrogels

“…The change of the gel volume is quite small (only ~20%) [66,67]. To increase the sensitivity of detection, interferometry and gel photonic crystals have been reported [68,69]. Another way to control gel swelling is shown in Figure 3B, where the gel is mainly crosslinked by conventional bis-acrylamide.…”

High resolution interferometry as a tool for characterization of swelling of weakly charged hydrogels subjected to amphiphile and cyclodextrin exposure

“…The three solutions were mixed together yielding 10 wt% of AAM, 0.22, 0.44 and 0.88 mol% AMPSA relative to AAM, 3, 6 or 12 mol% Bis relative to AAM, and 0.15 mol% of initiator relative to AAM in the pregel solutions. Aliquots of the pre-gel solutions were deposited on the tip of the functionalized fiber and polymerized as described [1][2][3][4]45].…”

“…It has already proved its potential in sensing such analytes as glucose [2,3] and oligonucleotides [4][5][6]. Herein we present the technique as a useful tool for label-free monitoring of swelling phenomena occurring in various hydrogelamphiphile and hydrogel-amphiphile-macrocycle cases.…”

Application of Synthetic Biology to Regenerative Medicine

“…If complementary ssDNA oligonucleotides are applied to the gel, they spontaneously hybridize to the crosslinks and change the overall conformation of the gel. This can alter the gel's stiffness [64], volume [65,66], or induce its dissolution [67].…”