@article {389, title = {A DNA turbine powered by a transmembrane potential across a nanopore}, journal = {Nature Nanotechnology}, volume = {19}, year = {2024}, month = {03/2024}, pages = {338--344}, chapter = {338}, 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 {397, title = {Dehydrated Biomimetic Membranes with Skinlike Structure and Function}, journal = {ACS Applied Materials \& Interfaces}, volume = {16}, year = {2024}, pages = {20865-20877}, 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 {386, title = {Super-Resolution Detection of DNA Nanostructures Using a Nanopore}, journal = {Advanced Materials}, year = {2023}, month = {01/2023}, pages = {2207434}, abstract = {

Abstract High-resolution analysis of biomolecules has brought unprecedented insights into fundamental biological processes and dramatically advanced biosensing. Notwithstanding the ongoing resolution revolution in electron microscopy and optical imaging, only a few methods are presently available for high-resolution analysis of unlabelled single molecules in their native states. Here, we demonstrate label-free electrical sensing of structured single molecules with a spatial resolution down to single-digit nanometres. Using a narrow solid-state nanopore, we detect the passage of a series of nanostructures attached to a freely translocating DNA molecule, resolving individual nanostructures placed as close as 6\ nm apart and with a surface-to-surface gap distance of only 2\ nm. We attribute such super-resolution ability to the nanostructure-induced enhancement of the electric field at the tip of the nanopore. Our work demonstrates a general approach to improving the resolution of single-molecule nanopore sensing and presents a critical advance towards label-free, high-resolution DNA sequence mapping and digital information storage independent of molecular motors.

}, keywords = {biosensing, DNA nanostructures, Nanopores, single molecule, super resolution}, doi = {https://doi.org/10.1002/adma.202207434}, author = {Chen, Kaikai and Choudhary, Adnan and Sandler, Sarah E. and Maffeo, Christopher and Ducati, Caterina and Aksimentiev, Aleksei and Keyser, Ulrich F.} } @article {364, title = {A nanoscale reciprocating rotary mechanism with coordinated mobility control.}, journal = {Nature Communications}, volume = {12}, year = {2021}, month = {12/2021}, pages = {7138}, chapter = {7138}, abstract = {

Biological molecular motors transform chemical energy into mechanical work by coupling cyclic catalytic reactions to large-scale structural transitions. Mechanical deformation can be surprisingly efficient in realizing such coupling, as demonstrated by the FoF1 ATP synthase. Here, we describe a synthetic molecular mechanism that transforms a rotary motion of an asymmetric camshaft into reciprocating large-scale transitions in a surrounding stator orchestrated by mechanical deformation. We design the mechanism using DNA origami, characterize its structure via cryo-electron microscopy, and examine its dynamic behavior using single-particle fluorescence microscopy and molecular dynamics simulations. While the camshaft can rotate inside the stator by diffusion, the stator{\textquoteright}s mechanics makes the camshaft pause at preferred orientations. By changing the stator{\textquoteright}s mechanical stiffness, we accelerate or suppress the Brownian rotation, demonstrating an allosteric coupling between the camshaft and the stator. Our mechanism provides a framework for manufacturing artificial nanomachines that function because of coordinated movements of their components.

}, keywords = {Cryoelectron Microscopy, DNA, Molecular Conformation, Molecular Dynamics Simulation, Nanostructures, Nanotechnology, Rotation}, issn = {2041-1723}, doi = {10.1038/s41467-021-27230-7}, author = {Bertosin, Eva and Maffeo, Christopher M and Drexler, Thomas and Honemann, Maximilian N and Aleksei Aksimentiev and Dietz, Hendrik} } @article {365, title = {Multiple rereads of single proteins at single{\textendash}amino acid resolution using nanopores}, journal = {Science}, volume = {374}, year = {2021}, month = {11/2021}, pages = {1509{\textendash}1513}, abstract = {

A proteomics tool capable of identifying single proteins would be important for cell biology research and applications. Here, we demonstrate a nanopore-based single-molecule peptide reader sensitive to single{\textendash}amino acid substitutions within individual peptides. A DNA-peptide conjugate was pulled through the biological nanopore MspA by the DNA helicase Hel308. Reading the ion current signal through the nanopore enabled discrimination of single{\textendash}amino acid substitutions in single reads. Molecular dynamics simulations showed these signals to result from size exclusion and pore binding. We also demonstrate the capability to {\textquotedblleft}rewind{\textquotedblright} peptide reads, obtaining numerous independent reads of the same molecule, yielding an error rate of \<10-6\ in single amino acid variant identification. These proof-of-concept experiments constitute a promising basis for the development of a single-molecule protein fingerprinting and analysis technology.

