DNA nanomechanics allows direct digital detection of complementary DNA and microRNA targets

Abstract

Techniques to detect and quantify DNA and RNA molecules in biological samples have played a central role in genomics research1–3. Over the past decade, several techniques have been developed to improve detection performance and reduce the cost of genetic analysis4–10. In particular, dramatic advances in label-free methods have been reported11–17. Yet, detection of DNA molecules at concentrations below femtomolar level requires amplified detection schemes1,8. Here we report a unique nanomechanical response of hybridized DNA and RNA molecules that serves as an intrinsic molecular label. Nanomechanical measurements on a microarray surface exhibit excellent background signal rejection that allows direct detection and counting of hybridized molecules. The digital response of the sensor provides a large dynamic range that is critical for gene expression profiling. We have measured differential expressions of miRNAs in tumor samples, which has been shown to help discriminate tissue origins of metastatic tumors18. 200 picograms of total RNA is found to be sufficient for this analysis. In addition, the limit of detection in pure samples is found to be 1 attomolar. These results suggest that nanomechanical readout of microarrays promises attomolar level sensitivity and large dynamic range for the analysis of gene expression, while eliminating biochemical manipulations, amplification, and labeling.

One-pot polymerase chain reaction with gold nanoparticles for rapid and ultrasensitive DNA detection

“…The ability to detect trace amounts of target deoxyribonucleic acid (DNA) sequences in a highly selective manner is of evergrowing interest for rapid detection of disease [1][2][3][4][5][6][7][8][9][10][11]. Herein, we report a method for rapid detection of DNA with ultrahigh sensitivity and specificity based on a novel strategy involving a combination of a polymerase chain reaction (PCR) and Au nanoparticles (Au NPs).…”

Low-concentration mechanical biosensor based on a photonic crystal nanowire array

“…A recently reported atomic force microscopy approach 32 showed attomolar DNA concentration resolution by label-free imaging of single hybridized DNA molecules, based on the stiff ness diff erences between single-and double-stranded DNA molecules. Compared with that, our method eliminates the requirement for direct contact with the molecules that might cause sample damage.…”

Molecular dynamic simulation of tip-polymer interaction in tapping-mode atomic force microscopy

“…13)). However, the link between the observables and the actual property is still not fully understood.…”

“…This new technique allows mapping the local elastic modulus 12 with very high sensitivity for variety of materials. 13 Despite the growing importance and potential of such techniques in material science, the link between the actual observables (amplitude, resonance frequency, phase shift, or even force-displacement curves) and the underlying material properties (e.g., local viscoelasticity) remains tenuous. As a consequence, it is still challenging to interpret AFM results and complex models are needed to relate observables to quantities of interest.…”