Investigating the kinetics of DNA–DNA and PNA–DNA interactions using surface plasmon resonance-enhanced fluorescence spectroscopy

Kambhampati, Dev; Nielsen, Peter; Knoll, Wolfgang

doi:10.1016/s0956-5663(01)00239-1

Cited by 94 publications

(89 citation statements)

References 14 publications

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“…In order to get a high fluorescence yield, the distance between the chromophores and the metal surface needs to be optimized by employing functional self-assembled architecture avoiding quenching effects. [16][17][18][19] This fluorescence signal shows sufficient sensitivity to allow for the analysis of the rate constants of biomolecular interactions quantitatively even in the picomolar ͑10 −12 M͒ concentration range of the target. 20 As the catcher probe layer, peptide nucleic acids ͑PNAs͒ as mimics of DNA show great potential for biosensor applications.…”

Section: Introductionmentioning

confidence: 99%

Effect of ionic strength on PNA-DNA hybridization on surfaces and in solution

et al. 2007

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Section: Introductionmentioning

confidence: 99%

Effect of ionic strength on PNA-DNA hybridization on surfaces and in solution

et al. 2007

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“…11 Many examples for the kinetic analysis of biomolecular interaction processes on a sensor surface using SPFS have been reported. [12][13][14][15][16][17][18] Most of these studies were based on a simple bimolecular interaction scheme:…”

Section: Introductionmentioning

confidence: 99%

Kinetic and affinity analyses of hybridization reactions between peptide nucleic acid probes and DNA targets using surface plasmon field-enhanced fluorescence spectroscopy

et al. 2006

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Peptide nucleic acid (PNA), a polyamide DNA mimic, has inspired the development of a variety of hybridization-based methods for the detection, quantification, purification, and characterization of nucleic acids owing to the stability of the PNA/DNA duplex. In this work, PNA probes complementary to a specific sequence of Roundup Ready® soybean were immobilized onto a sensor surface via a self-assembled matrix employing streptavidin/biotin binding. The specific hybridization of PNA and DNA has been monitored by applying the chromophore-labeled DNA target oligonucleotides to the PNA modified Au sensor surface in real time using surface plasmon field-enhanced fluorescence spectroscopy. The authors demonstrate three kinds of experiments called global, titration, and kinetic analyses for the determination of rate constants for the association (kon) and dissociation processes (koff, and the affinity constant (KA) of the PNA/DNA duplex formation by fitting the data to a simple Langmuir model. Discrimination of a single base mismatched DNA (15mer) target on a 15mer PNA probe was documented, with a difference of the affinity constant of two orders of magnitude. Finally, the affinity constant for the hybridization of a long polymerase chain reaction product (169mer) obtained by amplification of DNA extracted from genetically modified soybean reference material has been determined by a kinetic-titration analysis. The results show the influence of a Coulomb barrier at high target surface coverage even for the hybridization to PNA at low ionic strength.

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“…1 order of magnitude larger than that for the DNA/DNA binding. 26 In this case, the BPA molecules bind to the aptamer fragments more strongly, which leads to the displacement of the DNA linkers and disassembly of the supersandwich structures. As proved by the UV−vis spectroscopy ( Figure 2C), the DNA nanostructures are largely diminished (i.e., released from the magnetic beads into the solution) after treatment with BPA.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

DNA Nanostructure-Based Magnetic Beads for Potentiometric Aptasensing

Ding

et al. 2015

Anal. Chem.

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In this work, a simple, general, and sensitive potentiometric platform is presented, which allows potentiometric sensing to be applied to any class of molecule irrespective of the analyte charge. DNA nanostructures are self-assembled on magnetic beads via the incorporation of an aptamer into a hybridization chain reaction. The aptamer− target binding event leads to the disassembly of the DNA nanostructures, which results in a dramatic change in the surface charge of the magnetic beads. Such a surface charge change can be sensitively detected by a polycation-sensitive membrane electrode using protamine as an indicator. With an endocrine disruptor bisphenol A as a model, the proposed potentiometric method shows a wide linear range from 0.1 to 100 nM with a low detection limit of 80 pM (3σ). The proposed sensing strategy will lay a foundation for the development of potentiometric sensors for highly sensitive and selective detection of various targets.

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Investigating the kinetics of DNA–DNA and PNA–DNA interactions using surface plasmon resonance-enhanced fluorescence spectroscopy

Cited by 94 publications

References 14 publications

Effect of ionic strength on PNA-DNA hybridization on surfaces and in solution

Effect of ionic strength on PNA-DNA hybridization on surfaces and in solution

Kinetic and affinity analyses of hybridization reactions between peptide nucleic acid probes and DNA targets using surface plasmon field-enhanced fluorescence spectroscopy

DNA Nanostructure-Based Magnetic Beads for Potentiometric Aptasensing

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