@article {397, title = {Dehydrated Biomimetic Membranes with Skinlike Structure and Function}, journal = {ACS Applied Materials \& Interfaces}, year = {2024}, abstract = {

Novel vapor-permeable materials are sought after for applications in protective wear, energy generation, and water treatment. Current impermeable protective materials effectively block harmful agents but trap heat due to poor water vapor transfer. Here we present a new class of materials, vapor permeable dehydrated nanoporous biomimetic membranes (DBMs), based on channel proteins. This application for biomimetic membranes is unexpected as channel proteins and biomimetic membranes were assumed to be unstable under dry conditions. DBMs mimic human skin{\textquoteright}s structure to offer both high vapor transport and small molecule exclusion under dry conditions. DBMs feature highly organized pores resembling sweat pores in human skin, but at super high densities (\>1012\ pores/cm2). These DBMs achieved exceptional water vapor transport rates, surpassing commercial breathable fabrics by up to 6.2 times, despite containing \>2 orders of magnitude smaller pores (1 nm vs \>700 nm). These DBMs effectively excluded model biological agents and harmful chemicals both in liquid and vapor phases, again in contrast with the commercial breathable fabrics. Remarkably, while hydrated biomimetic membranes were highly permeable to liquid water, they exhibited higher water resistances after dehydration at values \>38 times that of commercial breathable fabrics. Molecular dynamics simulations support our hypothesis that dehydration induced protein hydrophobicity increases which enhanced DBM performance. DBMs hold promise for various applications, including membrane distillation, dehumidification, and protective barriers for atmospheric water harvesting materials.

}, doi = {10.1021/acsami.3c19572}, url = {https://doi.org/10.1021/acsami.3c19572}, author = {Oh, Hyeonji and Tu, Yu-Ming and Samineni, Laximicharan and De Respino, Sophie and Mehrafrooz, Behzad and Joshi, Himanshu and Massenburg, Lynnicia and Lopez-Marques, Horacio and Elessawy, Nada and Song, Woochul and Behera, Harekrushna and Dhiman, Raman and Boorla, Veda Sheersh and Kher, Kartik and Lin, Yi-Chih and Maranas, Costas and Aksimentiev, Aleksei and D. Freeman, Benny and Kumar, Manish} } @article {387, title = {DNA double helix, a tiny electromotor}, journal = {Nature Nanotechnology}, volume = {18}, year = {2023}, month = {12/2022}, pages = {238{\textendash}242}, chapter = {238}, abstract = {

Flowing fluid past chiral objects has been used for centuries to power rotary motion in man-made machines. By contrast, rotary motion in nanoscale biological or chemical systems is produced by biasing Brownian motion through cyclic chemical reactions. Here we show that a chiral biological molecule, a DNA or RNA duplex rotates unidirectionally at billions of revolutions per minute when an electric field is applied along the duplex, with the rotation direction being determined by the chirality of the duplex. The rotation is found to be powered by the drag force of the electro-osmotic flow, realizing the operating principle of a macroscopic turbine at the nanoscale. The resulting torques are sufficient to power rotation of nanoscale beads and rods, offering an engineering principle for constructing nanoscale systems powered by electric field.

}, issn = {1748-3387}, doi = {10.1038/s41565-022-01285-z}, url = {https://www.nature.com/articles/s41565-022-01285-z}, author = {Maffeo, Christopher and Quednau, Lauren and Wilson, James and Aksimentiev, Aleksei} } @article {389, title = {A DNA turbine powered by a transmembrane potential across a nanopore}, journal = {Nature Nanotechnology}, year = {2023}, month = {11/2023}, abstract = {

Rotary motors play key roles in energy transduction, from macroscale windmills to nanoscale turbines such as ATP synthase in cells. Despite our abilities to construct engines at many scales, developing functional synthetic turbines at the nanoscale has remained challenging. Here, we experimentally demonstrate rationally designed nanoscale DNA origami turbines with three chiral blades. These DNA nanoturbines are 24{\textendash}27 nm in height and diameter and can utilize transmembrane electrochemical potentials across nanopores to drive DNA bundles into sustained unidirectional rotations of up to 10 revolutions s-1. The rotation direction is set by the designed chirality of the turbine. All-atom molecular dynamics simulations show how hydrodynamic flows drive this turbine. At high salt concentrations, the rotation direction of turbines with the same chirality is reversed, which is explained by a change in the anisotropy of the electrophoretic mobility. Our artificial turbines operate autonomously in physiological conditions, converting energy from naturally abundant electrochemical potentials into mechanical work. The results open new possibilities for engineering active robotics at the nanoscale.

