Modeling and Analysis of Intercalant Effects on Circular DNA Conformation

Effect of surface functionalization on DNA sequencing using MXene-based nanopores

As one of the most promising types of label-free nanopores has great potential for DNA sequencing via fast detection of different DNA bases. As one of the most promising types of label-free nanopores, two-dimensional nanopore materials have been developed over the past two decades. However, how to detect different DNA bases efficiently and accurately is still a challenging problem. In the present work, the translocation of four homogeneous DNA strands (i.e., poly(A)20, poly(C)20, poly(G)20, and poly(T)20) through two-dimensional transition-metal carbide (MXene) membrane nanopores with different surface terminal groups is investigated via all-atom molecular dynamics simulations. Interestingly, it is found that the four types of bases can be distinguished by different ion currents and dwell times when they are transported through the Ti3C2(OH)2 nanopore. This is mainly attributed to the different orientation and position distributions of the bases, the hydrogen bonding inside the MXene nanopore, and the interaction of the ssDNA with the nanopore. The present study enhances the understanding of the interaction between DNA strands and MXene nanopores with different functional groups, which may provide useful guidelines for the design of MXene-based devices for DNA sequencing in the future.

Translocation of Proteins through Solid-State Nanopores Using DNA Polyhedral Carriers

The detection of biomolecules at the single molecule level has important applications in the fields of biosensing and biomedical diagnosis. The solid-state nanopore (SS nanopore) is a sensitive tool for detecting single molecules because of its unique label-free and low sample consumption properties. SS nanopore translocation of small biomolecules is typically driven by an electronic field force and is thus influenced by the charge, shape, and size of the target molecules. Therefore, it remains challenging to control the translocation of biomolecules through SS nanopores, particularly for different proteins with complex conformations and unique charges. Toward this problem, a DNA polyhedral carrier coating strategy to assist protein translocation through SS nanopores is developed, which facilitates target protein detection. The current signal-to-noise ratios are improved significantly using this DNA carrier loading strategy. The proposed method should aid the detection of proteins, which are difficult to translocate through nanopores. This coating-assisted method offers a wide range of applications for SS nanopore detection and promotes the development of single-molecule detection.

Structure-flexible DNA origami translocation through a solid-state nanopore

Nanopore detection is a label-free detection method designed to analyze single molecules by comparing specific translocation events with high signal-to-noise ratios. However, it is still challenging to understand the influences of structural flexibility of 100 nm DNA origami on nanopore translocations. Here, we used solid-state nanopores to characterize the translocation of “nunchaku” origami structures, the flexibility of which can be regulated by introducing specific DNA strands and streptavidin protein. The structural changes can result in significant variations in the translocation signals and distributions. It is anticipated that such a method of the flexible DNA origami translocation through a solid-state nanopore will find further applications in molecular detection as well as biosensing.

Using a solid-state nanopore to characterize the translocation of “nunchaku” origami with tunable-structures.

Ethidium bromide interactions with DNA: an exploration of a classic DNA-ligand complex with unbiased molecular dynamics simulations

Visualization of double stranded DNA in gels with the binding of the fluorescent dye ethidium bromide has been a basic experimental technique in any molecular biology laboratory for >40 years. The interaction between ethidium and double stranded DNA has been observed to be an intercalation between base pairs with strong experimental evidence. This presents a unique opportunity for computational chemistry and biomolecular simulation techniques to benchmark and assess their models in order to see if the theory can reproduce experiments and ultimately provide new insights. We present molecular dynamics simulations of the interaction of ethidium with two different double stranded DNA models. The first model system is the classic sequence d(CGCGAATTCGCG)₂ also known as the Drew–Dickerson dodecamer. We found that the ethidium ligand binds mainly stacked on, or intercalated between, the terminal base pairs of the DNA with little to no interaction with the inner base pairs. As the intercalation at the terminal CpG steps is relatively rapid, the resultant DNA unwinding, rigidification, and increased stability of the internal base pair steps inhibits further intercalation. In order to reduce these interactions and to provide a larger groove space, a second 18-mer DNA duplex system with the sequence d(GCATGAACGAACGAACGC) was tested. We computed molecular dynamics simulations for 20 independent replicas with this sequence, each with ∼27 μs of sampling time. Results show several spontaneous intercalation and base-pair eversion events that are consistent with experimental observations. The present work suggests that extended MD simulations with modern DNA force fields and optimized simulation codes are allowing the ability to reproduce unbiased intercalation events that we were not able to previously reach due to limits in computing power and the lack of extensively tested force fields and analysis tools.

