Vulnerability of DNA hybridization in soils is due to Mg2+ ion induced DNA aggregation
- 주제(키워드) Magnesium (Mg2+) ion , Gene quantification , DNA hybridization , NanoGene assay , Atomic force microscopy
- 주제(기타) Soil Science
- 설명문(일반) [Wang, Xiaofang] Auburn Univ, Dept Civil Engn, Auburn, AL 36849 USA; [Kweon, Hyojin; Son, Ahjeong] Ewha Womans Univ, Dept Environm Sci & Engn, Seoul 03760, South Korea; [Lee, Seokho] Hankuk Univ Foreign Studies, Dept Stat, Global Campus, Yongin 17035, Gyeonggi Do, South Korea; [Shin, Hyejin] Samsung Res, Seoul 06765, South Korea; [Chua, Beelee] Korea Univ, Sch Elect Engn, Seoul 02841, South Korea; [Liles, Mark R.] Auburn Univ, Dept Life Sci, Auburn, AL 36849 USA; [Lee, Ming-Kuo] Auburn Univ, Dept Geol, Auburn, AL 36849 USA
- 등재 SCIE, SCOPUS
- 발행기관 PERGAMON-ELSEVIER SCIENCE LTD
- 발행년도 2018
- URI http://www.dcollection.net/handler/ewha/000000156651
- 본문언어 영어
- Published As http://dx.doi.org/10.1016/j.soilbio.2018.08.003
초록/요약
The NanoGene assay is an inhibitor-resistant gene quantification assay based on magnetic bead and quantum dot nanoparticles. It employs a set of probe and signaling probe DNAs to capture target DNA via hybridization. Using simple DNA preparation that bypasses conventional DNA extraction, it was able to detect and quantify specific bacterial genes in environmental sample. In this study, the vulnerability of the NanoGene assay to the presence of various environmental factors was investigated. A total of 43 soil samples were inoculated with 10(9) CFU/mL of Pseudomonas putida prior to DNA isolation without purification. Subsequently, the NanoGene assay was performed for quantitative detection of P. putida with respect to 12 soil properties including pH, moisture, humic acids, organic matter, sand, silt, clay, cation exchange capability, sodium, potassium, magnesium, and calcium. Using multiple linear regression, the NanoGene assay was found to be particularly vulnerable to the presence of Mg2+, which was selected as a major variable (P = 0.001). The vulnerability of the NanoGene assay to Mg2+ was further explored by atomic force microscopy, which indicated significant Mg2+-mediated DNA aggregation. The inhibition of the NanoGene assay from some soil samples as a consequence of DNA aggregation could therefore be prevented by the use of me'' chelators such as EDTA, enabling application of this method across diverse soil types.
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