}, issn = {1748-3395}, doi = {10.1038/s41565-023-01527-8}, url = {https://doi.org/10.1038/s41565-023-01527-8}, author = {Shi, Xin and Pumm, Anna-Katharina and Maffeo, Christopher and Kohler, Fabian and Feigl, Elija and Zhao, Wenxuan and Verschueren, Daniel and Golestanian, Ramin and Aksimentiev, Aleksei and Dietz, Hendrik and Dekker, Cees} } @article {374, title = {Discrimination of RNA fiber structures using solid-state nanopores}, journal = {Nanoscale}, volume = {14}, year = {2022}, month = {05/2023}, pages = {6866-6875}, abstract = {

RNA fibers are a class of biomaterials that can be assembled using HIV-like kissing loop interactions. Because of the programmability of molecular design and low immunorecognition, these structures present an interesting opportunity to solve problems in nanobiotechnology and synthetic biology. However, the experimental tools to fully characterize and discriminate among different fiber structures in solution are limited. Herein, we utilize solid-state nanopore experiments and Brownian dynamics simulations to characterize and distinguish several RNA fiber structures that differ in their degrees of branching. We found that, regardless of the electrolyte type and concentration, fiber structures that have more branches produce longer and deeper ionic current blockades in comparison to the unbranched fibers. Experiments carried out at temperatures ranging from 20{\textendash}60 {\textdegree}C revealed almost identical distributions of current blockade amplitudes, suggesting that the kissing loop interactions in fibers are resistant to heating within this range.

}, issn = {2040-3364}, doi = {10.1039/D1NR08002D}, url = {http://pubs.rsc.org/en/content/articlepdf/2022/NR/D1NR08002D}, author = {Tripathi, Prabhat and Chandler, Morgan and Maffeo, Christopher Michael and Fallahi, Ali and Makhamreh, Amr and Halman, Justin and Aleksei Aksimentiev and Afonin, Kirill A. and Wanunu, Meni} } @article {369, title = {DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles.}, journal = {Nucleic Acids Res}, volume = {49}, year = {2021}, month = {11/2021}, pages = {11459-11475}, abstract = {

Eukaryotic genome and methylome encode DNA fragments{\textquoteright} propensity to form nucleosome particles. Although the mechanical properties of DNA possibly orchestrate such encoding, the definite link between {\textquoteright}omics{\textquoteright} and DNA energetics has remained elusive. Here, we bridge the divide by examining the sequence-dependent energetics of highly bent DNA. Molecular dynamics simulations of 42 intact DNA minicircles reveal that each DNA minicircle undergoes inside-out conformational transitions with the most likely configuration uniquely prescribed by the nucleotide sequence and methylation of DNA. The minicircles{\textquoteright} local geometry consists of straight segments connected by sharp bends compressing the DNA{\textquoteright}s inward-facing major groove. Such an uneven distribution of the bending stress favors minimum free energy configurations that avoid stiff base pair sequences at inward-facing major grooves. Analysis of the minicircles{\textquoteright} inside-out free energy landscapes yields a discrete worm-like chain model of bent DNA energetics that accurately account for its nucleotide sequence and methylation. Experimentally measuring the dependence of the DNA looping time on the DNA sequence validates the model. When applied to a nucleosome-like DNA configuration, the model quantitatively reproduces yeast and human genomes{\textquoteright} nucleosome occupancy. Further analyses of the genome-wide chromatin structure data suggest that DNA bending energetics is a fundamental determinant of genome architecture.