Fine-tuning the DNA conductance by intercalation of drug molecules

In this work we study the structure-transport property relationships of small ligand intercalated DNA molecules using a multiscale modeling approach where extensive ab initio calculations are performed on numerous MD-simulated configurations of dsDNA and dsDNA intercalated with two different intercalators, ethidium and daunomycin. DNA conductance is found to increase by one order of magnitude upon drug intercalation due to the local unwinding of the DNA base pairs adjacent to the intercalated sites, which leads to modifications of the density of states in the near-Fermi-energy region of the ligand-DNA complex. Our study suggests that the intercalators can be used to enhance or tune the DNA conductance, which opens new possibilities for their potential applications in nanoelectronics.

Fingerprinting branches on supercoiled plasmid DNA using quartz nanocapillaries

DNA conformation, in particular its supercoiling, plays an important structural and functional role in gene accessibility as well as in DNA condensation. Enzyme driven changes of DNA plasmids between their linear, circular and supercoiled conformations control the level of condensation and DNA distal-site interactions. Much effort has been made to quantify the branched supercoiled state of DNA to understand its ubiquitous contribution to many biological functions, such as packaging, transcription, replication etc. Nanopore technology has proven to be an excellent label-free single-molecule method to investigate the conformations of the translocating DNA in terms of the current pulse readout. In this paper, we present a comprehensive study to detect different branched-supercoils on individual plasmid DNA molecules. Using a detailed event charge deficit (ECD) analysis of the translocating molecules, we reveal, for the first time, the distributions in size and the position of the plectoneme branches on the supercoiled plasmid. Additionally, this analysis also gives an independent measure of the effective nanopore length. Finally, we use our nanopore platform for measurement of enzyme-dependent linearization of these branched-supercoiled plasmids. By simultaneous measurement of both single-molecule DNA supercoiled conformations and enzyme-dependent bulk conformational changes, we establish nanopore sensing as a promising platform for an in-depth understanding of the structural landscapes of supercoiled DNA to decipher its functional role in different biological processes.

Effects of Intercalating Molecules on the Polymer Properties of DNA

Atomic force microscopy (AFM) enables determination of physical properties from single DNA molecules. Insertion of aromatic molecules into the structure of DNA results in morphological changes. However, the accompanying changes to elastic properties due to this insertion are not fully understood. AFM was used to examine the morphological effects of intercalator binding and report changes in the elastic properties of intrinsically straight DNA molecules. The persistence length and polymer extension were characterized in the presence of three intercalating molecules: ethidium bromide and the less well studied chloroquine and acridine. It was found that all three intercalators significantly increased the bending persistence length. In addition, an analysis of the normal bending modes of the static molecules corroborated these results. This approach of measuring binding effects of intercalators on DNA physical properties using a model system of intrinsically straight DNA is applicable to other DNA binding ligands and other modes of DNA interaction.

