Browsing by Author "Huang, Chun-Jen"

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Improved DNA detection by utilizing electrically neutral DNA probe in field-effect transistor measurements as evidenced by surface plasmon resonance imaging
(2013-03-15)
Chen, Wen-Yih
;
Chen, Hon-Chen
;
Yang, Yuh-Shyong
;
Huang, Chun-Jen
;
Chan, Hardy Wai-Hong
Intensive efforts have been focused on the development of ultrasensitive DNA biosensors capable of quantitative gene expression analysis. Various neutralized nucleic acids have been demonstrated as alternative and attractive probe for the design of a DNA chip. However, the mechanism of the improvements has not been clearly revealed. In this investigation, we used a newly developed neutral ethylated DNA (E-DNA), a DNA analog with the "RO-P-O" backbone (wherein R could be methyl, ethyl, aryl, or alkyl group) obtained from synthetic procedures, and a silicon nanowire (SiNW) field-effect transistor (FET) to evaluate the difference in DNA detection performance while using E-DNA and DNA as probes. It is demonstrated that using the E-DNA probe in the FET measurement could have a significantly enhanced effect upon the detection sensitivity. Surface plasmon resonance imaging (SPRi) was used to evidence the mechanism of the improved detection sensitivity. SPRi analysis showed the amounts of probe immobilization on the sensor surface and the hybridization efficiency were both enhanced with the use of E-DNA. Consequently, neutral ethylated DNA probe hold a great promise for DNA sensing, especially in the electrical-based sensor. (C) 2012 Elsevier B.V. All rights reserved.
Neutralized chimeric DNA probe for detection of single nucleotide polymorphism on surface plasmon resonance biosensor
(2018-01-15)
Huang, Chun-Jen
;
Lin, Zhong-En
;
Yang, Yuh-Shyong
;
Chan, Hardy Wai-Hong
;
Chen, Wen-Yih
An implementation of neutralized chimeric DNA oligomer as a probe for sensitive detection of single nucleotide polymorphisms (SNPs) on a surface plasmon resonance imaging sensor is investigated. The chimeric DNA oligomer was synthesized in a conventional DNA synthesizer, containing neutral nucleotides with a methylated phosphate group. The secondary structures and melting points of the chimeric DNA fragment and its complexes with perfect-matched and single-mismatched complementary DNA molecules were examined by using circular dichroism and UV vis spectroscopy in comparison with the native probe DNA counterpart. The results indicate that the chimeric DNA complexes can form a B-form structure and exhibit high thermostability. Moreover, the hybridization and discrimination efficiency of the chimeric probe DNA for the SNP genotyping were verified by using the SPRi sensor under different experimental conditions. The data reveal the effects of the ionic strength and operation temperature on the selectivity of the chimeric probe DNA for the SNP detection. The hybridization condition with a low ionic strength and high temperature allows the chimeric probe DNA distinguishing perfect-matched and single-mismatched target DNA molecules to the best extent, likely due to the reduced electrostatic repulsive force and presence of the additional methyl group on the backbone. Consequently, the direct and label-free detection with the SPR technique and neutralized chimeric probe DNA can be realized for the SNP genotyping by optimizing the operation condition and sequence design.