}, keywords = {DNA Methylation, DNA, Circular, Molecular Dynamics Simulation, Nucleic Acid Conformation}, issn = {1362-4962}, doi = {10.1093/nar/gkab967}, author = {Yoo, Jejoong and Park, Sangwoo and Maffeo, Christopher and Ha, Taekjip and Aleksei Aksimentiev} } @article {362, title = {DNA Origami Voltage Sensors for Transmembrane Potentials with Single-Molecule Sensitivity}, journal = {Nano Letters}, volume = {21}, year = {2021}, month = {10/2021}, pages = {8634-8641}, chapter = {8634}, abstract = {

Signal transmission in neurons goes along with changes in the transmembrane potential. To report them, different approaches, including optical voltage-sensing dyes and genetically encoded voltage indicators, have evolved. Here, we present a DNA nanotechnology-based system and demonstrate its functionality on liposomes. Using DNA origami, we incorporated and optimized different properties such as membrane targeting and voltage sensing modularly. As a sensing unit, we used a hydrophobic red dye anchored to the membrane and an anionic green dye at the DNA to connect the nanostructure and the membrane dye anchor. Voltage-induced displacement of the anionic donor unit was read out by fluorescence resonance energy transfer (FRET) changes of single sensors attached to liposomes. A FRET change of \~{}5\% for ΔΨ = 100 mV was observed. The working mechanism of the sensor was rationalized by molecular dynamics simulations. Our approach holds potential for an application as nongenetically encoded membrane sensors.

}, doi = {10.1021/acs.nanolett.1c02584}, url = {https://pubs.acs.org/doi/10.1021/acs.nanolett.1c02584?fig=tgr1\&ref=pdf}, author = {Ochmann, Sarah E and Joshi, Himanshu and Büber, Ece and Franquelim, Henri G and Stegemann, Pierre and Sacc{\`a}, Barbara and Keyser, Ulrich F and Aleksei Aksimentiev and Tinnefeld, Philip} } @article {343, title = {Determining the In-Plane Orientation and Binding Mode of Single Fluorescent Dyes in DNA Origami Structures}, journal = {ACS Nano}, volume = {15}, year = {2021}, month = {03/2021}, pages = {5109-5117}, chapter = {5109}, abstract = {

We present a technique to determine the orientation of single fluorophores attached to DNA origami structures based on two measurements. First, the orientation of the absorption transition dipole of the molecule is determined through a polarization-resolved excitation measurement. Second, the orientation of the DNA origami structure is obtained from a DNA-PAINT nanoscopy measurement. Both measurements are performed consecutively on a fluorescence wide-field microscope. We employed this approach to study the orientation of single ATTO 647N, ATTO 643, and Cy5 fluorophores covalently attached to a 2D rectangular DNA origami structure with different nanoenvironments, achieved by changing both the fluorophores{\textquoteright} binding position and immediate vicinity. Our results show that when fluorophores are incorporated with additional space, for example, by omitting nucleotides in an elsewise doublestranded environment, they tend to stick to the DNA and to adopt a preferred orientation that depends more on the specific molecular environment than on the fluorophore type. With the aid of all-atom molecular dynamics simulations, we rationalized our observations and provide insight into the fluorophores{\textquoteright} probable binding modes. We believe this work constitutes an important step toward manipulating the orientation of single fluorophores in DNA origami structures, which is vital for the development of more efficient and reproducible self-assembled nanophotonic devices.\ 

}, keywords = {DNA Nanotechnology, DNA-PAINT, Single-molecule fluorescence polarization-resolved microscopy, Super-resolution microscopy}, doi = {https://doi.org/10.1021/acsnano.0c10259}, url = {https://pubs.acs.org/doi/10.1021/acsnano.0c10259}, author = {Hübner, Kristina and Joshi, Himanshu and Aleksei Aksimentiev and Stefani, Fernando D and Tinnefeld, Philip and Acuna, Guillermo P} } @article {293, title = {Dynamic Interactions between Lipid-Tethered DNA and Phospholipid Membranes}, journal = {Langmuir}, volume = {34}, year = {2018}, month = {11/2018}, pages = {15084-15092}, chapter = {15084}, abstract = {