}, doi = {10.1021/acs.nanolett.1c04203}, author = {Brinkerhoff, Henry and Kang, Albert SW and Liu, Jingqian and Aleksei Aksimentiev and Dekker, Cees} } @article {356, title = {The emerging landscape of single-molecule protein sequencing technologies}, journal = {Nature Methods}, volume = {18}, year = {2021}, month = {06/2021}, chapter = {604-617}, abstract = {

Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell profiling. These technologies will in turn facilitate biological discovery and open new avenues for ultrasensitive disease diagnostics.

}, doi = {10.1038/s41592-021-01143-1}, url = {https://doi.org/10.1038/s41592-021-01143-1}, author = {Javier Antonio Alfaro and Peggy Bohl{\"a}nder and Mingjie Dai and Mike Filius and Cecil J. Howard and Xander F. van Kooten and Shilo Ohayon and Adam Pomorski and Sonja Schmid and Aleksei Aksimentiev and Eric V. Anslyn and Georges Bedran and Chan Cao and Mauro Chinappi and Etienne Coyaud and Cees Dekker and Gunnar Dittmar and Nicholas Drachman and Rienk Eelkema and David Goodlett and S{\'e}bastien Hentz and Umesh Kalathiya and Neil L. Kelleher and Ryan T. Kelly and Zvi Kelman and Sung Hyun Kim and Bernhard Kuster and David Rodriguez-Larrea and Stuart Lindsay and Giovanni Maglia and Edward M. Marcotte and John P. Marino and Christophe Masselon and Michael Mayer and Patroklos Samaras and Kumar Sarthak and Lusia Sepiashvili and Derek Stein and Meni Wanunu and Mathias Wilhelm and Peng Yin and Amit Meller and Chirlmin Joo} } @article {350, title = {Cations Regulate Membrane Attachment and Functionality of DNA Nanostructures}, journal = {Journal of the American Chemical Society}, volume = {143}, year = {2021}, month = {05/2021}, pages = {7358-7367}, chapter = {7358}, abstract = {

The interplay between nucleic acids and lipids\ underpins several key processes in molecular biology, synthetic biotechnology, vaccine technology, and nanomedicine. These interactions are often electrostatic in nature, and much of their rich phenomenology remains unexplored in view of the chemical diversity of lipids, the heterogeneity of their phases, and the broad range of relevant solvent conditions. Here we unravel the electrostatic interactions between zwitterionic lipid membranes and DNA nanostructures in the presence of physiologically relevant\ cations, with the purpose of identifying new routes to program DNA-lipid complexation and membrane-active nanodevices. We demonstrate that this interplay is influenced by both the phase of the lipid membranes and the valency of the ions and observe divalent cation bridging between nucleic acids and gel-phase bilayers. Furthermore, even in the presence of hydrophobic modifications on the DNA, we find that cations are still required to enable DNA adhesion to liquid-phase membranes. We show that the latter mechanism can be exploited to control the degree of attachment of cholesterol-modified DNA nanostructures by modifying their overall hydrophobicity and charge. Besides their biological relevance, the interaction mechanisms we explored hold great practical potential in the design of biomimetic nanodevices, as we show by constructing an ion-regulated DNA-based synthetic enzyme.

}, doi = {10.1021/jacs.1c00166}, url = {https://doi.org/10.1021/jacs.1c00166}, author = {Morzy, Diana and Rubio-S{\'a}nchez, Roger and Joshi, Himanshu and Aleksei Aksimentiev and Di Michele, Lorenzo and Keyser, Ulrich F.} } @article {341, title = {Translocation of DNA through Ultrathin Nanoslits}, journal = {Advanced Materials}, volume = {33}, year = {2021}, month = {02/2021}, pages = {2007682}, chapter = {2007682}, abstract = {

2D nanoslit devices, where two crystals with atomically flat surfaces are separated by only a few nanometers, have attracted considerable attention because their tunable control over the confinement allows for the discovery of unusual transport behavior of gas, water, and ions. Here, the passage of double-stranded DNA molecules is studied through nanoslits fabricated from exfoliated 2D materials, such as graphene or hexagonal boron nitride, and the DNA polymer behavior is examined in this tight confinement. Two types of events are observed in the ionic current: long current blockades that signal DNA translocation and short spikes where DNA enters the slits but withdraws. DNA translocation events exhibit three distinct phases in their current-blockade traces{\textemdash}loading, translation, and exit. Coarse-grained molecular dynamics simulation allows the different polymer configurations of these phases to be identified. DNA molecules, including folds and knots in their polymer structure, are observed to slide through the slits with near-uniform velocity without noticeable frictional interactions of DNA with the confining graphene surfaces. It is anticipated that this new class of 2D-nanoslit devices will provide unique ways to study polymer physics and enable lab-on-a-chip biotechnology.

