Quantitative Measurements and Modeling of Kinetics in Nucleic Acid Monolayer Films Using SPR Spectroscopy

Georgiadis, R.; Peterlinz, K. P.; Peterson, Alexander W.

doi:10.1021/ja9930824

Cited by 277 publications

(267 citation statements)

References 27 publications

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“…In this section, we examine the effect of electrostatic charging on target͞probe hybridization. The DNA monolayer films used in this work have been extensively characterized by SPR, neutron scattering, and surface melting experiments and are found to be robust and reusable (8,9,25). For these experiments, hybridization was allowed to proceed with no potential applied, then the potential was swept at a rate of 50 mV s Ϫ1 to the desired potential (ϩ300 mV or Ϫ300 mV), and hybridization allowed to continue.…”

Section: Spr Detection In the Presence Of An Applied Electrochemical mentioning

confidence: 99%

“…The ordinate is given as percentage of steady-state hybridization. That is, the DNA coverage is calculated from analysis of the SPR reflectance curves as described previously (8,9,24,25). The progress of hybridization is shown as the percent of the duplex DNA surface coverage relative to the steady state coverage achieved after Ϸ14 h of hybridization at open circuit.…”

Section: Spr Detection In the Presence Of An Applied Electrochemical mentioning

confidence: 99%

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Electrostatic surface plasmon resonance: Direct electric field-induced hybridization and denaturation in monolayer nucleic acid films and label-free discrimination of base mismatches

Heaton

Peterson

Georgiadis

2001

Proc. Natl. Acad. Sci. U.S.A.

214

210

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We demonstrate that in situ optical surface plasmon resonance spectroscopy can be used to monitor hybridization kinetics for unlabeled DNA in tethered monolayer nucleic acid films on gold in the presence of an applied electrostatic field. The dc field can enhance or retard hybridization and can also denature surfaceimmobilized DNA duplexes. Discrimination between matched and mismatched hybrids is achieved by simple adjustment of the electrode potential. Although the electric field at the interface is extremely large, the tethered single-stranded DNA thiol probes remain bound and can be reused for subsequent hybridization reactions without loss of efficiency. Only capacitive charging currents are drawn; redox reactions are avoided by maintaining the gold electrode potential within the ideally polarizable region. Because of potential-induced changes in the shape of the surface plasmon resonance curve, we account for the full curve rather than simply the shift in the resonance minimum.electrochemistry ͉ DNA hybridization ͉ DNA mismatch discrimination I ncreasing research efforts are directed toward the detection of nucleic acid interactions with immobilized oligonucleotide probes for DNA microarray applications (1, 2). Limitations of most current technologies include complex DNA immobilization procedures, the need for fluorescence or other labeling, and slow hybridization kinetics that require long incubation times. In addition, those experimental conditions that optimize DNA duplex formation often also reduce the stringency of hybridization. That is, for oligonucleotides that are sufficiently long to distinguish a particular sequence in the presence of unrelated DNA, a mismatched base pair has only a marginal effect on the stability of the duplex (3). In DNA microarray applications, mismatched hybrids lead to ''false positives.''The use of an electric field to easily control the electrostatic forces on surface-immobilized polyelectrolytes such as DNA has not yet been fully exploited as a means for improving the speed and stringency of biomolecular interactions at interfaces.In this paper, we investigate the effect of simple electrostatic charging on the interactions of surface-bound monolayer nucleic acid films with unlabeled DNA target oligonucleotides by using a combination of electrochemical control and in situ real-time surface plasmon resonance (SPR) spectroscopy detection.The monolayer DNA thiol films used in this work are tethered directly to the SPR metal sensor surface through a gold-thiol covalent attachment. Therefore, the immobilized DNA hybrids are exposed to a field gradient at the metal͞electrolyte interface on the order of 10 9 V͞m. We show that this field can be used, in a reversible manner, to increase or decrease the rate of oligonucleotide hybridization. In addition, we show that a repulsive potential preferentially denatures mismatched DNA hybrids within a few minutes, while leaving the fully complementary hybrids largely intact. This sequence selectivity in hybrid denaturation imparts an extr...

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Section: Spr Detection In the Presence Of An Applied Electrochemical mentioning

confidence: 99%

Section: Spr Detection In the Presence Of An Applied Electrochemical mentioning

confidence: 99%

Electrostatic surface plasmon resonance: Direct electric field-induced hybridization and denaturation in monolayer nucleic acid films and label-free discrimination of base mismatches

Heaton

Peterson

Georgiadis

2001

Proc. Natl. Acad. Sci. U.S.A.

