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 had a central role in genomics research1,2,3. Over the past decade, several techniques have been developed to improve detection performance and reduce the cost of genetic analysis4,5,6,7,8,9,10. In particular, significant advances in label-free methods have been reported11,12,13,14,15,16,17. Yet detection of DNA molecules at concentrations below the 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 have sufficient background signal rejection to allow 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 microRNAs in tumour samples; such measurements have been shown to help discriminate between the tissue origins of metastatic tumours18. Two hundred 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 one attomolar. These results suggest that nanomechanical read-out of microarrays promises attomolar-level sensitivity and large dynamic range for the analysis of gene expression, while eliminating biochemical manipulations, amplification and labelling.

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Figure 1: Nanomechanical detection of DNA hybridization.
Figure 2: Direct detection and quantification of miRNA expression in cancer tissues.
Figure 3: High-throughput, robust nanomechanical read-out for multiplexed detection.

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Acknowledgements

This research is supported by the Rowland Junior Fellows Program. H.H.J.P. was supported in part by US National Institutes of Health grant HG000205. We thank R. W. Davis for discussions.

Author Contributions S.H. performed the experiments, prepared gold substrates and developed experimental protocols; H.H.J.P. and O.S. contributed to the experiments. S.H. and H.H.J.P. designed and performed the surface chemistry, O.S. designed the cantilevers and wrote the stiffness calculation program, and H.H.J.P. and O.S. designed the biological assay. O.S. directed the research and wrote the paper; all authors discussed the results and commented on the manuscript.

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Correspondence to Ozgur Sahin.

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This file contains Supplementary Data, Supplementary Notes and Supplementary Figures 1-4 and 6-8 with Legends. (PDF 1407 kb)

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Husale, S., Persson, H. & Sahin, O. DNA nanomechanics allows direct digital detection of complementary DNA and microRNA targets. Nature 462, 1075–1078 (2009). https://doi.org/10.1038/nature08626

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