Lipid-anchored DNA can attach functional cargo to bilayer membranes in DNA nanotechnology, synthetic biology, and cell biology research. To optimize DNA anchoring, an understanding of DNA-membrane interactions in terms of binding strength, extent, and structural dynamics is required. Here we use experiments and molecular dynamics (MD) simulations to determine how the membrane binding of cholesterol-modified DNA depends on electrostatic and steric factors involving the lipid headgroup charge, duplexed or single-stranded DNA, and the buffer composition. The experiments distinguish between free and membrane vesicle-bound DNA and thereby reveal the surface density of anchored DNA and its binding affinity, something which had previously not been known. The Kd values range from 8.5 {\textpm} 4.9 to 466 {\textpm} 134 μM whereby negatively charged headgroups led to weak binding due to the electrostatic repulsion with respect to the negatively charged DNA. Atomistic MD simulations explain the findings and elucidate the dynamic nature of anchored DNA such as the mushroom-like conformation of single-stranded DNA hovering over the bilayer surface in contrast to a straight-up conformation of double-stranded DNA. The biophysical insight into the binding strength to membranes as well as the molecular accessibility of DNA for hybridization to molecular cargo is expected to facilitate the\  creation of biomimetic DNA versions of natural membrane nanopores and cytoskeletons for research and nanobiotechnology.

}, keywords = {DNA Nanotechnology, Lipid Bilayer anchored DNA, Lipid-DNA binding affinity}, doi = {10.1021/acs.langmuir.8b02271}, url = {https://doi.org/10.1021/acs.langmuir.8b02271}, author = {Arnott, Patrick M. and Joshi, Himanshu and Aleksei Aksimentiev and Howorka, Stefan} } @article {291, title = {Dynamics of a Molecular Plug Docked onto a Solid-State Nanopore}, journal = {The Journal of Physical Chemistry Letters}, volume = {9}, year = {2018}, month = {08/2018}, pages = {4686-4694}, chapter = {4686}, abstract = {

Docking of a protein- DNA complex onto a nanopore can provide ample observation time, and has enabled collection of analytic applications of biological nanopores, including DNA sequencing. However, the application of the same principle to solid-state nanopores is tempered by poor understanding of the docking process. Here, we elucidate the behavior of individual protein- DNA complexes docked onto a solid-state nanopore by monitoring the nanopore ionic current. Repeat docking of monovalent streptavidin- DNA complexes is found to produce ionic current blockades that fluctuate between discrete levels. We elucidate the roles of the protein plug and the DNA tether in the docking process, finding the docking configurations to determine the multitude of the current blockade levels, whereas the frequency of the current level switching is determined by the interactions between the molecules and the solid-state membrane. Finally, we prove the feasibility of using the nanopore docking principle for single-molecule sensing using solid-state nanopores by detecting conformational changes of a tethered DNA molecule from a random coil to an i-motif state.

}, doi = {10.1021/acs.jpclett.8b01755}, author = {Xin Shi and Qiao Li and Rui Gao and Wei Si and Shao-Chuang Liu and Aleksei Aksimentiev and Yi-Tao Long} } @article {246, title = {DNA sequence-dependent ionic currents in ultra-small solid-state nanopores}, journal = {Nanoscale}, volume = {18}, year = {2016}, month = {04/2016}, pages = {9600-9613}, abstract = {

Measurements of ionic currents through nanopores partially blocked by DNA have emerged as a powerful method for characterization of the DNA nucleotide sequence. Although the effect of the nucleotide sequence on the nanopore blockade current has been experimentally demonstrated, prediction and interpretation of such measurements remain a formidable challenge. Using atomic resolution computational approaches, here we show how the sequence, molecular conformation, and pore geometry affect the blockade ionic current in model solid-state nanopores. We demonstrate that the blockade current from a DNA molecule is determined by the chemical identities and conformations of at least three consecutive nucleotides. We find the blockade currents produced by the nucleotide triplets to vary considerably with their nucleotide sequence despite having nearly identical molecular conformations. Encouragingly, we find blockade current differences as large as 25\% for single-base substitutions in ultra small (1.6 nm x 1.1 nm cross section; 2 nm length) solid-state nanopores. \ Despite the complex dependence of the blockade current on the sequence and conformation of the DNA triplets, we find that, under many conditions, the number of thymine bases is positively correlated with the current, whereas the number of purine bases and the presence of both purine and pyrimidines in the triplet \ are negatively correlated with the current. Based on these observations, we construct a simple theoretical model that relates the ion current to the base content of a solid-state nanopore. Furthermore, we show that compact \ conformations of DNA in narrow pores provide the greatest signal-to-noise ratio for single base detection, whereas reduction of the nanopore length \ increases the ionic current noise.\ Thus, the sequence dependence of nanopore blockade current can be theoretically rationalized, although the predictions will likely need to be customized for each nanopore type.

