Protected DNA strand displacement for enhanced single nucleotide discrimination in double-stranded DNA

被引：23
作者：
Khodakov, Dmitriy A. [1 ]
Khodakova, Anastasia S. [2 ]
Huang, David M. [3 ]
Linacre, Adrian [2 ]
Ellis, Amanda V. [1 ]
机构：
[1] Flinders Univ S Australia, Flinders Ctr Nanoscale Sci & Technol, Adelaide, SA 5001, Australia
[2] Flinders Univ S Australia, Dept Biol Sci, Adelaide, SA 5001, Australia
[3] Univ Adelaide, Sch Chem & Phys, Ctr Adv Nanomat, Adelaide, SA, Australia
来源：
SCIENTIFIC REPORTS | 2015年 / 5卷
基金：
澳大利亚研究理事会;
关键词：
MOLECULAR BEACONS; BASE MISMATCHES; HYBRIDIZATION; KINETICS; PLATFORM; PROBES; POLYMORPHISMS; AMPLIFICATION; RNA; LNA;
D O I：
10.1038/srep08721
中图分类号：
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号：
07 ; 0710 ; 09 ;
摘要：
Single nucleotide polymorphisms (SNPs) are a prime source of genetic diversity. Discriminating between different SNPs provides an enormous leap towards the better understanding of the uniqueness of biological systems. Here we report on a new approach for SNP discrimination using toehold-mediated DNA strand displacement. The distinctiveness of the approach is based on the combination of both 3- and 4-way branch migration mechanisms, which allows for reliable discrimination of SNPs within double-stranded DNA generated from real-life human mitochondrial DNA samples. Aside from the potential diagnostic value, the current study represents an additional way to control the strand displacement reaction rate without altering other reaction parameters and provides new insights into the influence of single nucleotide substitutions on 3- and 4-way branch migration efficiency and kinetics.
引用
收藏
页数：8
相关论文
共 50 条
[41]   Dual-Color Emissive AIEgen for Specific and Label-Free Double-Stranded DNA Recognition and Single-Nucleotide Polymorphisms Detection [J].
Gao, Yuting ;
He, Zhenyan ;
He, Xuewen ;
Zhang, Haoke ;
Weng, Jun ;
Yang, Xiangliang ;
Meng, Fanling ;
Luo, Liang ;
Tang, Ben Zhong .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2019, 141 (51) :20097-20106
[42]   Fluorescent Double-Stranded DNA-Templated Copper Nanoprobes for Rapid Diagnosis of Tuberculosis [J].
Tsai, Tsung-Ting ;
Chen, Chung-An ;
Ho, Natalie Yi-Ju ;
Yang, Shuan ;
Chen, Chien-Fu .
ACS SENSORS, 2019, 4 (11) :2885-2892
[43]   Nanoparticle carrying a single probe for target DNA detection and single nucleotide discrimination [J].
Qin, Wei Jie ;
Yung, Lin Yue Lanry .
BIOSENSORS & BIOELECTRONICS, 2009, 25 (02) :313-319
[44]   CVD Graphene Electrode for Direct Electrochemical Detection of Double-Stranded DNA [J].
Bardaoui, Afrah ;
Hammami, Asma ;
Elkarous, Rabiaa ;
Ali Aloui, Mohamed ;
Oueslati, Rania ;
Messaoud, Olfa ;
Santos, Diogo M. F. ;
Chtourou, Radhouane .
INORGANICS, 2023, 11 (04)
[45]   Surface plasmon resonance study of PNA interactions with double-stranded DNA [J].
Ananthanawat, Cheeraporn ;
Hoven, Voravee P. ;
Vilaivan, Tirayut ;
Su, Xiaodi .
BIOSENSORS & BIOELECTRONICS, 2011, 26 (05) :1918-1923
[46]   A new fluorescence labeling method for molecular analysis of double-stranded DNA [J].
Takahashi, Shunsuke ;
Oshige, Masahiko ;
Katsura, Shinji ;
Nagahara, Yukitoshi .
ANALYTICAL BIOCHEMISTRY, 2023, 662
[47]   Molecular conductance of double-stranded DNA evaluated by electrochemical capacitance spectroscopy [J].
Ribeiro, W. C. ;
Goncalves, L. M. ;
Liebana, S. ;
Pividori, M. I. ;
Bueno, P. R. .
NANOSCALE, 2016, 8 (16) :8931-8938
[48]   Using double-stranded DNA probes to promote specificity in target capture [J].
Baker, Bryan A. ;
Mahmoudabadi, Gita ;
Milam, Valeria T. .
COLLOIDS AND SURFACES B-BIOINTERFACES, 2013, 102 :884-890
[49]   Optimization of on-chip elongation for fabricating double-stranded DNA microarrays [J].
Bai, YF ;
Ge, QY ;
Wang, JK ;
Li, TX ;
Liu, QJ ;
Lu, ZH .
COLLOIDS AND SURFACES B-BIOINTERFACES, 2005, 40 (3-4) :153-158
[50]   Stretching of Long Double-Stranded DNA and RNA Described by the Same Approach [J].
Afanasyev, Alexander Y. ;
Onufriev, Alexey, V .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2022, 18 (06) :3911-3920
12345