}, keywords = {2D nanoslits, biopolymers, DNA translocation, graphene, Nanofluidics}, doi = {https://doi.org/10.1002/adma.202007682}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/adma.202007682}, author = {Yang, Wayne and Radha, Boya and Choudhary, Adnan and You, Yi and Mettela, Gangaiah and Geim, Andre K. and Aleksei Aksimentiev and Keerthi, Ashok and Dekker, Cees} } @article {357, title = {A tetrahedral DNA nanorobot with conformational change in response to molecular trigger}, journal = {Nanoscale}, year = {2021}, month = {01/2021}, abstract = {

Dynamic DNA origami nanostructures that respond to external stimuli are promising platforms for cargo delivery and nanoscale sensing. However, the low stability of such nanostructures under physiological conditions presents a major obstacle for their use in biomedical applications. This article describes a stable tetrahedral DNA nanorobot (TDN) programmed to undergo a controlled conformational change in response to epithelial cell adhesion molecule (EpCAM), a molecular biomarker specifically expressed on the circulating tumor cells. Multiresolution molecular dynamics simulations verified the overall stability of the folded TDN design and characterized local distortions in the folded structure. Atomic force microscopy and gel electrophoresis results showed that tetragonal structures are more stable than unfolded DNA origami sheets. Live cell experiments demonstrated the low cytotoxicity and target specificity of TDN. In summary, the proposed TDN can not only effectively resist nuclease catalysis but also has the potential to monitor EpCAM-positive cells precisely.

}, issn = {2040-3364}, doi = {10.1039/D1NR02757C}, url = {http://xlink.rsc.org/?DOI=D1NR02757Chttp://pubs.rsc.org/en/content/articlepdf/2021/NR/D1NR02757Chttp://pubs.rsc.org/en/content/articlepdf/2021/NR/D1NR02757C}, author = {Liu, Fengyu and Liu, Xiaoming and Shi, Qing and Maffeo, Christopher and Kojima, Masaru and Dong, Lixin and Aleksei Aksimentiev and Huang, Qiang and Fukuda, Toshio and Arai, Tatsuo} } @article {308, title = {Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism}, journal = {Cell}, volume = {179}, year = {2019}, month = {11/2019}, pages = {1098 - 1111.e23}, abstract = {

We report a 100-million atom-scale model of an entire cell organelle, a photosynthetic chromatophore vesicle from a purple bacterium, that reveals the cascade of energy conversion steps culminating in the generation of ATP from sunlight. Molecular dynamics simulations of this vesicle elucidate how the integral membrane complexes influence local curvature to tune photoexcitation of pigments. Brownian dynamics of small molecules within the chromatophore probe the mechanisms of directional charge transport under various pH and salinity conditions. Reproducing phenotypic properties from atomistic details, a kinetic model evinces that low-light adaptations of the bacterium emerge as a spontaneous outcome of optimizing the balance between the chromatophore{\textquoteright}s structural integrity and robust energy conversion. Parallels are drawn with the more universal\ mitochondrial bioenergetic machinery, from whence molecular-scale insights into the mechanism of cellular aging are inferred. Together, our integrative method and spectroscopic experiments pave the way to first-principles modeling of whole living cells.

}, keywords = {bioenergetics, biological membranes, charge transport, chromatophore, integrative model, MD, mitochondria, Molecular Dynamics Simulation, optical spectroscopy, photosynthesis}, issn = {0092-8674}, doi = {10.1016/j.cell.2019.10.021}, url = {http://www.sciencedirect.com/science/article/pii/S0092867419311717}, author = {Abhishek Singharoy and Christopher Maffeo and Karelia H. Delgado-Magnero and David J.K. Swainsbury and Melih Sener and Ulrich Kleinekath{\"o}fer and John W. Vant and Jonathan Nguyen and Andrew Hitchcock and Barry Isralewitz and Ivan Teo and Danielle E. Chandler and John E. Stone and James C. Phillips and Taras V. Pogorelov and M. Ilaria Mallus and Christophe Chipot and Zaida Luthey-Schulten and D. Peter Tieleman and C. Neil Hunter and Emad Tajkhorshid and Aleksei Aksimentiev and Klaus Schulten} } @article {301, title = {The Oligomerization Landscape of Histones}, journal = {Biophysical Journal}, volume = {116}, year = {2019}, month = {05/2019}, pages = {1845--1855}, doi = {doi.org/10.1016/j.bpj.2019.03.021}, url = {https://www.sciencedirect.com/science/article/pii/S0006349519302784}, author = {Zhao, Haiqing and Winogradoff, David and Dalal, Yamini and Papoian, Garegin A} } @article {295, title = {Electro-Mechanical Conductance Modulation of a Nanopore Using a Removable Gate}, journal = {ACS Nano}, volume = {13}, year = {2019}, month = {02/2019}, pages = {2398--2409}, chapter = {2398}, abstract = {

