Comparison of multiple DNA dyes for real-time PCR: effects of dye concentration and sequence composition on DNA amplification and melting temperature

Guðnason, Haukur; Dufva, Martin; Bang, Dang Duong; Wolff, Anders

doi:10.1093/nar/gkm671

Cited by 266 publications

(239 citation statements)

References 36 publications

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“…The Tm values obtained in this experiment are higher than those in the AuNP case because SYBR Green I is known to increase DNA Tm. 60 To confirm our conclusion, we also did an independent experiment where the hyperchromic effect of DNA melting at 260 nm was measured (see…”

Section: Melting As a Function Of Gap Size One Of The Most Importantmentioning

confidence: 66%

Assembly of DNA-Functionalized Gold Nanoparticles with Gaps and Overhangs in Linker DNA

et al. 2011

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DNA-directed assembly of gold nanoparticles (AuNPs) has been extensively studied because of its important applications in analytical chemistry, materials science, and nanomedicine. In a typical system, two DNA-functionalized AuNPs are assembled via a linker DNA to form large aggregates. In majority of the previous reports, the linker DNA is fully base paired with no gaps or overhangs present. Introducing such non-base-paired regions in the linker DNA has been recently shown to be important for making stimuli-responsive materials and in crystallization of such AuNPs. In this work, we systematically studied the effect of introducing gaps and overhangs in the linker DNA to understand the kinetics of assembly and the melting transition of these aggregates. We found that the assembly kinetics decreased with increasing linker DNA length. The melting temperature decreased with the loss of base stacking by introducing gaps as well as the steric effect of overhangs. Additional insights were obtained by measuring the melting curves of the free DNAs in the absence of AuNPs. For example, it appeared that DNA base stacking at the nick site was favored in assembled nanoparticles compared to that in free DNA. Our results indicate that while it is possible to form AuNP assemblies with linker DNAs containing various types of unpaired regions, these kinetic and thermodynamic factors need to be considered when designing related sensors and materials.

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Section: Melting As a Function Of Gap Size One Of The Most Importantmentioning

confidence: 66%

Assembly of DNA-Functionalized Gold Nanoparticles with Gaps and Overhangs in Linker DNA

et al. 2011

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“…This was possible by using a real-time turbidimeter 22 or by measuring the signals from DNA produced via fluorescent intercalating dyes 21,23 . Fluorescent detection is by far the most sensitive method, however, in a previous study, the intercalating dyes were shown to partially or completely inhibit PCR-based amplification, which compromised the advantages of using fluorescence measurement 24 . To our best knowledge, only a limited number of intercalating dyes such as SYTO 9 21 , SYTO 82 14 or SYBR Green 21 have been used rtLAMP.…”

Section: Comparison Of Multiple Dna Intercalating Dyes For Real-time mentioning

confidence: 98%

A lab-on-a-chip system with integrated sample preparation and loop-mediated isothermal amplification for rapid and quantitative detection of Salmonella spp. in food samples

et al. 2015

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Foodborne disease is a major public health threat worldwide. Salmonellosis, an infectious disease caused by Salmonella spp., is one of the most common foodborne diseases. Isolation and identification of Salmonella by conventional bacterial culture or molecular-based methods are time consuming and usually take a few hours to days to complete. In response to the demand for rapid on line or at site detection of pathogens, in this study, we describe for the first time an eight-chamber lab-on-a-chip (LOC) system with integrated magnetic beads-based sample preparation and loop-mediated isothermal amplification (LAMP) for rapid and quantitative detection of Salmonella spp. in food samples. The whole diagnostic procedures including DNA isolation, isothermal amplification, and real-time detection were accomplished in a single chamber. Up to eight samples could be handled simultaneously and the system was capable to detect Salmonella at concentration of 50 cells per test within 40 min. The simple design, together with high level of integration, isothermal amplification, and quantitative analysis of multiple samples in short time will greatly enhance the practical applicability of the LOC system for rapid on-site screening of Salmonella for applications in food safety control, environmental surveillance, and clinical diagnostics.

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“…Non-target amplifications resulting from primer-dimer artefacts were produced in the absence of template molecules in both negative control and unknown samples. They were excluded from the results through melt-curve analysis (Gudnason et al 2007). A subset (n = 8) of positive samples were confirmed as wood frog DNA via Sanger sequencing (GenBank accession #MG002391-MG002398).…”

Section: Abstract Edna · Wood Frog · Rana Sylvatica · Cytochrome B · mentioning

confidence: 99%

Development, validation, and evaluation of an assay for the detection of wood frogs (Rana sylvatica) in environmental DNA

Spangler

Huettmann

Herriott

et al. 2017

Conservation Genet Resour

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Comparison of multiple DNA dyes for real-time PCR: effects of dye concentration and sequence composition on DNA amplification and melting temperature

Cited by 266 publications

References 36 publications

Assembly of DNA-Functionalized Gold Nanoparticles with Gaps and Overhangs in Linker DNA

Assembly of DNA-Functionalized Gold Nanoparticles with Gaps and Overhangs in Linker DNA

A lab-on-a-chip system with integrated sample preparation and loop-mediated isothermal amplification for rapid and quantitative detection of Salmonella spp. in food samples

Development, validation, and evaluation of an assay for the detection of wood frogs (Rana sylvatica) in environmental DNA

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