Electrical detection and quantification of single and mixed DNA nucleotides in suspension.

Mahmoud Al Ahmad,Farah Mustafa,Neena G Panicker,Tahir A Rizvi

doi:10.1038/srep34016

Abstract

High speed sequential identification of the building blocks of DNA, (deoxyribonucleotides or nucleotides for short) without labeling or processing in long reads of DNA is the need of the hour. This can be accomplished through exploiting their unique electrical properties. In this study, the four different types of nucleotides that constitute a DNA molecule were suspended in a buffer followed by performing several types of electrical measurements. These electrical parameters were then used to quantify the suspended DNA nucleotides. Thus, we present a purely electrical counting scheme based on the semiconductor theory that allows one to determine the number of nucleotides in a solution by measuring their capacitance-voltage dependency. The nucleotide count was observed to be similar to the multiplication of the corresponding dopant concentration and debye volume after de-embedding the buffer contribution. The presented approach allows for a fast and label-free quantification of single and mixed nucleotides in a solution.

Highlights

Quick, label-free screening and quantification of DNA bases is becoming increasingly important[1,2,3]
To detect the individual nucleotides electrically and extract relevant parameters, the four nucleotides were diluted individually in control TE buffer (10 mM Tris-Cl, 1 mM EDTA, pH 8) and loaded inside an open-ended coaxial cable[20] of Gamry 3000 instrument (USA)[21] that has a wide range of electrical measurement capabilities
One way to demonstrate the electrical polarization of DNA nucleotides is through the electrical charging-discharging measurements

Summary

Introduction

Label-free screening and quantification of DNA bases is becoming increasingly important[1,2,3]. Nano pores are being used within which each nucleotide in a DNA strand can translocate through[7,8,9] This modulates the ionic current being passed through the nano device which allows identification of each nucleotide, and eventually the sequence of the entire stretch of DNA10–11. Nucleotides are randomly distributed at the molecular level within a suspension When these suspended nucleotides are subjected to an electric field, they get polarized to different degrees depending upon their molecular structures. The capacitance contribution of the control buffer was subtracted from that of the samples since the buffer can act as a linear superposition to that of sample or, equivalently, the capacitance value of the control can be parallel to that of the sample This “parallel model” was based on our observations that the effective capacitance of the nucleotide suspension (nucleotide +control buffer) was higher than the capacitance of the nucleotide-free control medium. If the effective capacitance of the suspension was lower than the reference, a “series model” would have been considered

Methods

Results

Conclusion