Ion channels form the basis of information processing in livings cells by facilitating exchange of electrical signals across and along cellular membranes. Applying the same principles to man-made systems requires development of synthetic ion channels that can alter their conductance in response to a variety of external manipulations. By combining single-molecule electrical recordings with all-atom molecular dynamics simulations, we here demonstrate a new hybrid nanopore system that allows for both a stepwise change of its conductance and a non-linear current-voltage dependence. The conductance modulation is realized by using a short flexible peptide gate that carries opposite electric charge at its ends. We show that a constant transmembrane bias can position, and in a later stage remove, the peptide gate right at the most sensitive sensing region of a biological nanopore FraC, thus partially blocking its channel and producing a stepwise change in the conductance. Increasing or decreasing the bias while having the peptide gate trapped in the pore stretches or compresses the peptide within the nanopore, thus modulating its conductance in a non-linear but reproducible manner. We envision a range of applications of this removable-gate nanopore system, e.g. from an element of biological computing circuits to a test bed for probing the elasticity of intrinsically disordered proteins.

}, doi = {10.1021/acsnano.8b09266}, url = {https://doi.org/10.1021/acsnano.8b09266}, author = {Shidi Zhao and Restrepo-Perez, Laura and Maglia, Giovanni and Misha Soskine and Chirlmin Joo and Cees Dekker and Aleksei Aksimentiev} } @article {290, title = {PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {09/2018}, pages = {3661}, abstract = {

Monodispersed angstrom-size pores embedded in a suitable matrix are promising for highly selective membrane-based separations. They can provide substantial energy savings in water treatment and small molecule bioseparations. Such pores present as membrane proteins (chiefly aquaporin-based) are commonplace in biological membranes but difficult to implement in synthetic industrial membranes and have modest selectivity without tunable selectivity. Here we present PoreDesigner, a design workflow to redesign the robust beta-barrel Outer Membrane Protein F as a scaffold to access three specific pore designs that exclude solutes larger than sucrose (\>360 Da), glucose (\>180 Da), and salt (\>58 Da) respectively. PoreDesigner also enables us to design any specified pore size (spanning 3{\textendash}10 {\r A}), engineer its pore profile, and chemistry. These redesigned pores may be ideal for conducting sub-nm aqueous separations with permeabilities exceeding those of classical biological water channels,\ aquaporins, by more than an order of magnitude at over 10 billion water molecules per channel per second.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-06097-1}, url = {https://doi.org/10.1038/s41467-018-06097-1}, author = {Chowdhury, Ratul and Ren, Tingwei and Shankla, Manish and Decker, Karl and Grisewood, Matthew and Prabhakar, Jeevan and Baker, Carol and Golbeck, John H and Aleksei Aksimentiev and Kumar, Manish and Maranas, Costas D} } @article {268, title = {Nanoscale Ion Pump Derived from a Biological Water Channel}, journal = {The Journal of Physical Chemistry B }, volume = {121}, year = {2017}, month = {08/2017}, pages = {7899{\textendash}7906 }, abstract = {

Biological molecular machines perform the\ work of supporting life at the smallest of scales, including\ the work of shuttling ions across cell boundaries and against\ chemical gradients. Systems of artifi cial channels at the\ nanoscale can likewise control ionic concentration by way of\ ionic current rectifi cation, species selectivity, and voltage\ gating mechanisms. Here, we theoretically show that a voltagegated,\ ion species-selective, and rectifying ion channel can be\ built using the components of a biological water channel\ aquaporin. Through all-atom molecular dynamics simulations,\ we show that the ionic conductance of a truncated aquaporin\ channel nonlinearly increases with the bias magnitude, depends on the channel{\textquoteright} s orientation, and is highly cation specific but only\ for one polarity of the transmembrane bias. Further, we show that such an unusually complex response of the channel to\ transmembrane bias arises from mechanical motion of a positively charged gate that blocks cation transport. By combining two\ truncated aquaporins, we demonstrate a molecular system that pumps ions against their chemical gradients when subject to an\ alternating transmembrane bias. Our work sets the stage for future biomimicry eff orts directed toward reproducing the function\ of biological ion pumps using synthetic components.

}, doi = {10.1021/acs.jpcb.7b05568}, author = {Karl Decker and Martin Page and Aleksei Aksimentiev} } @article {266, title = {SDS-assisted protein transport through solid-state nanopores}, journal = {Nanoscale}, volume = {9}, year = {2017}, month = {05/2017}, pages = {11685-11693}, abstract = {

Using nanopores for single-molecule sequencing of proteins - similar to nanopore-based sequencing of DNA - faces multiple challenges, including unfolding of the complex tertiary structure of the proteins and enforcing their unidirectional translocation through nanopores. Here, we combine molecular dynamics (MD) simulations with single-molecule experiments to investigate the utility of SDS (Sodium Dodecyl Sulfate) to unfold proteins for solid-state nanopore translocation, while simultaneously endowing them with a stronger electrical charge. Our simulations and experiments prove that SDS-treated proteins show a considerable loss of the protein structure during the nanopore translocation. Moreover, SDS-treated proteins translocate through the nanopore in the direction prescribed by the electrophoretic force due to the negative charge impaired by SDS. In summary, our results suggest that SDS causes protein unfolding while facilitating protein translocation in the direction of the electrophoretic force; both characteristics being advantageous for future protein sequencing applications using solid-state nanopores.

