Electronic detection of DNA by its intrinsic molecular charge

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Original Entry: Nick Chisholm, AP 225, Fall 2009 (In Progress...)

General Information

Authors: Jurgen Fritz, Emily B. Cooper, Suzanne Gaudet, Peter K. Sorger, and Scott R. Manalis

Publication: PNAS 99, no. 22, 14142-14146 (2002)

Soft Matter Keywords

Concentration, DNA, Hybridization, Surface Charge

Summary

This paper provides a method for detecting DNA strands without attaching any labels to them, thus simplifying readout and lowering the time the experiment takes. Currently, the highest sensitivities are obtained by attaching a reporter molecule to the DNA, such as fluorescent, chemiluminescent, redox, or radioactive labels. The authors of this paper, however, show that their approach can detect and distinguish a single base mismatch in a 12-mer oligonucleotide (thus showing the accuracy of the process) within minutes using electronic readout.

To perform this experiment, the authors use two field-effect sensors which are able to detect changes in surface charge. When a DNA strand hybridizes onto the surface of the sensor, it causes a change in the surface charge (since DNA has one intrinsic negative charge per base at its sugar-phosphate backbone). This change in surface charge causes a change in capacitance in the silicon part of the field-effect sensor, which can then be measured.

The set-up for the experiment can be seen in Figure 1. In (a) and (b) of Figure 1, one notices a gray substrate on the sensor surface (yellow). This gray substrate is PLL (poly-L-lysine). In (a), the probe DNA (red) is bound electrostatically to the PLL; in this picture, the probe DNA is complimentary to the DNA being characterized (green), and thus they bind (hybridize). This hybridization changes the surface charge, thus increasing the depletion region (black arrow) in the silicon region (green), which is then measured as a change in capacitance of the silicon. In (b), the probe DNA (blue) is bound electrostatically to the PLL; however, this time, the probe DNA is not complimentary to the DNA being characterized, so there is a much smaller change in the depletion region (black arrow) and thus a smaller change in capacitance of the silicon (green). In (c), one sees an optical micrograph of the device used for measurement, and (d) shows a close-up of the cantilever field-effect sensor. One should note that this set-up is only used for testing the ability of the system to characterize a known DNA strand by two known probe DNA strands (one being its compliment, and the other not being its compliment). To actually characterize an unknown DNA strand, one would need to have a cantilever field-effect sensor for each possible complimentary strand.

Figure 1, taken from [1].

It should be noted that the authors explicitly experimented to make sure that layer thickness does not affect the capacitance read-out, and thus the system only measures the surface charge.

Soft Matter Discussion

This experiment shows the power of charged interfaces with regards to detection, in particular in biological applications. Beyond the obvious application presented here (characterizing genes and DNA sequences in general), one could also use this method to potentially characterize infectious agents (or really, for anything that requires nucleic assays).

Personally, I'm not entirely convinced that this is an appropriate direction for performing characterization of DNA sequences. My main concern would be scalability: for a DNA sequence of <math>n</math> bases, one would need <math>4^{n}</math> different sensors in order to test each possible chain sequence (assuming we could even determine how many bases we begin with!). As an example, if we have <math>n = 10</math>, then we need <math>4^{10} = 1 048 576</math> sensors, which would seem rather ridiculous. I would imagine that <math>n = 10</math> is a very conservative lower bound on the number of bases in the sequences we would wish to characterize.

Besides the scalability issue, this paper is still interesting from a fundamental point of view (just for the sake of showing that it can be done).

Reference

[1] Jurgen Fritz, Emily B. Cooper, Suzanne Gaudet, Peter K. Sorger, and Scott R. Manalis, "Electronic detection of DNA by its intrinsic molecular charge," PNAS 99, no. 22, 14142-14146 (2002).