Neutralized chimeric DNA probe for the improvement of GC-rich RNA detection specificity on the nanowire field-effect transistor

Wei-Cheng Chou,Hardy Wai-Hong Chan,Wen-Yih Chen,Yuh-Shyong Yang,Wen-Pin Hu

doi:10.1038/s41598-019-47522-9

Wei-Cheng Chou, Hardy Wai-Hong Chan + Show 3 more

Open Access

https://doi.org/10.1038/s41598-019-47522-9

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Abstract

Silicon nanowire (SiNW) field-effect transistors (FETs) is a powerful tool in genetic molecule analysis because of their high sensitivity, short detection time, and label-free detection. In nucleic acid detection, GC-rich nucleic acid sequences form self- and cross-dimers and stem-loop structures, which can easily obtain data containing signals from nonspecific DNA binding. The features of GC-rich nucleic acid sequences cause inaccuracies in nucleic acid detection and hinder the development of precision medicine. To improve the inaccurate detection results, we used phosphate-methylated (neutral) nucleotides to synthesize the neutralized chimeric DNA oligomer probe. The probe fragment originated from a primer for the detection of hepatitis C virus (HCV) genotype 3b, and single-mismatched and perfect-matched targets were designed for single nucleotide polymorphisms (SNP) detection on the SiNW FET device. Experimental results revealed that the HCV-3b chimeric neutralized DNA (nDNA) probe exhibited better performance for SNP discrimination in 10 mM bis-tris propane buffer at 25 °C than a regular DNA probe. The SNP discrimination of the nDNA probe could be further improved at 40 °C on the FET device. Consequently, the neutralized chimeric DNA probe could successfully distinguish SNP in the detection of GC-rich target sequences under optimal operating conditions on the SiNW FET device.

Highlights

Single nucleotide polymorphisms (SNPs) are the most common forms of genetic variations, which are important indicators to disclose individual susceptibility to disease and differences in treatment effect
The present work reports the applications of neutralized chimeric DNA probe for the detection of GC-rich nucleic acid sequences on the silicon nanowire (SiNW) field-effect transistors (FETs) device in order to get selective single nucleotide polymorphisms (SNP) genotyping
The results of circular dichroism (CD) measurements revealed that the neutralized chimeric DNA probe consisted of phosphate-methylated and regular nucleotides could hybridize with the RNA target to form a double-stranded structure

Summary

Introduction

Single nucleotide polymorphisms (SNPs) are the most common forms of genetic variations, which are important indicators to disclose individual susceptibility to disease and differences in treatment effect. Compared with regular DNA probes, our recent study revealed that neutralized chimeric DNAs close to the 5′ end for surface immobilization and alternately modified with phosphate-methylated nucleotides exhibit better sensitivity and specificity in the detection of target fragments[15]. The positions of embedded methylated neutral nucleotides must be close to the end of the probe for immobilizing on the sensing surface These sequences used in this study are different from the reports published previously[9,15]. The major goal of this study is to examine the performance of neutralized chimeric DNA oligomer in the SNP discrimination on the SiNW FET device, especially for the detection of the GC-rich sequence. We demonstrate that neutralized chimeric DNA oligomer is able for sensitive SNP genotyping of GC-rich sequence in the low ionic strength buffer and at a higher operating temperature on the SiNW FET device (Fig. 1)

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