}, doi = {10.1039/C6NR01061J}, url = {http://pubs.rsc.org/en/content/articlehtml/2016/nr/c6nr01061j}, author = {Jeffrey Comer and Aleksei Aksimentiev} } @article {214, title = {De Novo Reconstruction of DNA Origami Structures through Atomistic Molecular Dynamics Simulation}, journal = {Nucleic Acids Research}, volume = {44}, year = {2016}, month = {04/2016}, pages = {3013-3019}, chapter = {3013}, abstract = {

The DNA origami method has brought nanometer-precision fabrication to molecular biology labs, offering myriads of potential applications in the fields of synthetic biology, biomolecular medicine, molecular computation, etc. Advancing the method further requires controlling self-assembly down to the atomic scale. Here we demonstrate a computational method that allows the equilibrium structure of a large, complex DNA origami object to be determined to atomic resolution. Through direct comparison with the results of cryo-electron microscopy, we demonstrate de novo reconstruction of a 4.7 megadalton pointer structure by means of fully atomistic molecular dynamics simulations. Furthermore, we show that elastic network-guided simulations performed without solvent can yield similar accuracy at a fraction of the computational cost, making this method an attractive approach for prototyping and validation of self-assembled DNA nanostructures.

}, doi = {10.1093/nar/gkw155}, url = {http://nar.oxfordjournals.org/content/early/2016/03/14/nar.gkw155}, author = {Christopher Maffeo and Jejoong Yoo and Aleksei Aksimentiev} } @article {211, title = {Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation}, journal = {Nature Communications}, volume = {7}, year = {2016}, month = {03/2016}, pages = {11045}, abstract = {

Although proteins mediate highly ordered DNA organization\ in vivo, theoretical studies suggest that homologous DNA duplexes can preferentially associate with one another even in the absence of proteins. Here we combine molecular dynamics simulations with single-molecule fluorescence resonance energy transfer experiments to examine the interactions between duplex DNA in the presence of spermine, a biological polycation. We find that AT-rich DNA duplexes associate more strongly than GC-rich duplexes, regardless of the sequence homology. Methyl groups of thymine acts as a steric block, relocating spermine from major grooves to interhelical regions, thereby increasing DNA{\textendash}DNA attraction. Indeed, methylation of cytosines makes attraction between GC-rich DNA as strong as that between AT-rich DNA. Recent genome-wide chromosome organization studies showed that remote contact frequencies are higher for AT-rich and methylated DNA, suggesting that direct DNA{\textendash}DNA interactions that we report here may play a role in the chromosome organization and gene regulation.

}, doi = {10.1038/ncomms11045}, author = {Jejoong Yoo and Hajin Kim and Aleksei Aksimentiev and Taekjip Ha} } @article {27, title = {DNA base-calling from a nanopore using a Viterbi algorithm}, journal = {Biophys J}, volume = {102}, year = {2012}, month = {2012 May 16}, pages = {L37-9}, abstract = {

Nanopore-based DNA sequencing is the most promising third-generation sequencing method. It has superior read length, speed, and sample requirements compared with state-of-the-art second-generation methods. However, base-calling still presents substantial difficulty because the resolution of the technique is limited compared with the measured signal/noise ratio. Here we demonstrate a method to decode 3-bp-resolution nanopore electrical measurements into a DNA sequence using a Hidden Markov model. This method shows tremendous potential for accuracy (~98\%), even with a poor signal/noise ratio.

