A sub-nanometer field of vision, perfect for peeping DNA

A sub-nanometer field of vision, perfect for peeping DNA

The paper in Nature Communications is here: https://go.nature.com/2GERhNb

2016, Aug. 29, NASA released a big news: the first time ever, DNA was deciphered in the outer space, by a palmtop sequencer based on nanopores. 

Since 1980s when the nanopore was initially suggested for single-molecule sensing, numerous biological or solid-state nanopores have been investigated and developed. The footstone of most nanopore sensors is the physical interactions of pore-molecule, such as the size-induced blockage effect. And it usually needs a systematic calibration and dedicated pores. One may ask, would a nanopore directly read molecular features of analytes? You know, aliens may have completely different media for storing genomic data, which may need a more universal nanopore sensing mechanism. 

It sounds like a scene in a science fiction. But the answer could be yes. Here is an idea - simple and sweet: spectroscopic nanopore. When shining light onto a gold plasmonic nanoslit, a kind of elongated pore, the generation of surface enhanced Raman scattering (SERS) from DNA molecules adsorbed inside the nanoslit, enables the direct identification of individual bases through their spectroscopic fingerprints. The use of a plasmon-enhanced spectroscopy is just a simple physical method, which is in principle more transparent and tailorable than other enzyme-related processes. This so-far unproven strategy could be an emerging game thriller for the sequencing competition.

In this work, we study DNA bases, both individual in solutions and incorporated in DNA strands. As expected, we can observe alternative spectral fluctuations of mixed adenine isotopologues, representing the nature of single-molecule stochastic behaviour in a solution. Surprisingly, we further observe the remarkable asynchronous fluctuations of adjacent bases in a DNA strand, pointing toward true performance of sub-nanometer spatial resolution with rational designs of experiments. This nanoslit SERS does show the basic features required for becoming a universal and emerging mechanism to directly read molecular information of analytes.   

However, our journey to compass single-molecule sensitivity was joys with tears. First, such a geometrical confinement concentrates both photons and fluids at the same focus, conveying extra phenomena than one could expected. These include fluidic loading of analytes, bipolar electrochemistry, photothermal heating, to name a few. Second, the hot spots for molecule docking and SERS detection are highly dynamic and chemically active, therefore sensitive to unnoticeable changes. Fortunately, we next conquered this by the modulation of the static bias potentials. What we found striking finally is that nanoslit SERS becomes proficient for nucleobase detection at such high spatial resolution.

The remaining challenges of nanoslit SERS for DNA sequencing are still risky. The volume reduction of hot spots – although the resolution boosted – requires further efforts to precisely control bases moving in/out of the sweet hot spots. The current susceptive voltage-modulation on realizing stochastic fluctuations for displacing bases may not be straightforward. With our efforts, we hope the highlights in these results could stimulate researchers join into the community. And we are looking forward to the prospective ability of nanoslit SERS or other similar nanopore SERS, which reflects the glowing simplicity of the original spectroscopic nanopore idea.

More insights of the applications and background of this technology can also be found in a recent imec press: https://www.imec-int.com/en/articles/imec-demonstrates-direct-optical-reading-of-single-molecule-dna-bases-in-modified-nanopores
Written by Yi Li and Chang Chen

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