A DNA nanoswitch incorporating the fluorescent base analogue 2-aminopurine detects single nucleotide mismatches in unlabelled targets

Campbell, Colin J.; Mountford, C. P.; Stoquert, Helene C; Buck, Amy H.; Dickinson, Paul; Ferapontova, Elena E.; Terry, Jonathan G.; Beattie, John S.; Walton, A.J.; Crain, Jason; Ghazal, Peter; Mount, Andrew R.

doi:10.1039/b900325h

Cited by 3 publications

(4 citation statements)

References 29 publications

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“…use the fluorescence decay of 2AP positioned at the branchpoint to probe the conformation (switch state) and to detect structural differences arising from hybridization of matched and mis-matched targets (Campbell et al . 2009). The decay parameters reported enhanced base-stacking at the branchpoint on switch closure and could resolve variations in switch structure that enabled discrimination between target mutations that were indistinguishable from steady-state measurements.…”

Section: The Fluorescence Decay Of 2ap In Dna As a Reporter Of Conformentioning

confidence: 99%

“…There was good agreement between the quantum yields derived from the ultrafast decay parameters and those from the fluorescence intensities, showing that there remained no undetected decay processes faster than the 0.3-ps time resolution of the measurements. In further agreement with the observations of Mély and coworkers,(Avilov et al, 2008), the sub-5 ps decay components were found to be entirely suppressed in the presence of 70% glycerol.To assist in the development of a Holliday junction-based nanoswitch for detection of single-nucleotide mismatches in unlabelled targets, Campbell et al use the fluorescence decay of 2AP positioned at the branchpoint to probe the conformation (switch state) and to detect structural differences arising from hybridisation of matched and mis-matched targets(Campbell et al, 2009). The decay parameters reported enhanced base-stacking at the branchpoint on switch closure and could resolve variations in switch structure that enabled discrimination between target mutations that were indistinguishable from steady-state measurements.We used 2AP time-resolved fluorescence was used to complement single-molecule, multi-parameter Förster resonance energy transfer (FRET) measurements to investigate branchpoint expansion in a three-way junction(Sabir et al, 2012).…”

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confidence: 99%

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2-aminopurine as a fluorescent probe of DNA conformation and the DNA–enzyme interface

Jones

Neely

2015

Quart. Rev. Biophys.

125

130

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Nearly 50 years since its potential as a fluorescent base analogue was first recognized, 2-aminopurine (2AP) continues to be the most widely used fluorescent probe of DNA structure and the perturbation of that structure by interaction with enzymes and other molecules. In this review, we begin by considering the origin of the dramatic and intriguing difference in photophysical properties between 2AP and its structural isomer, adenine; although 2AP differs from the natural base only in the position of the exocyclic amine group, its fluorescence intensity is one thousand times greater. We then discuss the mechanism of interbase quenching of 2AP fluorescence in DNA, which is the basis of its use as a conformational probe but remains imperfectly understood. There are hundreds of examples in the literature of the use of changes in the fluorescence intensity of 2AP as the basis of assays of conformational change; however, in this review we will consider in detail only a few intensity-based studies. Our primary aim is to highlight the use of time-resolved fluorescence measurements, and the interpretation of fluorescence decay parameters, to explore the structure and dynamics of DNA. We discuss the salient features of the fluorescence decay of 2AP when incorporated in DNA and review the use of decay measurements in studying duplexes, single strands and other structures. We survey the use of 2AP as a probe of DNA-enzyme interaction and enzyme-induced distortion, focusing particularly on its use to study base flipping and the enhanced mechanistic insights that can be gained by a detailed analysis of the decay parameters, rather than merely monitoring changes in fluorescence intensity. Finally we reflect on the merits and shortcomings of 2AP and the prospects for its wider adoption as a fluorescence-decay-based probe.

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Section: The Fluorescence Decay Of 2ap In Dna As a Reporter Of Conformentioning

confidence: 99%

mentioning

confidence: 99%

2-aminopurine as a fluorescent probe of DNA conformation and the DNA–enzyme interface

Jones

Neely

2015

Quart. Rev. Biophys.

125

130

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“…71,72 Jones and co-workers used 2-aminopurine to investigate base-flipping in M.Hha1-DNA complexes (Fig. 5).…”

Section: Fluorescence-lifetime-based Biosensingmentioning

confidence: 99%

“…Fluorescent base analogs have little influence on the structure of host nucleic acids, but they show sensitive response to the change of the structures, which is well suited for investigating the structure changes of nucleic acids, especially when the change involves protein recognition. 71,72 Jones and co-workers used 2-aminopurine to investigate base-flipping in M.Hha1-DNA complexes (Fig. 5).…”

Section: Fluorescence-lifetime-based Biosensingmentioning

confidence: 99%

Nucleic Acid Fluorescent Probes for Biological Sensing

Xiao

Zhang

et al. 2012

Appl Spectrosc

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Nucleic acid fluorescent probes are playing increasingly important roles in biological sensing in recent years. In addition to the conventional functions of single-stranded DNA/RNA to hybridize with their complementary strands, affinity nucleic acids (aptamers) with specific target binding properties have also been developed, which has greatly broadened the application of nucleic acid fluorescent probes to the detection of a large variety of analytes, including small molecules, proteins, ions, and even whole cells. Another chemical property of nucleic acids is to act as substrates for various nucleic acid enzymes. This property can be utilized not only to detect those enzymes and screen their inhibitors, but also employed to develop effective signal amplification systems, which implies extensive applications. This review mainly covers the biosensing methods based on the above three types of nucleic acid fluorescent probes. The most widely used intensity-based biosensing assays are covered first, including nucleic acid probe-based signal amplification methods. Then fluorescence lifetime, fluorescence anisotropy, and fluorescence correlation spectroscopy assays are introduced, respectively. As a rapidly developing field, fluorescence imaging approaches are also briefly summarized.

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Base pair mismatch identification with DNA nanoswitch and long lifetime acridine fluorophore

McGuinness

Keszenman-Pereyra

Dickinson

et al. 2010

Sensors and Actuators B: Chemical

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A DNA nanoswitch incorporating the fluorescent base analogue 2-aminopurine detects single nucleotide mismatches in unlabelled targets

Cited by 3 publications

References 29 publications

2-aminopurine as a fluorescent probe of DNA conformation and the DNA–enzyme interface

2-aminopurine as a fluorescent probe of DNA conformation and the DNA–enzyme interface

Nucleic Acid Fluorescent Probes for Biological Sensing

Base pair mismatch identification with DNA nanoswitch and long lifetime acridine fluorophore

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