Factors and methods to modulate DNA hybridization kinetics

Wong, Kingsley; Liu, Juewen

doi:10.1002/biot.202000338

Cited by 25 publications

(26 citation statements)

References 96 publications

(156 reference statements)

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“…We report a very strong negative and significant correlation between the temperature and the amount of DNA extracted. Our finding is consisted with the previous reports [12,19,21]. It is, therefore, critical to establish an optimal range of moderate temperatures and DNA concentrations for better quality and desired yields.…”

Section: Discussionsupporting

confidence: 84%

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Protocol Optimization of DNA Extraction from Banana Fruits

Omara

Barugahare²

2022

JABB

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Background: DNA extraction is the process by which the DNA is extracted and purified from the living or dead cells or tissues. There are many different kits commercially available for DNA extraction, with varying protocols. This study aimed at determining the optimal conditions for the extraction of high yield DNA from banana fruits. Methodology: DNA was extracted from banana fruits by precipitation method. The DNA yield was determined using the Nanodrop DNA quantification technique. Results: The optimal sodium chloride salt concentration for DNA extraction from banana fruits was 4mM and the amount of DNA extracted increased as the temperature decreased. The highest yield was obtained between 4 0C to 0 0C. Conclusion: We report for the first time a protocol with an optimal salt concentration (NaCl, 4mM) for quality DNA yield from banana fruits. A critical consideration is required to establish an optimal range of moderate temperatures and DNA concentrations for better quality and desired yields. There may not be a universal protocol for DNA extraction from all plant materials.

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Section: Discussionsupporting

confidence: 84%

“…There are many different protocols and, kits commercially available for DNA extraction from different plant materials [2][3][4][5][6][7][8][9][10]. Varying amounts and integrity of DNA are obtained due to the inherent properties as it were, and, differences in the optimization of the protocols for DNA extraction [11,12].…”

Section: Introductionmentioning

confidence: 99%

Protocol Optimization of DNA Extraction from Banana Fruits

Omara

Barugahare²

2022

JABB

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“…Nucleation and diffusion are two main kinetic limiting steps in DNA hybridization. The nucleation step means taking single-stranded DNA to a nucleated duplex with two to four H-bonded and stacked bases (SS 1 ·SS 2 ), and this nucleation step is followed by a rapid zipping step in which the rest of the duplex base stacks and hydrogen bonds …”

Section: Resultsmentioning

confidence: 99%

Space-Confinment-Enhanced Fluorescence Detection of DNA on Hydrogel Particles Array

et al. 2022

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Fluorescent biosensors have been widely applied in DNA detection because of their reliability and reproducibility. However, low kinetics in DNA hybridization often brings out long test terms, thus restricting their practical use. Here, we demonstrate unexpected fast DNA fluorescence detection on the confined surface of hydrogel particles. When the pore size and surface charge of hydrogel particles are tailored, DNA molecules can be confined in the outer water layer of hydrogel particles. We fabricated a fluorescence-on DNA sensor based on the hydrogel particle array by utilizing the fluorescence quenching property of graphene oxide and its different adsorption behaviors toward single-strand DNA or double-strand DNA. Benefiting from the confinement effect of hydrogel particle surface and the enrichment effect of water evaporation, the DNA-recognition time was descreased significantly from 3000 s to less than 10 s under the target concentration of 400 nM. Moreover, rapid detection can be achieved at concentrations between 50 and 400 nM. The study provides another insight to fabricate fast biosensors and shows great potential in DNA diagnostics, gene analysis, and liquid biopsy.

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“…Noting that T tot (N ) scales linearly with N , we can write T tot (N ) = N T tot (1), where T tot (1) is the average time per collision. After N collisions there will be R…”

Section: Registry Stagementioning

confidence: 99%

“…These functions depend on the ability of DNA to separate into individual strands and then re-hybridize. The recognition of specific nucleotide sequences during hybridization also plays a fundamental role in medicine, biotechnology, and nanotechnology [1][2][3][4] by enabling techniques like PCR [5][6][7] , DNA-based nanostructures (DNA origami) [8][9][10][11][12] , and methods for the diagnosis of diseases like HPV, HIV, and cancer [13][14][15] . The specificity in DNA hybridization is encoded in the complementary H-bonding patterns of the A-T and G-C Watson-Crick-Franklin (WCF) base pairs.…”

Section: Introductionmentioning

confidence: 99%

Beneficial and Detrimental Effects of Nonspecific Binding During DNA Hybridization

Phan

Schmit

2022

Preprint

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DNA strands have to sample numerous states to find the alignment that maximizes Watson-Crick-Franklin base pairing. This process depends strongly on sequence, which affects the stability of the native duplex as well as the prevalence of non-native inter- and intra-molecular helices. We present a theory which describes DNA hybridization as a three stage process: diffusion, registry search, and zipping. We find that non-specific binding affects each of these stages in different ways. Mis-registered intermolecular binding in the registry search stage helps DNA strands sample different alignments and accelerates the hybridization rate. Non-native intramolecular structure affects all three stages by rendering portions of the molecule inert to intermolecular association, limiting mis-registered alignments to be sampled, and impeding the zipping process. Once in register base-pairs are formed, the stability of the native structure is important to hold the molecules together long enough for non-native contacts to break.

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Factors and methods to modulate DNA hybridization kinetics

Cited by 25 publications

References 96 publications

Protocol Optimization of DNA Extraction from Banana Fruits

Protocol Optimization of DNA Extraction from Banana Fruits

Space-Confinment-Enhanced Fluorescence Detection of DNA on Hydrogel Particles Array

Beneficial and Detrimental Effects of Nonspecific Binding During DNA Hybridization

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