scholarly journals Sensitive and Selective Detection of DNA Fragments Associated with Ganoderma Boninense by DNA-Nanoparticle Conjugate Hybridisation

2020 ◽  
Author(s):  
Ekta Rani ◽  
Siti Akhtar Mohshim ◽  
Nor Hidayat Yusof ◽  
Muhammad Zamharir Ahmad ◽  
Royston Goodacre ◽  
...  
Keyword(s):  
Colorimetric Assay ◽  
Colour Change ◽  
Dna Fragments ◽  
Label Free ◽  
Ganoderma Boninense ◽  
Large Excess ◽  
Single Nucleotide ◽  
Free System ◽  
Complementary Dna ◽  
Double Stranded Dna

<u><strong> </strong></u><p>A colorimetric assay for the detection of DNA fragments associated with the oil palm pathogen Ganoderma boninense is reported, which is based on the aggregation of DNA-nanoparticle conjugated in the presence of complementary DNA from the pathogen. Here, various designs of DNA-nanoparticle conjugates were evaluated, and it was found that the best design gave a visually observable colour change with as little as 2 pmol of double-stranded DNA analyte even in the presence of a large excess of a mixture of non-complementary DNA. The assay was also able to differentiate analyte sequences with three or more single nucleotide mismatches. Overall, this label-free system is rapid, sensitive, selective, simple in design and easy to carry out. It does not require specialist equipment or specialist training for the interpretation of the results and therefore has the potential to be deployed of agricultural diagnostics in the field.</p><u><strong></strong></u>

scholarly journals Sensitive and Selective Detection of DNA Fragments Associated with Ganoderma Boninense by DNA-Nanoparticle Conjugate Hybridisation

2020 ◽  
Author(s):  
Ekta Rani ◽  
Siti Akhtar Mohshim ◽  
Nor Hidayat Yusof ◽  
Muhammad Zamharir Ahmad ◽  
Royston Goodacre ◽  
...  
Keyword(s):  
Colorimetric Assay ◽  
Colour Change ◽  
Dna Fragments ◽  
Label Free ◽  
Ganoderma Boninense ◽  
Large Excess ◽  
Single Nucleotide ◽  
Free System ◽  
Complementary Dna ◽  
Double Stranded Dna

<u><strong> </strong></u><p>A colorimetric assay for the detection of DNA fragments associated with the oil palm pathogen Ganoderma boninense is reported, which is based on the aggregation of DNA-nanoparticle conjugated in the presence of complementary DNA from the pathogen. Here, various designs of DNA-nanoparticle conjugates were evaluated, and it was found that the best design gave a visually observable colour change with as little as 2 pmol of double-stranded DNA analyte even in the presence of a large excess of a mixture of non-complementary DNA. The assay was also able to differentiate analyte sequences with three or more single nucleotide mismatches. Overall, this label-free system is rapid, sensitive, selective, simple in design and easy to carry out. It does not require specialist equipment or specialist training for the interpretation of the results and therefore has the potential to be deployed of agricultural diagnostics in the field.</p><u><strong></strong></u>

scholarly journals Sensitive and Selective Detection of DNA Fragments Associated with Ganoderma Boninense by DNA-Nanoparticle Conjugate Hybridisation

2020 ◽  
Author(s):  
Ekta Rani ◽  
Siti Akhtar Mohshim ◽  
Nor Hidayat Yusof ◽  
Muhammad Zamharir Ahmad ◽  
Royston Goodacre ◽  
...  
Keyword(s):  
Colorimetric Assay ◽  
Colour Change ◽  
Dna Fragments ◽  
Label Free ◽  
Ganoderma Boninense ◽  
Large Excess ◽  
Single Nucleotide ◽  
Free System ◽  
Complementary Dna ◽  
Double Stranded Dna

<u><strong> </strong></u><p>A colorimetric assay for the detection of DNA fragments associated with the oil palm pathogen Ganoderma boninense is reported, which is based on the aggregation of DNA-nanoparticle conjugated in the presence of complementary DNA from the pathogen. Here, various designs of DNA-nanoparticle conjugates were evaluated, and it was found that the best design gave a visually observable colour change with as little as 2 pmol of double-stranded DNA analyte even in the presence of a large excess of a mixture of non-complementary DNA. The assay was also able to differentiate analyte sequences with three or more single nucleotide mismatches. Overall, this label-free system is rapid, sensitive, selective, simple in design and easy to carry out. It does not require specialist equipment or specialist training for the interpretation of the results and therefore has the potential to be deployed of agricultural diagnostics in the field.</p><u><strong></strong></u>

scholarly journals Sensitive and Selective Detection of DNA Fragments Associated with Ganoderma Boninense Pathogen by DNA-Nanoparticle Conjugate Hybridisation

2019 ◽  
Author(s):  
Ekta Rani ◽  
Siti Akhtar Mohshim ◽  
Nor Hidayat Yusof ◽  
Muhammad Zamharir Ahmad ◽  
Royston Goodacre ◽  
...  
Keyword(s):  
Colorimetric Assay ◽  
Colour Change ◽  
Dna Fragments ◽  
Label Free ◽  
Ganoderma Boninense ◽  
Large Excess ◽  
Single Nucleotide ◽  
Free System ◽  
Complementary Dna ◽  
Double Stranded Dna