}, doi = {10.1039/C7NR02450A}, url = {http://dx.doi.org/10.1039/C7NR02450A}, author = {Restrepo-Perez*, Laura and John*, Shalini and Aleksei Aksimentiev and Joo, Chirlmin and Dekker, Cees} } @article {251, title = {Selective Permeability of Truncated Aquaporin 1 in Silico}, journal = {ACS Biomaterials Science \& Engineering}, volume = {3}, year = {2017}, month = {02/2017}, pages = {342-348}, chapter = {342}, abstract = {

Aquaporin (AQP) proteins function as highly efficient water transport channels that support homeostasis in many types of living cells. Their structure-function relationships have been characterized extensively in fundamental and applied research, primarily via structural analysis, mutational studies, and computational approaches. The present study evaluates the effects of progressive truncations on the permeability and ionic conductivity of AQP-1 (bovine). The use of truncations to determine critical features has not been considered previously, as physical truncation of AQP is likely not technically feasible due to the ornate arrangement of six interwoven alpha helices in a single pore structure. However, structures not obtainable through protein assembly can be realized via synthetic chemistry approaches and studied using molecular dynamics (MD) simulations. Here, we apply the MD method to characterize the permeability of AQP variants truncated along the pore axis from both cytoplasmic and extracellular sides of the channel. The simulation results suggest that AQP-1 can retain its function even after deletion of up to 50\% of the channel{\textquoteright}s length, representing 50\% of proteins{\textquoteright}s molecular mass. Deletions such as these are expected to greatly simplify future biomimicry efforts of reproducing the AQP functionality using synthetic macromolecules. This study demonstrates the potential of in silico approaches to support the creation of streamlined functional analogs of biological molecular machines.

}, doi = {10.1021/acsbiomaterials.6b00583 }, author = {Karl Decker and Martin Page and Ashley Boyd and Irene MacAllister and Mark Ginsberg and Aleksei Aksimentiev} } @article {253, title = {Interference-free detection of genetic biomarkers using synthetic dipole-facilitated nanopore dielectophoresis.}, journal = {ACS Nano}, volume = {11}, year = {2017}, month = {01/2017}, pages = {1204-1213}, chapter = {1204}, abstract = {

The motion of polarizable particles in a non-uniform electric field, i.e., dielectrophoresis, has been extensively used for concentration, separation, sorting, and transport of biological particles, from cancer cells and viruses to biomolecules such as DNAs and proteins. However, current approaches to dielectrophoretic manipulation are not sensitive enough to selectively target individual molecular species. Here we describe the application of the dielectrophoretic principle for selective detection of DNA and RNA molecules using an engineered biological nanopore. The key element of our approach is a synthetic polycationic nanocarrier that selectively binds to the target biomolecules, dramatically increasing their dielectrophoretic response to the electric field gradient generated by the nanopore. The dielectrophoretic capture of the nanocarrier-target complexes is detected as a transient blockade of the nanopore ionic current while any non-target nucleic acids are repelled from the nanopore by electrophoresis and thus do not interfere with the signal produced by the target{\textquoteright}s capture. Strikingly, we show that even modestly charged nanocarriers can be used to capture DNA or RNA molecules of any length or secondary structure and simultaneously detect several molecular targets. Such selective, multiplex molecular detection technology would be highly desirable for real-time analysis of complex clinical samples.

}, doi = {10.1021/acsnano.6b07570}, author = {Kai Tian and Karl Decker and Aleksei Aksimentiev and Li-Qun Gu} } @article {250, title = {Mechanical Trapping of DNA in a Double-Nanopore System}, journal = {Nano Letters}, volume = {16}, year = {2016}, month = {11/2016}, pages = {8021-8028 }, abstract = {

Nanopores have become ubiquitous components of systems for single-molecule manipulation and detection, in particular DNA sequencing where electric field driven translocation of DNA through a nanopore is used to read out the DNA molecule. Here, we present a double-pore system where two nanopores are drilled in parallel through the same solid-state membrane, which offers new opportunities for DNA manipulation. Our experiments and molecular dynamics simulations show that simultaneous electrophoretic capture of a DNA molecule by the two nanopores mechanically traps the molecule, increasing its residence time within the nanopores by orders of magnitude. Remarkably, by using two unequal-sized nanopores, the pore of DNA entry and exit can be discerned from the ionic current blockades, and the translocation direction can be precisely controlled by small differences in the effective force applied to DNA. The mechanical arrest of DNA translocation using a double-pore system can be straightforwardly integrated into any solid-state nanopore platform, including those using optical or transverse-current readouts.

