Barley haplotyping using biplex deoxyribozyme nanomachine
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 he...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-11-01
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| Series: | Sensors and Actuators Reports |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666053922000595 |
| _version_ | 1811201739670421504 |
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| author | Maria M. Akhmetova Maria S. Rubel Olga S. Afanasenko Dmitry M. Kolpashchikov |
| author_facet | Maria M. Akhmetova Maria S. Rubel Olga S. Afanasenko Dmitry M. Kolpashchikov |
| author_sort | Maria M. Akhmetova |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T02:26:59Z |
| format | Article |
| id | doaj.art-ba2899cdcfa34a19883b0fda4666a84c |
| institution | Directory Open Access Journal |
| issn | 2666-0539 |
| language | English |
| last_indexed | 2024-04-12T02:26:59Z |
| publishDate | 2022-11-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Sensors and Actuators Reports |
| spelling | doaj.art-ba2899cdcfa34a19883b0fda4666a84c2022-12-22T03:51:56ZengElsevierSensors and Actuators Reports2666-05392022-11-014100132Barley haplotyping using biplex deoxyribozyme nanomachineMaria M. Akhmetova0Maria S. Rubel1Olga S. Afanasenko2Dmitry M. Kolpashchikov3Laboratory of DNA-Nanosensor Diagnostics, SCAMT Institute, ITMO University, Saint-Petersburg 191002, Russian FederationLaboratory of DNA-Nanosensor Diagnostics, SCAMT Institute, ITMO University, Saint-Petersburg 191002, Russian FederationDepartment of Plant Resistance to Diseases, All-Russian Institute of Plant Protection (VIZR), St. Petersburg 196608, Russian FederationChemistry Department, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, United States; Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, United States; Center for Forensic Science, University of Central Florida, Orlando, FL, United States; Corresponding author at: Chemistry Department, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, United States.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.http://www.sciencedirect.com/science/article/pii/S2666053922000595Split probesCrop haplotypingDetection of dsDNASNV selectivitybinary probeDNA machine |
| spellingShingle | Maria M. Akhmetova Maria S. Rubel Olga S. Afanasenko Dmitry M. Kolpashchikov Barley haplotyping using biplex deoxyribozyme nanomachine Sensors and Actuators Reports Split probes Crop haplotyping Detection of dsDNA SNV selectivity binary probe DNA machine |
| title | Barley haplotyping using biplex deoxyribozyme nanomachine |
| title_full | Barley haplotyping using biplex deoxyribozyme nanomachine |
| title_fullStr | Barley haplotyping using biplex deoxyribozyme nanomachine |
| title_full_unstemmed | Barley haplotyping using biplex deoxyribozyme nanomachine |
| title_short | Barley haplotyping using biplex deoxyribozyme nanomachine |
| title_sort | barley haplotyping using biplex deoxyribozyme nanomachine |
| topic | Split probes Crop haplotyping Detection of dsDNA SNV selectivity binary probe DNA machine |
| url | http://www.sciencedirect.com/science/article/pii/S2666053922000595 |
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