Temperature dependence of DNA translocations through solid-state nanopores

Verschueren, Daniel; Jonsson, Magnus P.; Dekker, Cees

doi:10.1088/0957-4484/26/23/234004

Cited by 49 publications

(42 citation statements)

References 54 publications

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“…Thus, it is unlikely that the increase in frequency is entirely due to reduced solution viscosity and other effects, which induce sensitivity to polymer size, will have to be considered. On the other hand, mean blockade duration is shown to decrease exponentially with temperature in the case of PEG 1500, in agreement with the classical behavior observed in previous work2742434445464748, while increasing exponentially in the case of PEG 3400 (Fig. 3).…”

Section: Resultssupporting

confidence: 91%

“…On the one hand, blockade frequency increases exponentially with temperature for the two PEG molar masses, saturating above 35 °C for PEG 3400 because the pore is mostly occupied due to the increasing duration of blocks. A frequency increase with temperature has previously been observed with various pores and analytes42434445 and is, here, to be expected from the lower solution viscosity if entry of PEG molecules into the pore is limiting for the on-rate of the interaction27. However, like Reiner et al 27,.…”

Section: Resultssupporting

confidence: 53%

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High Temperature Extends the Range of Size Discrimination of Nonionic Polymers by a Biological Nanopore

Piguet¹,

Ouldali²,

Discala³

et al. 2016

Sci Rep

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We explore the effect of temperature on the interaction of polydisperse mixtures of nonionic poly(ethylene glycol) (PEG) polymers of different average molar masses with the biological nanopore α-hemolysin. In contrast with what has been previously observed with various nanopores and analytes, we find that, for PEGs larger than a threshold molar mass (2000 g/mol, PEG 2000), increasing temperature increases the duration of the PEG/nanopore interaction. In the case of PEG 3400 the duration increases by up to a factor of 100 when the temperature increases from 5 °C to 45 °C. Importantly, we find that increasing temperature extends the polymer size range of application of nanopore-based single-molecule mass spectrometry (Np-SMMS)-type size discrimination. Indeed, in the case of PEG 3400, discrimination of individual molecular species of different monomer number is impossible at room temperature but is achieved when the temperature is raised to 45 °C. We interpret our observations as the consequence of a decrease of PEG solubility and a collapse of PEG molecules with higher temperatures. In addition to expanding the range of application of Np-SMMS to larger nonionic polymers, our findings highlight the crucial role of the polymer solubility for the nanopore detection.

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Section: Resultssupporting

confidence: 91%

Section: Resultssupporting

confidence: 53%

High Temperature Extends the Range of Size Discrimination of Nonionic Polymers by a Biological Nanopore

Piguet¹,

Ouldali²,

Discala³

et al. 2016

Sci Rep

View full text Add to dashboard Cite

show abstract

“…This is too high for reliable detection of different nucleotides. Several methods have been developed to slow down translocation: modifying the DNA molecule (19,20), immobilizing DNA (21,22), adding hairpins or double-stranded DNA to the end of the ssDNA (23)(24)(25), employing dumbbell structures (26)(27)(28), modifying the viscosity of the solvent (29,30), varying temperature (31)(32)(33), adding charge modifications to the nanopore (12,(34)(35)(36), and controlling the speed by mechanical force (10). Aside from charge-modified nanopores, these techniques are usually very complex and can modify the analytes or the buffer solution, which affects the ionic current signal.…”

Section: Introductionmentioning

confidence: 99%

Effects of Nanopore Charge Decorations on the Translocation Dynamics of DNA

Jou

Muthukumar

2017

Biophysical Journal

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We have investigated the dynamics of single-stranded DNA as it translocates through charge-mutated protein nanopores. Translocation of DNA is a crucial step in nanopore-based sequencing platforms, where control over translocation speed remains one of the main challenges. Taking advantage of the interactions between negatively charged DNA and positively charged amino acid residues, the translocation speed of DNA can be manipulated by deliberate charge decorations inside the nanopore. We employed coarse-grained Langevin dynamics simulations to monitor the step-by-step movement of DNA through different mutations of α-hemolysin protein nanopores. We found that although the average translocation time per nucleotide is longer, in agreement with experiments, the DNA nucleotides do not translocate with a uniform speed. Furthermore, the location and spacing of the charge decorations can alter the translocation dynamics significantly, trapping DNA in some cases. Our findings can give insights when designing charge patterns in nanopores.

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“…It also agreed with other previous parameter's studies where small nanopore exhibited a strong effect of each parameters on translocation time, while large pore showed less effect on almost all those parameters. Recent report demonstrated a strong effect of temperature on the DNA dynamic in large nanopore (10 nm) [50]. Decreasing temperature to 0 ℃ could prolong the translocation speed down to 7.5 mm/s.…”

Section: Temperaturementioning

confidence: 98%

Speculation of Nano-gap Sensor for DNA sequencing technology: A Review on Synthetic Nanopores

Pungetmongkol

2018

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Nano-gap sensor is the next generation of single molecule analysis that consumes less resources, costs, times and spaces. The ultimate goal of this technology is rendering the ability to determine any living genetic code in several seconds using this portable device. In principle, DNA decryption was determined by tracking electrical signal change when DNA is passed through either natural or synthetic nanometer size gap. This review focuses on the synthetic nanopore, which is more robust, reliable and manageable with ease. Biological nanopore has been researched in parallel; however, the device reproducibility is a controversial issue. The history and development toward the future of this prospect technology will be elaborated attentively. The main limitation of nanopore sensor device is the controlling of DNA translocation dynamic through tiny pore. Many attempts had been tried and the synopsis will be contemplated in the review. Nonetheless, the present results of DNA sequencing have not been satisfied, the development of nanogap sensor is promising for genomic sequencing and molecular biology.

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Temperature dependence of DNA translocations through solid-state nanopores

Cited by 49 publications

References 54 publications

High Temperature Extends the Range of Size Discrimination of Nonionic Polymers by a Biological Nanopore

High Temperature Extends the Range of Size Discrimination of Nonionic Polymers by a Biological Nanopore

Effects of Nanopore Charge Decorations on the Translocation Dynamics of DNA

Speculation of Nano-gap Sensor for DNA sequencing technology: A Review on Synthetic Nanopores

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