}, doi = {10.1021/acs.nanolett.6b04642}, author = {Sergii Pud and Shu-Han Chao and Maxim Belkin and Daniel Verschueren and Teun Huijben and Casper van Engelenburg and Cees Dekker and Aleksei Aksimentiev} } @article {316, title = {Promiscuous Histone Mis-Assembly Is Actively Prevented by Chaperones.}, journal = {J Am Chem Soc}, volume = {138}, year = {2016}, month = {10/2016}, pages = {13207-13218}, abstract = {

Histone proteins are essential for the organization, expression, and inheritance of genetic material for eukaryotic cells. A centromere-specific H3 histone variant, centromere protein A (CENP-A), shares about 50\% amino acid sequence identity with H3. CENP-A is required for packaging the centromere and for the proper separation of chromosomes during mitosis. Despite their distinct biological functions, previously reported crystal structures of the CENP-A/H4 and H3/H4 dimers reveal a high degree of similarity. In this work, we characterize the structural dynamics of CENP-A/H4 and H3/H4 dimers based on a dual-resolution approach, using both microsecond-scale explicit-solvent all-atom and coarse-grained (CG) molecular dynamics (MD) simulations. Our data show that the H4 histone is significantly more rigid compared with the H3 histone and its variant CENP-A, hence, serving as a reinforcing structural element within the histone core. We report that the CENP-A/H4 dimer is significantly more dynamic than its canonical counterpart H3/H4, and our results provide a physical explanation for this flexibility. Further, we observe that the centromere-specific chaperone Holliday Junction Recognition Protein (HJURP) stabilizes the CENP-A/H4 dimer by forming a specific electrostatic interaction network. Finally, replacing CENP-A S68 with E68 disrupts the binding interface between CENP-A and HJURP in all-atom MD simulation, and consistently, in vivo experiments demonstrate that replacing CENP-A S68 with E68 disrupts CENP-A{\textquoteright}s localization to the centromere. Based on all our results, we propose that, during the CENP-A/H4 deposition process, the chaperone HJURP protects various substructures of the dimer, serving both as a folding and binding chaperone.

}, keywords = {Centromere Protein A, DNA-Binding Proteins, HeLa Cells, Histones, Humans, Molecular Dynamics Simulation, Protein Folding, Protein Multimerization, Protein Structure, Quaternary, Substrate Specificity}, doi = {10.1021/jacs.6b05355}, author = {Zhao*, Haiqing and Winogradoff*, David and Bui, Minh and Dalal, Yamini and Papoian, Garegin A} } @article {313, title = {Promiscuous histone mis-assembly is actively prevented by chaperones.}, journal = {Journal of the American Chemical Society}, volume = {138}, year = {2016}, pages = {13207--13218}, doi = {10.1021/jacs.6b05355}, author = {Zhao*, Haiqing and Winogradoff*, David and Minh Bui and Yamini Dalal and Garegin Papoian} } @article {210, title = {Effect of Cytosine Modifications on DNA Flexibility and Nucleosome Mechanical Stability}, journal = {Nature Communications}, volume = {7}, year = {2016}, pages = {10813}, chapter = {10813}, abstract = {

Cytosine can undergo modifications, forming 5-methylcytosine (5-mC) and its oxidized products 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC). Despite their importance as epigenetic markers and as central players in cellular processes, it is not well understood how these modifications influence physical properties of DNA and chromatin. Here we report a comprehensive survey of the effect of cytosine modifications on DNA flexibility. We find that even a single copy of 5-fC increases DNA flexibility markedly. 5-mC reduces and 5-hmC enhances flexibility, and 5-caC does not have a measurable effect. Molecular dynamics simulations show that these modifications promote or dampen structural fluctuations, likely through competing effects of base polarity and steric hindrance, without changing the average structure. The increase in DNA flexibility increases the mechanical stability of the nucleosome and vice versa, suggesting a gene regulation mechanism where cytosine modifications change the accessibility of nucleosomal DNA through their effects on DNA flexibility.

}, doi = {10.1038/ncomms10813}, author = {Thuy Ngo and Jejoong Yoo and Dai, Q and Zhang, Q and He, C and Aleksei Aksimentiev and Taekjip Ha} } @article {204, title = {Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA}, journal = {ACS Nano}, volume = {9}, year = {2015}, month = {09/2015}, pages = {10598--10611}, type = {Article}, abstract = {

\ \ \ \ \ \ With the aim of developing a DNA sequencing methodology, we theoretically examine the feasibility of using nanoplasmonics to control the translocation of a DNA molecule through a solid-state nanopore and to read off sequence information using surface-enhanced Raman spectroscopy. Using molecular dynamics\ simulations, we show that high-intensity optical hot spots produced by a metallic nanostructure can arrest DNA translocation through a solid-state nanopore, thus providing a physical knob for controlling the DNA speed. Switching the plasmonic field on and off can displace the DNA molecule in discrete steps, sequentially exposing neighboring fragments of a DNA molecule to the pore as well as to the plasmonic hot spot. Surface-enhanced Raman scattering from the exposed DNA fragments contains information about their nucleotide composition, possibly allowing the identification of the nucleotide sequence of a DNA molecule transported through the hot spot. The principles of plasmonic nanopore sequencing can be extended to detection of DNA modifications and RNA characterization.

