A strategy for establishing accurate quantitation standards of oligonucleotides: quantitation of phosphorus of DNA phosphodiester bonds using inductively coupled plasma–optical emission spectroscopy

Yang, Inchul; Han, Myung-Sub; Yim, Yong‐Hyeon; Hwang, Euijin; Park, Sang-Ryoul

doi:10.1016/j.ab.2004.08.038

Cited by 50 publications

(27 citation statements)

References 24 publications

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“…Phosphorus exists stoichiometrically in DNA and can be quantified using ICP–OES with an accuracy of ∼1% (45). Quantification of the amount of phosphorus by ICP–OES and gold by ICP–MS in the same sample provides a new approach to deduce the ratio of phosphorus to gold and hence the number of oligonucleotides to GNPs.…”

Section: Resultsmentioning

confidence: 99%

Efficient self-assembly of DNA-functionalized fluorophores and gold nanoparticles with DNA functionalized silicon surfaces: the effect of oligomer spacers

Milton

Patole

Yin

et al. 2013

Nucleic Acids Research

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Although strategies for the immobilization of DNA oligonucleotides onto surfaces for bioanalytical and top-down bio-inspired nanobiofabrication approaches are well developed, the effect of introducing spacer molecules between the surface and the DNA oligonucleotide for the hybridization of nanoparticle–DNA conjugates has not been previously assessed in a quantitative manner. The hybridization efficiency of DNA oligonucleotides end-labelled with gold nanoparticles (1.4 or 10 nm diameter) with DNA sequences conjugated to silicon surfaces via hexaethylene glycol phosphate diester oligomer spacers (0, 1, 2, 6 oligomers) was found to be independent of spacer length. To quantify both the density of DNA strands attached to the surfaces and hybridization with the surface-attached DNA, new methodologies have been developed. Firstly, a simple approach based on fluorescence has been developed for determination of the immobilization density of DNA oligonucleotides. Secondly, an approach using mass spectrometry has been created to establish (i) the mean number of DNA oligonucleotides attached to the gold nanoparticles and (ii) the hybridization density of nanoparticle–oligonucleotide conjugates with the silicon surface–attached complementary sequence. These methods and results will be useful for application with nanosensors, the self-assembly of nanoelectronic devices and the attachment of nanoparticles to biomolecules for single-molecule biophysical studies.

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Section: Resultsmentioning

confidence: 99%

Efficient self-assembly of DNA-functionalized fluorophores and gold nanoparticles with DNA functionalized silicon surfaces: the effect of oligomer spacers

Milton

Patole

Yin

et al. 2013

Nucleic Acids Research

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“…HPD was fragmented by sonication to an average size of 3,000 bp and absolutely quantified by ICP-OES [26]. Calibration standards for real-time PCR were prepared by gravimetric ten-fold serial dilutions of HPD in TE buffer.…”

Section: Methodsmentioning

confidence: 99%

Quantification of Trace-Level DNA by Real-Time Whole Genome Amplification

Kang

Kim

et al. 2011

PLoS ONE

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Quantification of trace amounts of DNA is a challenge in analytical applications where the concentration of a target DNA is very low or only limited amounts of samples are available for analysis. PCR-based methods including real-time PCR are highly sensitive and widely used for quantification of low-level DNA samples. However, ordinary PCR methods require at least one copy of a specific gene sequence for amplification and may not work for a sub-genomic amount of DNA. We suggest a real-time whole genome amplification method adopting the degenerate oligonucleotide primed PCR (DOP-PCR) for quantification of sub-genomic amounts of DNA. This approach enabled quantification of sub-picogram amounts of DNA independently of their sequences. When the method was applied to the human placental DNA of which amount was accurately determined by inductively coupled plasma-optical emission spectroscopy (ICP-OES), an accurate and stable quantification capability for DNA samples ranging from 80 fg to 8 ng was obtained. In blind tests of laboratory-prepared DNA samples, measurement accuracies of 7.4%, −2.1%, and −13.9% with analytical precisions around 15% were achieved for 400-pg, 4-pg, and 400-fg DNA samples, respectively. A similar quantification capability was also observed for other DNA species from calf, E. coli, and lambda phage. Therefore, when provided with an appropriate standard DNA, the suggested real-time DOP-PCR method can be used as a universal method for quantification of trace amounts of DNA.

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“…When dealing with very low quantities, neither spectrophotometric nor fluorometric methods can accurately quantify nucleic acids. Other methods, such as elemental analysis and traceable phosphorus, have circumvented this issue and are discussed elsewhere [52][53][54]. Commercially available systems for routine clinical work, developed by Nanodrop Technologies (Wilmington, DE), offer the ability to quantify nucleic acid using only 1 μL of purified sample.…”

Section: Part Iii: Assessment Of Nucleic Acid Quality and Quantitymentioning

confidence: 99%

Molecular Techniques in Hematopathology

Boyanton

Rushton

2010

Hematopathology

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A strategy for establishing accurate quantitation standards of oligonucleotides: quantitation of phosphorus of DNA phosphodiester bonds using inductively coupled plasma–optical emission spectroscopy

Cited by 50 publications

References 24 publications

Efficient self-assembly of DNA-functionalized fluorophores and gold nanoparticles with DNA functionalized silicon surfaces: the effect of oligomer spacers

Efficient self-assembly of DNA-functionalized fluorophores and gold nanoparticles with DNA functionalized silicon surfaces: the effect of oligomer spacers

Quantification of Trace-Level DNA by Real-Time Whole Genome Amplification

Molecular Techniques in Hematopathology

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