Complementary and partially complementary DNA duplexes tethered to a functionalized substrate: a molecular dynamics approach to biosensing

Monti, Susanna; Cacelli, Ivo; Ferretti, Alessandro; Prampolini, Giacomo; Barone, Vincenzo

doi:10.1039/c1cp21115c

Cited by 4 publications

(4 citation statements)

References 51 publications

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“…On the other hand, some classical molecular dynamics (MD) simulations with the DNA tethered onto the solid state have been carried out [14][15][16][17][18][19][20][21]. They contributed to the comprehension of the dynamics of tethered DNA, but the ionic or water molecular behavior at the solid/liquid interface has not been considered.…”

Section: Introductionmentioning

confidence: 99%

Effect of double-stranded DNA on electrical double layer structure at oxide/electrolyte interface in classical molecular dynamics simulation

Maekawa

Shibuta

Sakata

2015

Chemical Physics Letters

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The elucidation of the electrical double layer (EDL) structure including biomolecules is helpful in controlling biointerfacial functions in biosensing devices. In this study, the effect of double-stranded DNA (ds-DNA) on the EDL structure at the SiO2/NaClaq interface in a concentrated solution was investigated by classical molecular dynamics (MD) simulation. In 1.0 M NaClaq, negatively charged ds-DNA shielded electrically by cations did not affect the potential profile of the EDL structure. This finding indicates that the simulated bio-interfacial structure allows the detection of ionic charges adsorbed directly onto substrates in a concentrated solution regardless of the presence of shielded biomolecular charges.

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Section: Introductionmentioning

confidence: 99%

Effect of double-stranded DNA on electrical double layer structure at oxide/electrolyte interface in classical molecular dynamics simulation

Maekawa

Shibuta

Sakata

2015

Chemical Physics Letters

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“…Simulations of interfaces between tethered DNA and oxide or metal surfaces have been reported to analyze ionic behaviors around the gate oxide/electrolyte interface. [13][14][15][16][17][18] We also simulated the aqueous structure around the SiO 2 /solution interface without or with a DNA duplex in the previous papers. [19][20][21] As one of the experimental results, DNA molecular charges were detected inside the Debye length by varying the extended base lengths, but no quantitative signals were obtained for DNA molecules more than 40 bases, the lengths of which were longer than the Debye length.…”

mentioning

confidence: 99%

Effect of Ionic Atmosphere around DNA/Electrolyte Interface on Potentiometric Signal

Maekawa

Shibuta

Sakata

2017

J. Electrochem. Soc.

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Biomolecular recognitions with an ion sensitive field effect transistor (ISFET) are mostly reported to strongly depend on the structure and dynamics of the electric double layer (EDL) at the gate electrode/electrolyte interface, while the effect of an ionic behavior around a biomolecule/electrolyte interface on the potentiometric detection has not been clarified. In this study, we investigated the behavior of water and ions around a DNA/electrolyte interface using molecular dynamics (MD) simulations, where the charge distribution may induce a field effect contributing to electrical signals of a DNA-modified ISFET sensor. As a result, MD simulations showed that the interfacial charge distribution with a gentle slope (ionic atmosphere) was more clearly found around the DNA duplex at a lower concentration of NaCl electrolyte, while the counter ion condensation was observed nearby the DNA duplex with increasing the concentration of NaCl electrolyte. This means the EDL structure was found at the DNA/electrolyte interface. Such an ionic atmosphere around the DNA duplex would cause the shift in the threshold voltage for DNA molecular recognition events such as hybridization on the gate of ISFET. Our knowledge based on the MD simulation for the biomolecule/electrolyte interface contributes to design and develop an optimum device on potentiometric biosensors.

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“…Molecular dynamics simulations of surface-immobilized simple DNA complexes provide similar possibilities even though the time scale of simulated events and the length of the DNA complexes are still far from those involved in standard SPRi assays. 53 A further interesting aspect is SPRi signal sampling and management.…”

mentioning

confidence: 99%

“…It is also expected that more sophisticated in silico models, designed on purpose, may better mimic the biochip environment, thus providing a useful tool for the design of even more efficient SPRi assays. Molecular dynamics simulations of surface-immobilized simple DNA complexes provide similar possibilities even though the time scale of simulated events and the length of the DNA complexes are still far from those involved in standard SPRi assays . A further interesting aspect is SPRi signal sampling and management.…”

mentioning

confidence: 99%

Surface Plasmon Resonance Imaging: What Next?

Spoto

Minunni

2012

J. Phys. Chem. Lett.

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This Perspective discusses recent advances in the field of surface plasmon resonance imaging (SPRi) for the label-free, multiplex, and sensitive study of biomolecular systems. Large efforts have been made during the past decade with the aim of developing even more sensitive and specific SPRi-based platforms. Metal nanostructures have been used to enhance SPRi sensitivity and to build a specific SPR-active surface, while special effects such as long-range SPR have been investigated to develop more effective SPRi platforms. Here, we review some of the significant work performed with SPRi for the ultrasensitive detection of biomolecular systems and provide a perspective on the challenges that need to be overcome to enable the wide use of SPRi in emerging key areas such as health diagnostics and antidoping controls.

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Complementary and partially complementary DNA duplexes tethered to a functionalized substrate: a molecular dynamics approach to biosensing

Cited by 4 publications

References 51 publications

Effect of double-stranded DNA on electrical double layer structure at oxide/electrolyte interface in classical molecular dynamics simulation

Effect of double-stranded DNA on electrical double layer structure at oxide/electrolyte interface in classical molecular dynamics simulation

Effect of Ionic Atmosphere around DNA/Electrolyte Interface on Potentiometric Signal

Surface Plasmon Resonance Imaging: What Next?

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