}, doi = {10.1021/acsnano.5b04173}, url = {http://pubs.acs.org/doi/10.1021/acsnano.5b04173}, author = {Maxim Belkin and Shu-Han Chao and Magnus P. Jonsson and Cees Dekker and Aleksei Aksimentiev} } @article {202, title = {Highly permeable artificial water channels that self-assemble into two-dimensional arrays}, journal = {Proceedings of the National Academy of Science}, volume = {112}, year = {2015}, month = {07/2015}, pages = {9810-9815}, chapter = {9810}, abstract = {

Bioinspired artificial water channels aim to combine the high permeability and selectivity of biological aquaporin (AQP) water channels with chemical stability. We characterized a new architecture of artificial water channels, peptide-appended pillar[5]arenes (PAPs). The average single-channel osmotic water permeability for PAPs is 1.0({\textpm} 0.3){\texttimes}10-14\ cm3/s or 3.5({\textpm} 1.0){\texttimes}108\ water molecules/s, which is in the range of AQPs (3.4~40.3{\texttimes}108\ water molecules/s) and their current synthetic analogs, carbon nanotubes (CNTs, 9.0{\texttimes}108\ water molecules/s). This permeability is an order of magnitude higher than first-generation artificial water channels (20 to ~107\ water molecules/s). Furthermore, within lipid bilayers, PAP channels can self-assemble into two-dimensional arrays. Importantly for permeable membrane design, the pore density of PAP channel arrays (~2.6{\texttimes}105\ pores/μm2) is two orders of magnitude higher than CNT membranes (0.1~2.5{\texttimes}103\ pores/μm2). PAP channels thus combine the advantages of biological channels and CNTs and improve upon them through their relatively simple synthesis, chemical stability and propensity to form arrays.

}, keywords = {membrane, nanochannel, permeation}, doi = {10.1073/pnas.1508575112}, author = {Yue-xiao Shen and Wen Si and Mustafa Erbakan and Karl Decker and Rita De Zorzi and Patrick O. Saboe and You Jung Kang and Sheereen Majd and Peter J. Butler and Thomas Walz and Aleksei Aksimentiev and Jun-li Hou and Manish Kumar} } @article {220, title = {Shearing of the CENP-A dimerization interface mediates plasticity in the octameric centromeric nucleosome}, journal = {Scientific reports}, volume = {5}, year = {2015}, doi = {10.1038/srep17038}, author = {Winogradoff, David and Zhao, Haiqing and Dalal, Yamini and Papoian, Garegin A} } @article {doi:10.1021/jp501492g, title = {Rectification of Ion Current in Nanopores Depends on the Type of Monovalent Cations: Experiments and Modeling}, journal = {The Journal of Physical Chemistry C}, volume = {118}, number = {18}, year = {2014}, pages = {9809-9819}, abstract = {Rectifying nanopores feature ion currents that are higher for voltages of one polarity compared to the currents recorded for corresponding voltages of the opposite polarity. Rectification of nanopores has been found to depend on the pore opening diameter and distribution of surface charges on the pore walls as well as pore geometry. Very little is known, however, on the dependence of ionic rectification on the type of transported ions of the same charge. We performed experiments with single conically shaped nanopores in a polymer film and recorded current-voltage curves in three electrolytes: LiCl, NaCl, and KCl. Rectification degrees of the pores, quantified as the ratio of currents recorded for voltages of opposite polarities, were the highest for KCl and the lowest for LiCl. The experimental observations could not be explained by a continuum modeling based on the Poisson-Nernst-Planck equations. All-atom molecular dynamics simulations revealed differential binding between Li+, Na+, and K+ ions and carboxyl groups on the pore walls, resulting in changes to both the effective surface charge of the nanopore and cation mobility within the pore.}, doi = {10.1021/jp501492g}, url = {http://dx.doi.org/10.1021/jp501492g}, author = {Gamble, Trevor and Karl Decker and Plett, Timothy S. and Pevarnik, Matthew and Pietschmann, Jan-Frederik and Vlassiouk, Ivan and Aleksei Aksimentiev and Siwy, Zuzanna S.} } @article {135, title = {Single-base DNA discrimination via transverse ionic transport.}, journal = {Nanotechnology}, volume = {24}, year = {2013}, month = {10/2013}, pages = {415101}, abstract = {

We suggest the discrimination of single DNA bases via transverse ionic transport, namely by detecting the ionic current that flows in a channel while a single-stranded DNA is driven through an intersecting nanochannel. Our all-atom molecular dynamics simulations indeed show that the ionic currents of the four bases are statistically distinct, thus offering another possible approach to sequencing DNA.