Translocation of a Polyelectrolyte through a Nanopore in the Presence of Trivalent Counterions: A Comparison with the Cases in Monovalent and Divalent Salt Solutions

A polyelectrolyte threading through a nanopore in a trivalent salt solution is investigated by means of molecular dynamics simulations under a reflective wall boundary. By varying the chain length N and the strength E of the driving electric field applied inside the pore, the translocation time is carefully calculated to get rid of the bouncing effect because of the boundary. The results are analyzed under the scaling form ⟨τ⟩ ∼ N ^α E ^-δ and four driving force regimes; namely, the unbiased, the weakly driven, the strongly driven trumpet, and the strongly driven isoflux regime, are distinguished. The exponents are calculated in each regime and compared with the cases in the monovalent and divalent salt solutions. Owing to strong condensation of counter ions, the changes of the exponents in the force regimes are found to be nontrivial. A large increase in translocation time can be, however, achieved as the driving field is weak. The variations of the chain size, the ion condensation, and the effective chain charge show that the process is proceeded in a quasi-equilibrium way in the unbiased regime and deviated to exhibit strong nonequilibrium characteristics as E increases. Several astonishing scaling behaviors of the waiting time function, the translocation velocity, and the diffusion properties are discovered in the study. The results provide deep insights into the phenomena of polyelectrolyte translocation in various salt solutions at different driving forces.

Computational investigation on DNA sequencing using functionalized graphene nanopores

Fast, low-cost and reliable DNA sequencing is one of the most desirable innovations in recent years, which can pave the way for high throughput, label-free and inexpensive personalized genome sequencing techniques. Although graphene-based nanopore devices hold great promise for next-generation DNA sequencing, it is still a challenging problem to detect different DNA sequences efficiently and accurately. In the present work, the translocation of four homogeneous DNA strands (i.e., poly(A)20, poly(C)20, poly(G)20, and poly(T)20) through the functionalized graphene nanopores is investigated by all-atom molecular dynamic simulations. Interestingly, it is found that the four types of bases could be identified by different ionic currents when they pass through the hydrogenated and hydroxylated pores. For the hydrogenated nanopore, the difference in the ionic current for the four bases is mainly attributed to the different electrostatic interactions between the base and the ion. For the hydroxylated nanopore, apart from the electrostatic interactions, the position of a nucleotide inside the nanopore and the dwell time of an ion around the nucleotide also play an important role in the ionic current. The present study could be helpful to better design a novel device for DNA sequencing in the future.

Clog and Release, and Reverse Motions of DNA in a Nanopore

Motions of circular and linear DNA molecules of various lengths near a nanopore of 100 or 200 nm diameter were experimentally observed and investigated by fluorescence microscopy. The movement of DNA molecules through nanopores, known as translocation, is mainly driven by electric fields near and inside the pores. We found significant clogging of nanopores by DNA molecules, particularly by circular DNA and linear T4 DNA (165.65 kbp). Here, the probabilities of DNA clogging events, depending on the DNA length and shape—linear or circular—were determined. Furthermore, two distinct DNA motions were observed: clog and release by linear T4 DNA, and a reverse direction motion at the pore entrance by circular DNA, after which both molecules moved away from the pore. Finite element method-based numerical simulations were performed. The results indicated that DNA molecules with pores 100–200 nm in diameter were strongly influenced by opposing hydrodynamic streaming flow, which was further enhanced by bulky DNA configurations.

Translocation of Charged Polymers through a Nanopore in Monovalent and Divalent Salt Solutions: A Scaling Study Exploring over the Entire Driving Force Regimes

Langevin dynamics simulations are performed to study polyelectrolytes driven through a nanopore in monovalent and divalent salt solutions. The driving electric field E is applied inside the pore, and the strength is varied to cover the four characteristic force regimes depicted by a rederived scaling theory, namely the unbiased (UB) regime, the weakly-driven (WD) regime, the strongly-driven trumpet (SD(T)) regime and the strongly-driven isoflux (SD(I)) regime. By changing the chain length N, the mean translocation time is studied under the scaling form 〈 τ 〉 ∼ N α E - δ . The exponents α and δ are calculated in each force regime for the two studied salt cases. Both of them are found to vary with E and N and, hence, are not universal in the parameter's space. We further investigate the diffusion behavior of translocation. The subdiffusion exponent γ p is extracted. The three essential exponents ν s , q, z p are then obtained from the simulations. Together with γ p , the validness of the scaling theory is verified. Through a comparison with experiments, the location of a usual experimental condition on the scaling plot is pinpointed.