Barley haplotyping using biplex deoxyribozyme nanomachine

• Published in: Sensors and actuators reports Vol. 4; p. 100132
• Main Authors: Akhmetova, Maria M., Rubel, Maria S., Afanasenko, Olga S., Kolpashchikov, Dmitry M.
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01-11-2022; Elsevier
• Subjects: binary probe; Crop haplotyping; Deoxyribozyme; Detection of dsDNA; DNA machine; DNAzyme; Fluorescent DNA sensor; SNV selectivity; Split probes; DNAzyme; Crop haplotyping; Split probes; SNV selectivity; Fluorescent DNA sensor; DNA machine; Deoxyribozyme; Detection of dsDNA; binary probe
• ISSN: 2666-0539; 2666-0539
• DOI: 10.1016/j.snr.2022.100132

•Biplex deoxyribozyme nanomachine detects two alleles in one reaction mixture by producing fluorescent signal in two channels.•The system can recognize dsDNA amplicon with selectivity toward a single nucleotide difference.•The system responses faster and with greater to the presence of short than long dsDNA amplicons.•The system accurately genotypes plans specimens.
Direct sequencing is the gold standard for genome haplotyping, while PCR is used for detection of limited number of genetic variations. However, these methods are not suitable for fast low-cost in-field testing of plant specimens. Here, we developed a two-color florescent nanosensor system (named here biplex deoxyribozyme nanomachine or bixDNM) that can haplotype dsDNA amplicons. The sensor is based on fluorescent binary deoxyribozyme embedded in a nanostructure containing together four DNA binding arms. Two allele specific sensors were tailored for producing signals at two different wavelengths (525 and 662 nM) only in the presence of fully matched analytes. Accurate haplotyping of seven barley samples was achieved. This is the first technique showing detected of both short (146 bp) and long (1348 bp) dsDNA amplicons with single nucleotide specificity. The study demonstrated bixDNM can become a foundation for future development of a plant haplotyping technology that can be used in field or at the low resource agricultural settings.
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