<u><strong> </strong></u><p>A colorimetric assay for the detection of DNA fragments associated with the oil palm pathogen Ganoderma boninense is reported, which is based on the aggregation of DNA-nanoparticle conjugated in the presence of complementary DNA from the pathogen. Here, various designs of DNA-nanoparticle conjugates were evaluated, and it was found that the best design gave a visually observable colour change with as little as 2 pmol of double-stranded DNA analyte even in the presence of a large excess of a mixture of non-complementary DNA. The assay was also able to differentiate analyte sequences with three or more single nucleotide mismatches. Overall, this label-free system is rapid, sensitive, selective, simple in design and easy to carry out. It does not require specialist equipment or specialist training for the interpretation of the results and therefore has the potential to be deployed of agricultural diagnostics in the field.</p><u><strong></strong></u>

scholarly journals Specificity-Enhanced Hot-Start PCR: Addition of Double-Stranded DNA Fragments Adapted to the Annealing Temperature

BioTechniques ◽  
2000 ◽  
Vol 28 (2) ◽  
pp. 278-282 ◽  
Author(s):  
Peter Kainz ◽  
Angela Schmiedlechner ◽  
Hans Bernd Strack
Keyword(s):  
Annealing Temperature ◽  
Dna Fragments ◽  
Double Stranded Dna ◽  
Hot Start

scholarly journals Improving the Precision of Base Editing by Bubble Hairpin Single Guide RNA

mBio ◽  
2021 ◽  
Vol 12 (2) ◽  
Author(s):  
Zhiwei Hu ◽  
Yannan Wang ◽  
Qian Liu ◽  
Yan Qiu ◽  
Zhiyu Zhong ◽  
...  
Keyword(s):  
Genome Editing ◽  
Dna Breaks ◽  
Single Nucleotide ◽  
Base Editing ◽  
Guide Rna ◽  
Guide Rnas ◽  
Double Stranded Dna ◽  
Target Sites ◽  
Guide Sequence ◽  
Sgrna Design

ABSTRACT Base editing is a powerful genome editing approach that enables single-nucleotide changes without double-stranded DNA breaks (DSBs). However, off-target effects as well as other undesired editings at on-target sites remain obstacles for its application. Here, we report that bubble hairpin single guide RNAs (BH-sgRNAs), which contain a hairpin structure with a bubble region on the 5′ end of the guide sequence, can be efficiently applied to both cytosine base editor (CBE) and adenine base editor (ABE) and significantly decrease off-target editing without sacrificing on-target editing efficiency. Meanwhile, such a design also improves the purity of C-to-T conversions induced by base editor 3 (BE3) at on-target sites. Our results present a distinctive and effective strategy to improve the specificity of base editing. IMPORTANCE Base editors are DSB-free genome editing tools and have been widely used in diverse living systems. However, it is reported that these tools can cause substantial off-target editings. To meet this challenge, we developed a new approach to improve the specificity of base editors by using hairpin sgRNAs with a bubble. Furthermore, our sgRNA design also dramatically reduced indels and unwanted base substitutions at on-target sites. We believe that the BH-sgRNA design is a significant improvement over existing sgRNAs of base editors, and our design promises to be adaptable to various base editors. We expect that it will make contributions to improving the safety of gene therapy.

Patents on random complementary DNA fragments?

Science ◽  
1992 ◽  
Vol 257 (5072) ◽  
pp. 915-918 ◽  
Author(s):  
T. Kiley
Keyword(s):  
Dna Fragments ◽  
Complementary Dna

A colorimetric method for the sequence-specific recognition of double-stranded DNA on the surface of a silver-coated glass slide

2018 ◽  
Vol 96 (5) ◽  
pp. 466-470
Author(s):  
Xiaoting Guo ◽  
Jing Wang ◽  
Zhifang Zhu ◽  
Manjun Zhang ◽  
Haigang Li ◽  
...  
Keyword(s):  
Colorimetric Method ◽  
Colour Change ◽  
Glass Slide ◽  
Coated Glass ◽  
Specific Recognition ◽  
Double Stranded Dna ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Good Sequence ◽  
Coated Glass Slide

In this study, a colorimetric method for sequence-specific recognition of double-stranded DNA (dsDNA) was established on the surface of a silver-coated glass slide. Oligo-1 was assembled on the surface of a silver-coated glass slide through an Ag–S bond, and Oligo-2 as reporter was used to bind with streptavidin-horseradish peroxidase (SA–HRP). They could bind with target dsDNA that was composed of Oligo-3 and Oligo-4 on the surface of a silver-coated glass slide through triplex formation. The bound HRP could be moved into the solution by DNase I and catalyze the oxidation of 3,3′,5,5′-tetramethylbenzidine (TMB). Therefore, the concentration of target dsDNA could be determined with the colour change of TMB. Under the optimum conditions, the absorbance was proportional to the concentration of target dsDNA over the range of 100 pmol/L to 2.0 nmol/L, with a detection limit of 13 pmol/L. In addition, this method showed good sequence selectivity, enabling it to be further developed for the detection of other polymerase chain reaction (PCR) products.

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