}, keywords = {Algorithms, Base Sequence, DNA, Electricity, Genome, Human, Humans, Markov Chains, Nanopores, Sequence Analysis, DNA, Signal-To-Noise Ratio}, issn = {1542-0086}, doi = {10.1016/j.bpj.2012.04.009}, author = {Timp, Winston and Jeffrey Comer and Aleksei Aksimentiev} } @article {17, title = {DNA-DNA interactions in tight supercoils are described by a small effective charge density}, journal = {Phys Rev Lett}, volume = {105}, year = {2010}, month = {2010 Oct 8}, pages = {158101}, abstract = {

DNA-DNA interactions are important for genome compaction and transcription regulation. In studies of such complex processes, DNA is often modeled as a homogeneously charged cylinder and its electrostatic interactions are calculated within the framework of the Poisson-Boltzmann equation. Commonly, a charge adaptation factor is used to address limitations of this theoretical approach. Despite considerable theoretical and experimental efforts, a rigorous quantitative assessment of this parameter is lacking. Here, we comprehensively characterized DNA-DNA interactions in the presence of monovalent ions by analyzing the supercoiling behavior of single DNA molecules held under constant tension. Both a theoretical model and coarse-grained simulations of this process revealed a surprisingly small effective DNA charge of 40\% of the nominal charge density, which was additionally supported by all-atom molecular dynamics simulations.

}, keywords = {Biomechanical Phenomena, DNA, Superhelical, Molecular Dynamics Simulation, Monte Carlo Method, Salts, Static Electricity}, issn = {1079-7114}, doi = {10.1103/PhysRevLett.105.158101 }, url = {http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.105.158101}, author = {Christopher Maffeo and Sch{\"o}pflin, Robert and Brutzer, Hergen and Stehr, Ren{\'e} and Aleksei Aksimentiev and Wedemann, Gero and Seidel, Ralf} } @article {105, title = {Dehydration and ionic conductance quantization in nanopores}, journal = {J Phys Condens Matter}, volume = {22}, year = {2010}, month = {2010 Nov 17}, pages = {454126}, abstract = {

There has been tremendous experimental progress in the last decade in identifying the structure and function of biological pores (ion channels) and fabricating synthetic pores. Despite this progress, many questions still remain about the mechanisms and universal features of ionic transport in these systems. In this paper, we examine the use of nanopores to probe ion transport and to construct functional nanoscale devices. Specifically, we focus on the newly predicted phenomenon of quantized ionic conductance in nanopores as a function of the effective pore radius--a prediction that yields a particularly transparent way to probe the contribution of dehydration to ionic transport. We study the role of ionic species in the formation of hydration layers inside and outside of pores. We find that the ion type plays only a minor role in the radial positions of the predicted steps in the ion conductance. However, ions with higher valency form stronger hydration shells, and thus, provide even more pronounced, and therefore, more easily detected, drops in the ionic current. Measuring this phenomenon directly, or from the resulting noise, with synthetic nanopores would provide evidence of the deviation from macroscopic (continuum) dielectric behavior due to microscopic features at the nanoscale and may shed light on the behavior of ions in more complex biological channels.

}, keywords = {Computer Simulation, Ions, Models, Chemical, Models, Molecular, Nanostructures, Particle Size, Porosity, Water}, issn = {1361-648X}, doi = {10.1088/0953-8984/22/45/454126}, author = {Zwolak, Michael and James Wilson and Massimiliano Di Ventra} } @article {42, title = {Deciphering ionic current signatures of DNA transport through a nanopore}, journal = {Nanoscale}, volume = {2}, year = {2010}, month = {2010 Apr}, pages = {468-83}, abstract = {

Within just a decade from the pioneering work demonstrating the utility of nanopores for molecular sensing, nanopores have emerged as versatile systems for single-molecule manipulation and analysis. In a typical setup, a gradient of the electrostatic potential captures charged solutes from the solution and forces them to move through a single nanopore, across an otherwise impermeable membrane. The ionic current blockades resulting from the presence of a solute in a nanopore can reveal the type of the solute, for example, the nucleotide makeup of a DNA strand. Despite great success, the microscopic mechanisms underlying the functionality of such stochastic sensors remain largely unknown, as it is not currently possible to characterize the microscopic conformations of single biomolecules directly in a nanopore and thereby unequivocally establish the causal relationship between the observables and the microscopic events. Such a relationship can be determined using molecular dynamics-a computational method that can accurately predict the time evolution of a molecular system starting from a given microscopic state. This article describes recent applications of this method to the process of DNA transport through biological and synthetic nanopores.

