Label-free detection of DNA hybridization based on hydration-induced tension in nucleic acid films

Abstract

The properties of water at the nanoscale are crucial in many areas of biology, but the confinement of water molecules in sub-nanometre channels in biological systems has received relatively little attention. Advances in nanotechnology make it possible to explore the role played by water molecules in living systems, potentially leading to the development of ultrasensitive biosensors. Here we show that the adsorption of water by a self-assembled monolayer of single-stranded DNA on a silicon microcantilever can be detected by measuring how the tension in the monolayer changes as a result of hydration. Our approach relies on the microcantilever bending by an amount that depends on the tension in the monolayer. In particular, we find that the tension changes dramatically when the monolayer interacts with either complementary or single mismatched single-stranded DNA targets. Our results suggest that the tension is mainly governed by hydration forces in the channels between the DNA molecules and could lead to the development of a label-free DNA biosensor that can detect single mutations. The technique provides sensitivity in the femtomolar range that is at least two orders of magnitude better than that obtained previously with label-free nanomechanical biosensors and with label-dependent microarrays.

Hydration Induced Stress on DNA Monolayers Grafted on Microcantilevers

“…11 We do not consider the effect of electrostatic interactions in this study, as previous work with uncharged PNA molecules did not show remarkable differences in the surface stress response with relative humidity of this uncharged DNA mimic. 7 The surface stress variation of ssDNA films as a function of the RH, shown in figure 1, reveals distinct hydration/dehydration features after incubation with the target solution depending on the hybridization conditions. For the sake of simplicity, we will focus from this point onwards only on the swelling curve to study the behavior of the oligonucleotide monolayer after incubation with a target solution.…”

“…3,4 Hydration driven structural changes in DNA have recently gained further attention for the generation of responsive biomaterials. 5,6 We have also previously demonstrated exsitu hybridization detection in air after incubation with the sample solutions by harnessing the hydration-induced tension in nucleic acid films 7 or water desorption. 8 Surface stress biosensors have proven high sensitivity that adds to the advantages of a label-free technology.…”

“…19,[20][21][22][23] One singularly limiting difficulty has been to accomplish the anchoring of the ssDNA probes with a well-defined uniform density and a standing up conformation. 19,24 For such purpose, sophisticated nanografting methods need to be applied. 25,26 Alternatively, the gold layer needs to comply with very restrictive conditions regarding surface roughness 13 and surface electrostatics, 16 while long incubation times are also applied, 24 which bans the use of technologies for high multiplexing, such as ink-jet low volume dispensing.…”

Gold coating of micromechanical DNA biosensors by pulsed laser deposition

“…17,18 There is an increasing interest in using micromechanical sensors functionalized with SAMs of DNA to detect complementary DNA sequence with high sensitivity and specificity. In this type of sensors, a gold layer of few nanometers is used as an intermediate layer between the surface of the mechanical sensor and DNA.…”

“…This provides a way to detect DNA hybridization with improved sensitivity and larger reproducibility and robustness in the response. 17 In this work, we describe the gold-coating of silicon cantilever sensors by PLD and characterize their performance as DNA biosensors. PLD experiments were first carried out on silicon substrates in order to identify the optimum deposition conditions for coating the sensors.…”