Gold nanoparticle-assisted single base-pair mismatch discrimination on a microfluidic microarray device

Wang, Lin; Li, Paul C. H.

doi:10.1063/1.3463720

Cited by 23 publications

(6 citation statements)

References 43 publications

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“…colorimetric, fluorescence) can result from the close proximity between AuNPs released upon DNA hybridization with complementary ssDNA. [15][16][17][18][19][20][21] Previous work by Li et al demonstrated the use of binding of DNA to AuNPs for applications in which the AuNPs were used to hold onto the ssDNA as a cargo in assisting single base pair discrimination, 24,25 but the mechanism of this discrimination is yet to be determined (vide infra).…”

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confidence: 99%

“…[10][11][12][13] Through further research, Li et al have determined that AuNP-loaded DNA targets (AuNPtargets), in contrast to the DNA targets freely dissolved in the buffer solution (free-targets), were able to discriminate between the PM immobilized probe from the single base-pair mismatched (MM) probes when unaided by thermal stringency at room temperature. 24,25 We hypothesized that AuNPs compete with the immobilized probes to gain the target binding, which increases the stringency of the hybridization process. During this competitive process the MM duplex formation with a lower hybridization affinity would be influenced more strongly by the presence of AuNPs than the formation of PM duplex.…”

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confidence: 99%

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A Proposed Mechanism of the Influence of Gold Nanoparticles on DNA Hybridization

Sedighi

Pekcevik

et al. 2014

ACS Nano

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A combination of gold nanoparticles (AuNPs) and nucleic acids has been used in biosensing applications. However, there is a poor fundamental understanding of how gold nanoparticle surfaces influence the DNA hybridization process. Here, we measured the rate constants of the hybridization and dehybridization of DNA on gold nanoparticle surfaces to enable the determination of activation parameters using transition state theory. We show that the target bases need to be detached from the gold nanoparticle surfaces before zipping. This causes a shift of the rate-limiting step of hybridization to the mismatch-sensitive zipping step. Furthermore, our results propose that the binding of gold nanoparticles to the single-stranded DNA segments (commonly known as bubbles) in the duplex DNA stabilizes the bubbles and accelerates the dehybridization process. We employ the proposed mechanism of DNA hybridization/dehybridization to explain the ability of 5 nm diameter gold nanoparticles to help discriminate between single base-pair mismatched DNA molecules when performed in a NanoBioArray chip. The mechanistic insight into the DNA-gold nanoparticle hybridization/dehybridization process should lead to the development of new biosensors.

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A Proposed Mechanism of the Influence of Gold Nanoparticles on DNA Hybridization

Sedighi

Pekcevik

et al. 2014

ACS Nano

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“…In our group, we have previously employed the MMA chip for detection of DNA [37][38][39] and RNA targets. 40 The microfluidic microarray chip offers several advantages to other designs (e.g.…”

Section: R a F Tmentioning

confidence: 99%

Effect of buffer composition on PNA–RNA hybridization studied in the microfluidic microarray chip

et al. 2018

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Herein, we report that peptide nucleic acid sequences (PNAs) have been used as the probe species for detection of RNA and that a microfluidic microarray (MMA) chip is used as the platform for detection of hybridizations between immobilized PNA probes and RNA targets. The RNA targets used are derived from influenza A sequences. This paper discusses the optimization of two probe technologies used for RNA detection and investigates how the composition of the probe buffer and the content of the hybridization solution can influence the overall results. Our data show that the PNA probe is a better choice than the DNA probe when there is low salt in the probe buffer composition. Furthermore, we show that the absence of salt (NaCl) in the hybridization buffer does not hinder the detection of RNA sequences. The results provide evidence that PNA probes are superior to DNA probes in term of sensitivity and adaptability, as PNA immobilization and PNA–RNA hybridization are less affected by salt content in the reaction buffers unlike DNA probes.

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“…Some of the common polymer materials used include polycarbonates (PCs) 14,15 and polydimethylsiloxane. 12,16,17 For this research, a polycarbonate compact disc base material was selected. Studies have shown that polycarbonate is PCR friendly.…”

Section: B Pcr Sample Chamber Design and Fabricationmentioning

confidence: 99%

Rapid multi sample DNA amplification using rotary-linear polymerase chain reaction device (PCRDisc)

Sugumar

Kong

Ismail³

et al. 2012

Biomicrofluidics

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Multiple sample DNA amplification was done by using a novel rotary-linear motion polymerase chain reaction (PCR) device. A simple compact disc was used to create the stationary sample chambers which are individually temperature controlled. The PCR was performed by shuttling the samples to different temperature zones by using a combined rotary-linear movement of the disc. The device was successfully used to amplify up to 12 samples in less than 30 min with a sample volume of 5 ll. A simple spring loaded heater mechanism was introduced to enable good thermal contact between the samples and the heaters. Each of the heater temperatures are controlled by using a simple proportional-integral-derivative pulse width modulation control system. The results show a good improvement in the amplification rate and duration of the samples. The reagent volume used was reduced to nearly 25% of that used in conventional method. V C 2012 American Institute of Physics. [http://dx

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Gold nanoparticle-assisted single base-pair mismatch discrimination on a microfluidic microarray device

Cited by 23 publications

References 43 publications

A Proposed Mechanism of the Influence of Gold Nanoparticles on DNA Hybridization

A Proposed Mechanism of the Influence of Gold Nanoparticles on DNA Hybridization

Effect of buffer composition on PNA–RNA hybridization studied in the microfluidic microarray chip

Rapid multi sample DNA amplification using rotary-linear polymerase chain reaction device (PCRDisc)

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