214

210

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“…Modeling studies with thiolated DNA have demonstrated that efficient hybridization occurs in the well-controlled condition of surface-attached probes with large interprobe distances and upright conformations. [13][14][15][16][17][18][19][20][21][22][23][24] However, constructing a reproducible DNA recognition layer with both of these properties is a critical challenge owing to unexpected surface adsorptions, disordered conformations, inconsistencies in grafting density and the flexibility of probe molecules. It is thus imperative to obtain an in-depth understanding of the factors that influence the structure of immobilized DNA layers.…”

Section: Introductionmentioning

confidence: 99%

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confidence: 99%

Scaffolded biosensors with designed DNA nanostructures

et al. 2013

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In addition to its fundamental function as a genetic code carrier, the utilization of DNA in various material applications has been actively explored over the past several decades. DNA is intrinsically an excellent type of self-assembly nanomaterial owing to its predictable base-pairing, high chemical stability and the convenience it possesses for synthesis and modification. Because of these unparalleled properties, DNA is widely used as excellent recognition elements in biosensors and as unique building blocks in nanodevices. A critical challenge in surface-based DNA biosensors lies in the reduced accessibility of target molecules to the DNA probes arranged on heterogeneous surfaces, especially when compared to probe-target recognition in homogeneous solutions. To improve the recognition abilities of these heterogeneous surface-confined DNA probes, much effort has been devoted to controlling the surface chemistry, conformation and packing density of the probe molecules, as well as the size and geometry of the surface. In this review, we aim to summarize the recent progress on the improvement of the probetarget recognition properties by introducing DNA nanostructure scaffolds. A range of new strategies have proven to provide a significantly enhanced range in the spatial positioning and the accessibility of the probes to the surface over previously reported linear structures. We will also describe the applications of DNA nanostructure scaffold-based biosensors. INTRODUCTIONDetection of nucleic acids (DNA or RNA) is an integral step in many applications, including in clinical diagnosis, environmental monitoring and antibioterrorism. 1 With these applications in mind, significant efforts have been made to develop sensitive, selective, rapid and cost-effective DNA (or RNA) biosensors. In parallel, DNAbased devices have also attracted a significant, recent interest owing to their promising applications in nanoelectronics, 2,3 biomolecular computations, 4-8 cellular imaging 9 and drug delivery. [10][11][12] In a typical design of DNA biosensors and nanodevices, oligonucleotides are often used as the molecular recognition layer. Because DNA is comprised of only four bases with A-T and G-C pairing, DNA hybridization processes are highly predictable and can be finely tuned with a rational design of the sequence. In addition, DNA oligonucleotides are usually easy to design, chemically stable and cost-effective.Understanding the physical structure of a DNA probe immobilized on a surface is critical in applications using DNA as a molecular recognition element. The properties of the DNA molecular recognition layer (such as selectivity, sensitivity and reproducibility) highly depend on the structure of the self-assembled DNA film. Modeling studies with thiolated DNA have demonstrated that efficient hybridization occurs in the well-controlled condition of surface-attached probes with large interprobe distances and upright conformations. [13][14][15][16][17][18][19][20][21][22][23][24]

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“…Adsorption of DNA oligomers on gold electrode is a complicated kinetic process [32]. Until now one of the most common strategies for DNA immobilization on gold electrode is the formation of thiolated DNA self-assembly monolayer (SAM) via the strong Au-S bond.…”

Section: Resultsmentioning

confidence: 99%

Fast assembly of non-thiolated DNA on gold surface at lower pH

Jiang¹,

Materón²,

Sotomayor³

et al. 2013

Journal of Colloid and Interface Science

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In a typical protocol for attaching DNA to a gold electrode, thiolated DNA is incubated with the electrode at neutral pH overnight. Here we report fast adsorption of non-thiolated DNA oligomers on gold electrodes at acidic pH (i.e., pH ~3.0). The peak-to-peak potential difference and the redox peak currents in typical cyclic voltammetry of [Fe(CN)6] 3-are investigated to monitor the attachment. Compared with incubation at neutral pH, the lower pH can significantly promote the adsorption processes, enabling efficient adsorption even in 30 min. The adsorption rate is DNA concentration-dependent, while the ionic strength shows no influence. Moreover, the adsorption is base-discriminative, with a preferred order of A >C>>G, T, which is attributed to the protonation of A and C at low pH and their higher binding affinity to gold surface. The immobilized DNA is functional and can hybridize with its complementary DNA but not a random DNA. This work is promising to provide a useful time-saving strategy for DNA assembly on gold electrodes, allowing fast fabrication of DNA-based biosensors and devices.3

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Quantitative Measurements and Modeling of Kinetics in Nucleic Acid Monolayer Films Using SPR Spectroscopy

Cited by 277 publications

References 27 publications

Electrostatic surface plasmon resonance: Direct electric field-induced hybridization and denaturation in monolayer nucleic acid films and label-free discrimination of base mismatches

Electrostatic surface plasmon resonance: Direct electric field-induced hybridization and denaturation in monolayer nucleic acid films and label-free discrimination of base mismatches

Scaffolded biosensors with designed DNA nanostructures

Fast assembly of non-thiolated DNA on gold surface at lower pH

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