Nanopore Translocation of DNA Knots and its Applications to Measure DNA-DNA Interaction and Sharply Bent DNA Properties

Project: Research

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Nanopore devices can be utilized to measure not only the sequences of single-stranded DNA but also the conformational properties of double-stranded DNA. Recent nanopore experiments have detected DNA knots, which spontaneously form in long double-stranded DNA. Because DNA knots are sensitive to DNA properties, nanopore measurement of DNA knots provides unique opportunities to precisely determine relevant DNA properties. However, extracting DNA properties from DNA knots is not straightforward, and critically relies on the quantitative relationships between DNA properties and observation of DNA knots by nanopores. In this project,these quantitative relationships will be established using multiscale computer simulations, which can handle the wide length and time scales of relevant DNA structures and interactions. Three tasks will be implemented synergistically. First, nanopore experimental results of equilibrium DNA knotting probability, Pknot, will be used to determine DNA-DNA interaction strength, which can be quantified by an effective DNA hardcore diameter, deff . The relationship between Pknot and deff  will be established by Monte Carlo simulations. Our preliminary result shows deff < 2 nm at 3 mol/L LiCl, which indicates DNA-DNA electrostatic attraction, a counterintuitive phenomenon. Second, the minimum voltage or driving force required to squeeze a DNA knot into a small pore will be used to investigate sharply bent DNA properties. Recent nanopore experiments observed that a voltage of only 250 mV can squeeze a DNA knot into a 5 nm pore, which suggests DNA is much softer than expected. Our simulations will reveal the mechanism of such DNA softening and quantify this softening. Third, with the above results, we will build a pseudo phase diagram for knot jamming, sliding, and passing during nanopore translocation. To build this diagram, we will systematically vary the pore diameter and driving force in Langevin dynamics simulations of nanopore translocation of DNA knots. The diagram can be utilized to rationally choose experimental conditions for differentpurposes. Overall, this project will establish quantitative relationships between DNA properties and the observation of DNA knots by nanopores, which should enable nanopore devices to precisely measure DNA-DNA interaction and sharply bent DNA properties. As shown by our preliminary analysis, counterintuitive DNA-DNA electrostatic interaction and non-harmonic bending elasticity of sharply bent DNA will be extracted from nanopore results of DNA knots. Besides facilitating the development of DNA analysis technology, the results can be applied to quantitatively understand DNA packaging in vivo, which is largely determined by DNA-DNA interaction and sharply bent DNA properties. 


Project number9043390
Grant typeGRF
StatusNot started
Effective start/end date1/01/23 → …