Research Article: Detection of DNA oligonucleotides with base mutations by terahertz spectroscopy and microstructures

Date Published: January 24, 2018

Publisher: Public Library of Science

Author(s): Mingjie Tang, Mingkun Zhang, Shihan Yan, Liangping Xia, Zhongbo Yang, Chunlei Du, Hong-Liang Cui, Dongshan Wei, Oksana Ostroverkhova.

http://doi.org/10.1371/journal.pone.0191515

Abstract

DNA oligonucleotides with a 5-base mutation at the 3′-terminus were investigated by terahertz (THz) spectroscopy in a marker-free manner. The four single-stranded oligonucleotides with 17nt have been detected with specificity on a microfluidic chip, and corroborated by spectral measurements with split-ring resonators. The number of hydrogen bonds formed between the oligonucleotide and its surrounding water molecules, deemed a key contribution to the THz absorption of biological solutions, was explored by molecular dynamics simulations to explain the experimental findings. Our work underlies the feasibility of THz spectroscopy combined with microstructures for marker-free detection of DNA, which may form the basis of a prospective diagnostic tool for studying genic mutation.

Partial Text

Gene mutation can change the whole structure of a gene through the addition, deletion, or alteration of one or more bases in the DNA sequence. It is generally harmful and will give rise to genetic diseases and cancers, yet it is beneficial for the biological evolution on the other hand. Therefore, detection of the gene mutation is very important for many biomedical applications, such as genetic analysis [1,2] and cancer research [3,4]. To diagnose the gene mutation, it is crucial to detect DNA oligonucleotides generated after mutation. Current techniques for DNA detection, e.g., hybridization assay, usually require complicated and costly fluorescent labeling processes which affect the precision of gene detection due to the degradable labels [5–7]. In recent years, marker-free gene detection techniques are garnering more and more attention and beginning to be recognized as the development trend of gene detection [8,9].

In this study, measurement techniques combining the THz spectroscopy and microstructures were proposed to try to detect the DNA oligonucleotides with 5-base mutation. Based on the experimental results and the simulation analysis, we can draw the following conclusions: (1) A microfluidic chip can be used as a carrier device suitable for THz detection of biomolecular solutions to reduce the strong absorption of water in the THz frequency range; (2) The four oligonucleotides with the 5-base mutation (Ter-5A, Ter-5C, Ter-5T, Ter-5G) can be detected with specificity according to their different THz absorption spectra. (3) The four oligonucleotides were found to exhibit different red-shifts in resonance frequency because of their different effective dielectric constants; (4) Difference in the number of hydrogen bonds formed by the oligonucleotide molecules and their surrounding water molecules can be well used to interpret the difference in the THz absorption coefficients of these four oligonucleotide solutions. Therefore, the investigation results reported in this work indicate that THz spectroscopy may be an effective and marker-free technique to explore and diagnose the genic mutation of DNA molecules.

 

Source:

http://doi.org/10.1371/journal.pone.0191515