Precisely Manipulating Steric Hindrance Effect on DNA Walker for Tunable Detection of MicroRNA Using Enzymatic Strand Displacement Amplification

The spatial constraints imposed by the DNA structure have significant implications for the walking efficiency of three-dimensional DNA walkers. However, accurately quantifying and manipulating steric hindrance remains a challenging task. This study presents a steric hindrance-controlled DNA walker u...

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Bibliographic Details
Published in:Analytical chemistry (Washington) 2024-09, Vol.96 (36), p.14471-14479
Main Authors: Dong, Jiang Xue, Zhang, Sai Mei, Zhang, Yi Lin, Fan, Ya Jie, Li, Yan Lei, Su, Ming, Wang, Zhen Guang, Shen, Shi Gang, Gao, Zhong Feng, Wei, Qin, Xia, Fan
Format: Article
Language:English
Subjects:
Amplification
analytical chemistry
Biosensing Techniques
blood serum
Deoxyribonucleic acid
detection limit
Disease detection
DNA
DNA - chemistry
DNA structure
Drug development
Dynamic range
Humans
Limit of Detection
microRNA
MicroRNAs
MicroRNAs - analysis
MicroRNAs - blood
miRNA
Nucleic Acid Amplification Techniques
Precision medicine
quantitative analysis
Steric hindrance
Walking
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Summary:The spatial constraints imposed by the DNA structure have significant implications for the walking efficiency of three-dimensional DNA walkers. However, accurately quantifying and manipulating steric hindrance remains a challenging task. This study presents a steric hindrance-controlled DNA walker utilizing an enzymatic strand displacement amplification (ESDA) strategy for detecting microRNA-21 (miR-21) with tunable dynamic range and sensitivity. The steric hindrance of the DNA walker was precisely manipulated by varying the length of empty bases from 6.5 Å to 27.4 Å at the end of the track strand and adjusting the volumetric dimensions of the hairpin structure from 9.13 nm3 to 26.2 nm3 at the terminus of the single-foot DNA walking strand. This method demonstrated a tunable limit of detection for miR-21 ranging from 3.6 aM to 35.6 nM, along with a dynamic range from ∼100-fold to ∼166 000-fold. Impressively, it exhibited successful identification of cancer cells and clinical serum samples with high miR-21 expression. The proposed novel strategy not only enables tunable detection of miRNA through the regulation of steric hindrance but also achieves accurate and quantitative analysis of the steric hindrance effect, promising broader applications in personalized medicine, early disease detection, and drug development.
ISSN:0003-2700
1520-6882
1520-6882
DOI:10.1021/acs.analchem.4c02565