Biophysical properties of nucleic acids at surfaces relevant to microarray performance

Rao, Archana N.; Grainger, David W.

doi:10.1039/c3bm60181a

Cited by 92 publications

(108 citation statements)

References 274 publications

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“…However, the undertaking of proteomics is time-consuming and costly, so rapid and high-throughput microarrays of proteins (protein arrays) are being developed by various researchers [1][2][3]. Immobilization strategy and designing of an ideal, local chemical environment for the proteins on the solid surface are essential for the success of protein arrays and biosensor systems [4,5]. Proteins almost inevitably lose their naturally high activities once immobilized.…”

Section: Introductionmentioning

confidence: 99%

Polymer brush biointerfaces for highly sensitive biosensors that preserve the structure and function of immobilized proteins

Takasu

Kushiro

Hayashi

et al. 2015

Sensors and Actuators B: Chemical

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Section: Introductionmentioning

confidence: 99%

Polymer brush biointerfaces for highly sensitive biosensors that preserve the structure and function of immobilized proteins

Takasu

Kushiro

Hayashi

et al. 2015

Sensors and Actuators B: Chemical

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“…However in this experiment, the DNA is at 75 nM, which is lower than the theoretical binding capacity of the particles. At this lower concentration the DNA is much more flexible and can exist in its condensed mushroom form 64 . Figure 4c and A.7.…”

Section: Figure 2 -Size and Zeta Potential Data Captured Simultaneousmentioning

confidence: 99%

Particle-by-Particle Charge Analysis of DNA-Modified Nanoparticles Using Tunable Resistive Pulse Sensing

2016

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Resistive pulse sensors, RPS, are allowing the transport mechanism of molecules, proteins and even nanoparticles to be characterised as they traverse pores. Previous work using RPS has shown that the size, concentration and zeta potential of the analyte can be measured. Here we use tunable resistive pulse sensing (TRPS) which utilises a tunable pore to monitor the translocation times of nanoparticles with DNA modified surfaces. We start by demonstrating that the translocation times of particles can be used to infer the zeta potential of known standards and then apply the method to measure the change in zeta potential of DNA modified particles. By measuring the translocation times of DNA modified nanoparticles as a function of packing density, length, structure, and hybridisation time, we observe a clear difference in zeta potential using both mean values, and population distributions as a function of the DNA structure. We demonstrate the ability to resolve the signals for ssDNA, dsDNA, small changes in base length for nucleotides between 15-40 bases long and even the discrimination between partial and fully complementary target sequences. Such a method has potential and applications in sensors for the monitoring of nanoparticles in both medical and environmental samples.

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“…7 In addition, long DNA sequences form thermodynamically stable secondary structures that render the detection even more difficult. 8 Therefore, there is an obvious need for new solutions to detect long DNA sequences.…”

mentioning

confidence: 99%

Nanoparticle-Based Discrimination of Single-Nucleotide Polymorphism in Long DNA Sequences

et al. 2017

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Circulating DNA (ctDNA) and specifically the detection cancer-associated mutations in liquid biopsies promises to revolutionize cancer detection. The main difficulty however is that the length of typical ctDNA fragments (~150 bases) can form secondary structures potentially obscuring the mutated fragment from detection. We show that an assay based on gold nanoparticles (65 nm) stabilized with DNA (Au@DNA) can discriminate single nucleotide polymorphism in clinically-relevant ssDNA sequences (70-140 bases). The preincubation step was crucial to this process, allowing sequential bridging of Au@DNA, so that single base mutation can be discriminated, down to 100 pM concentration.Detection of single nucleotide polymorphisms (SNP) in ssDNA sequences by selective aggregation of plasmonic nanoparticles carries the potential for rapid determination of cancer biomarkers in liquid biopsies such as blood.1-3 Although, the detection of sequences of up to 40 bases without any signal amplification has been demonstrated 4,5 the average size of circulating DNA is ~150 bases in length, 6 and these longer fragments are more problematic as the increase of the sequence length affects the plasmon coupling (larger gaps between the particles), that decrease the limit of detection. 7 In addition, long DNA sequences form thermodynamically stable secondary structures that render the detection even more difficult.8 Therefore, there is an obvious need for new solutions to detect long DNA sequences.In earlier studies, we have reported a plasmonic assay comprising DNA-coated gold nanoparticles (AuNPs) that could discriminate SNP in less than 10 min. 9 Even though relatively large particles may lead to plasmon coupling upon aggregation, the assay is limited to the detection of rather short sequences (up to 23 bases). We report here that large plasmonic particles (65 nm) functionalized with modified DNA 10 can be used to detect single-base mutation in clinically relevant sequences with 140 bases in length. We found out that premixing the AuNPs (batch 1) with the target DNA was sufficient to induce aggregation upon addition of batch 2 (Figure 1b). In contrast, the addition of the target DNA to the mixture of two batches (standard sandwich assay, Figure 1a) had no effect on the aggregation.As a target we choose the most common point mutation in non-small cell lung cancer (NSCLC), the L858R mutation that occurs in the Epidermal Growth Factor Receptor (EGFR) gene.11 Detection of this mutation is an FDA and EMA-approved biomarker for the administration of TKItherapy to NSCLC patients. Figure 1d-e show possible secondary structures of target sequences comprising 70 and 140 bases, with indication of the binding sites of Au@DNA and the location of a single-point mutation. As a signal transducer, we used AuNPs with 65 nm in diameter, stabilized by short sequences that were complementary to either a mutation-free region in the target DNA (WT) or to a region that contained a single-base mutation (MUT) (Figure 1c). Each AuNP was stabilised by ~15...

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Biophysical properties of nucleic acids at surfaces relevant to microarray performance

Cited by 92 publications

References 274 publications

Polymer brush biointerfaces for highly sensitive biosensors that preserve the structure and function of immobilized proteins

Polymer brush biointerfaces for highly sensitive biosensors that preserve the structure and function of immobilized proteins

Particle-by-Particle Charge Analysis of DNA-Modified Nanoparticles Using Tunable Resistive Pulse Sensing

Nanoparticle-Based Discrimination of Single-Nucleotide Polymorphism in Long DNA Sequences

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