Numerical modeling of transport and accumulation of DNA on electronically active biochips

Kassegne, Sam; Reese, Howard R.; Hodko, Dalibor; Yang, Joon Mo; Sarkar, Kamal; Smolko, Dan; Swanson, Paul N.; Raymond, Daniel E.; Heller, Michael; Madou, Marc

doi:10.1016/s0925-4005(03)00322-8

Cited by 49 publications

(45 citation statements)

References 13 publications

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“…66,67 The use of an applied electric field to affect hybridization and to determine mutations by the application of a constant potential (-300 mV) followed by measuring the change in fluorescence with time has been described by Sosnowski et al 68 In their work, the probes were immobilized in a 1 µm thick gel-permeation layer coating the electrode, and denaturation was brought about by a complex mechanism involving a mixture of effects rather than as the result of simple electrostatic repulsion at the metal surface. 69,70 The use of electrochemical scanning dehybridization using fluorescence monitoring for SNP recognition has been recently demonstrated on silicon substrates with surface-bound hairpin (molecular beacons) probes. 71,72 However, in these experiments, the authors were unable to generate sufficient difference to distinguish SNP targets from the perfect match when using linear DNA probes.…”

Section: Introductionmentioning

confidence: 99%

SERS-Melting: A New Method for Discriminating Mutations in DNA Sequences

et al. 2008

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Abstract:The reliable discrimination of mutations, single nucleotide polymorphisms (SNPs), and other differences in genomic sequence is an essential part of DNA diagnostics and forensics. It is commonly achieved using fluorescently labeled DNA probes and thermal gradients to distinguish between the matched and mismatched DNA. Here, we describe a novel method that uses surface enhanced (resonance) Raman spectroscopy (SER(R)S) to follow denaturation of dsDNA attached to a structured gold surface. This denaturation is driven either electrochemically or thermally on SERS active sphere segment void (SSV) gold substrates. Using this method, we can distinguish between wild type, a single point mutation (1653C/ T), and a triple deletion (∆F 508) in the CFTR gene at the 0.02 attomole level, and the method can be used to differentiate the unpurified PCR products of the wild type and ∆F 508 mutation. Our method has the potential to provide small, rapid, sensitive, reproducible platforms for detecting genetic variations and sequencing genes.

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Section: Introductionmentioning

confidence: 99%

SERS-Melting: A New Method for Discriminating Mutations in DNA Sequences

et al. 2008

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“…This was done by forming a solution of eDc (1-ethyl-3-(3-dimethylaminopropyl) carbodiimide) at a concentration 40 mM and Sulfo-nhS (n-hydroxysulfosuccinimide) at a concentration of 100 mM. Phosphate buffered saline (PBS) and hydrochloric acid (hcl) are then mixed into this eDcSulfo-nhS solution so that the final solution possesses ph This was then followed by oligonucleotide attachment that involves applying 2 µl of oligonucleotide (Integrated Dna Technologies, coralville, Iowa) to the surface of microelectrode and then 5 V positive bias for 2 min (Vahidi et al 2014;Kassegne et al 2003Kassegne et al , 2009). The oligonucleotide was allowed to remain on the microelectrode for 12 h. Finally λ-Dna (new england Biolabs, Ipswich, Ma) attachment was done by using restriction enzyme ecorI to cut λ-Dna and create sticky ends.…”

Section: Dna Attachment To Polyferrocnt™ Electrodesmentioning

confidence: 99%

Manufacturing of high aspect-ratio 3-dimensional PolyFerroCNT nanocomposite polymer electrodes

2014

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“…Then DNA-containing aliquots were denatured at 95°C for 2 min, rapidly diluted in the SB solution, cooled to room temperature, and then immediately introduced into micro-electrochemical cell while holding the potential at +300 mV vs. Ag/AgCl. A positive potential was applied to the working electrode to facilitate diffusion of target DNA towards the ssDNA/ Ppy-modified electrode and to accelerate the accumulation of DNA on the surface of working electrode [38,39]. After the defined time the electrode was removed from the micro-electrochemical cell, thoroughly washed with buffer and deposited into a 2 mL electrochemical cell filled with SB.…”

Section: Detection Of Target Dnamentioning

confidence: 99%

Pulsed amperometric detection of DNA with an ssDNA/polypyrrole-modified electrode

Ramanavičienė

2004

Analytical and Bioanalytical Chemistry

116

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Pulsed amperometric detection (PAD) of target DNA with platinum electrodes modified by single-stranded DNA (ssDNA) entrapped within polypyrrole (ssDNA/Ppy) is reported for the first time. Single-stranded DNA 20-mers complementary to the target DNA were used to construct the DNA biosensors. Polymerase chain reaction (PCR) amplified bovine leukaemia virus (BLV) provirus DNA was used as target DNA. Electrochemical impedance spectroscopic (EIS) investigation of ssDNA/Ppy before and after incubation in target DNA-containing sample revealed significant changes in terms of an imaginary (Z") vs. a real (Z') component. The PAD results were in good agreement with EIS investigations. The PAD method was selected, because it does not require such sophisticated equipment as it is used to perform EIS and the results obtained can be more easily estimated. Optimum conditions for performing PAD and evaluating an analytical signal were elaborated. No label-binding step was necessary for detection of target DNA in PCR-amplified amplicons and detection time was reduced by as much as 30-35 min. The changes of PAD signals were at least 6-7 times higher if ssDNA/Ppy-modified electrodes instead of blank Ppy-modified electrodes were incubated in the target DNA solutions. If ssDNA/Ppy modified electrodes were incubated in non-complementary (control) DNA solution changes in PAD signals were smaller than those detected after incubation in complementary (target) DNA-containing solution by a factor of at least 6-8.

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Numerical modeling of transport and accumulation of DNA on electronically active biochips

Cited by 49 publications

References 13 publications

SERS-Melting: A New Method for Discriminating Mutations in DNA Sequences

SERS-Melting: A New Method for Discriminating Mutations in DNA Sequences

Manufacturing of high aspect-ratio 3-dimensional PolyFerroCNT nanocomposite polymer electrodes

Pulsed amperometric detection of DNA with an ssDNA/polypyrrole-modified electrode

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