}, keywords = {Biological Transport, DNA, Escherichia coli Proteins, Hemolysin Proteins, Kinetics, Molecular Dynamics Simulation, Monte Carlo Method, Nanostructures, Nanotubes, Porins, Review}, issn = {2040-3372}, doi = {10.1039/b9nr00275h}, author = {Aleksei Aksimentiev} } @article {53, title = {DNA attraction in monovalent and divalent electrolytes}, journal = {J Am Chem Soc}, volume = {130}, year = {2008}, month = {2008 Nov 26}, pages = {15754-5}, abstract = {

The dependence of the effective force on the distance between two DNA molecules was directly computed from a set of extensive all-atom molecular dynamics simulations. The simulations revealed that in a monovalent electrolyte the effective force is repulsive at short and long distances but can be attractive in the intermediate range. This attractive force is, however, too weak (approximately 5 pN per turn of a DNA helix) to induce DNA condensation in the presence of thermal fluctuations. In divalent electrolytes, DNA molecules were observed to form a bound state, where Mg(2+) ions bridged minor groves of DNA. The effective force in divalent electrolytes was predominantly attractive, reaching a maximum of 42 pN per one turn of a DNA helix.

}, keywords = {Computer Simulation, DNA, Electrolytes, Models, Molecular, Molecular Conformation}, issn = {1520-5126}, doi = {10.1021/ja804802u}, author = {Luan, Binquan and Aleksei Aksimentiev} } @article {62, title = {Detection of DNA sequences using an alternating electric field in a nanopore capacitor}, journal = {Nano Lett}, volume = {8}, year = {2008}, month = {2008 Jan}, pages = {56-63}, abstract = {

Molecular dynamics simulations revealed that back-and-forth motion of DNA strands through a 1 nm diameter pore exhibits sequence-specific hysteresis that arises from the reorientation of the DNA bases in the nanopore constriction. Such hysteresis of the DNA motion results in detectable changes of the electrostatic potential at the electrodes of the nanopore capacitor and in a sequence-specific drift of the DNA strand under an oscillating transmembrane bias. A strategy is suggested for sequencing DNA in a nanopore using the electric field that alternates periodically in time.

}, keywords = {DNA, Electricity, Nanostructures, Sequence Analysis, DNA}, issn = {1530-6984}, doi = {10.1021/nl071890k}, author = {G Sigalov and Jeffrey Comer and Gregory Timp and Aleksei Aksimentiev} } @article {65, title = {Detecting SNPs using a synthetic nanopore}, journal = {Nano Lett}, volume = {7}, year = {2007}, month = {2007 Jun}, pages = {1680-5}, abstract = {

We have discovered a voltage threshold for permeation through a synthetic nanopore of dsDNA bound to a restriction enzyme that depends on the sequence. Molecular dynamic simulations reveal that the threshold is associated with a nanonewton force required to rupture the DNA-protein complex. A single mutation in the recognition site for the restriction enzyme, i.e., a single nucleotide polymorphism (SNP), can easily be detected as a change in the threshold voltage. Consequently, by measuring the threshold voltage in a synthetic nanopore, it may be possible to discriminate between two variants of the same gene (alleles) that differ in one base.

}, keywords = {Deoxyribonuclease EcoRI, DNA, DNA Mutational Analysis, Electromagnetic Fields, Macromolecular Substances, Materials Testing, Molecular Conformation, Nanostructures, Nanotechnology, Particle Size, Polymorphism, Single Nucleotide, Porosity, Sequence Analysis, DNA, Surface Properties}, issn = {1530-6984}, doi = {10.1021/nl070668c}, author = {Zhao, Q and G Sigalov and Valentin Dimitrov and Dorvel, B and Mirsaidov, U and S Sligar and Aleksei Aksimentiev and Gregory Timp} } @article {78, title = {Diffusion on curved, periodic surfaces}, journal = {Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics}, volume = {60}, year = {1999}, month = {1999 Jul}, pages = {302-7}, abstract = {

We present a simulation algorithm for a diffusion on a curved surface given by the equation phi(r)=0. The algorithm is tested against analytical results known for diffusion on a cylinder and a sphere, and applied to the diffusion on the P, D, and G periodic nodal surfaces. It should find application in an interpretation of two-dimensional exchange NMR spectroscopy data of diffusion on biological membranes.

}, issn = {1063-651X}, author = {Robert Ho{\l}yst and Plewczy{\'n}ski, D and Aleksei Aksimentiev and Burdzy, K} }