}, keywords = {Base Sequence, DNA, Single-Stranded, Ion Transport, Ions, Molecular Dynamics Simulation, Nucleic Acid Conformation}, issn = {1361-6528}, doi = {10.1088/0957-4484/24/41/415101}, author = {James Wilson and Massimiliano Di Ventra} } @article {31, title = {Slowing down DNA translocation through a nanopore in lithium chloride.}, journal = {Nano Lett}, volume = {12}, year = {2012}, month = {2012 Feb 8}, pages = {1038-44}, abstract = {

The charge of a DNA molecule is a crucial parameter in many DNA detection and manipulation schemes such as gel electrophoresis and lab-on-a-chip applications. Here, we study the partial reduction of the DNA charge due to counterion binding by means of nanopore translocation experiments and all-atom molecular dynamics (MD) simulations. Surprisingly, we find that the translocation time of a DNA molecule through a solid-state nanopore strongly increases as the counterions decrease in size from K(+) to Na(+) to Li(+), both for double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA). MD simulations elucidate the microscopic origin of this effect: Li(+) and Na(+) bind DNA stronger than K(+). These fundamental insights into the counterion binding to DNA also provide a practical method for achieving at least 10-fold enhanced resolution in nanopore applications.

}, keywords = {DNA, Lithium Chloride, Models, Molecular, Molecular Dynamics Simulation, Nanopores, Nanotechnology, Particle Size, Surface Properties}, issn = {1530-6992}, doi = {10.1021/nl204273h}, author = {Kowalczyk, Stefan W and David B Wells and Aleksei Aksimentiev and Dekker, Cees} } @article {26, title = {Molecular dynamics study of MspA arginine mutants predicts slow DNA translocations and ion current blockades indicative of DNA sequence}, journal = {ACS Nano}, volume = {6}, year = {2012}, month = {2012 Aug 28}, pages = {6960-8}, abstract = {

The protein nanopore Mycobacteria smegmatis porin A (MspA), can be used to sense individual nucleotides within DNA, potentially enabling a technique known as nanopore sequencing. In this technique, single-stranded DNA electrophoretically moves through the nanopore and results in an ionic current that is nucleotide-specific. However, with a high transport velocity of the DNA within the nanopore, the ionic current cannot be used to distinguish signals within noise. Through extensive (~100 μs in total) all-atom molecular dynamics simulations, we examine the effect of positively charged residues on DNA translocation rate and the ionic current blockades in MspA. Simulation of several arginine mutations show a ~10-30 fold reduction of DNA translocation speed without eliminating the nucleotide induced current blockages. Comparison of our results with similar engineering efforts on a different nanopore (α-hemolysin) reveals a nontrivial effect of nanopore geometry on the ionic current blockades in mutant nanopores.

}, keywords = {Arginine, Base Sequence, Biosensing Techniques, Computer Simulation, Conductometry, DNA, Electric Conductivity, Ion Channel Gating, Models, Chemical, Models, Genetic, Models, Molecular, Molecular Sequence Data, Mutation, Porins, Sequence Analysis, DNA, Translocation, Genetic}, issn = {1936-086X}, doi = {10.1021/nn3019943}, author = {Bhattacharya, Swati and Derrington, Ian M and Pavlenok, Mikhail and Niederweis, Michael and Gundlach, Jens H and Aleksei Aksimentiev} } @article {32, title = {Nanopore analysis of individual RNA/antibiotic complexes.}, journal = {ACS Nano}, volume = {5}, year = {2011}, month = {2011 Dec 27}, pages = {9345-53}, abstract = {

Nanopores in thin solid-state membranes are used to rapidly analyze individual RNA/drug complexes. The interactions of a truncated A-site RNA model of the prokaryotic ribosome with aminoglycoside antibiotics are characterized by passing individual molecules through a 3-3.5 nm diameter pore fabricated in a 8-10 nm thick silicon nitride membrane. Complexes of the A-site RNA with aminoglycosides can be distinguished from unbound A-site based on the ion current signatures produced as they pass through the nanopores. Counting the fraction of free and drug-bound molecules affords label-free drug-RNA binding isotherms consistent with literature reports and with data generated using independent fluorescence-based assays. Our measurements are supported by molecular dynamics simulations, which illustrate the relationship between the ionic current and complexation of the A-site RNA with paramomycin, a prototypical aminoglycoside antibiotic.

}, keywords = {Anti-Bacterial Agents, Binding Sites, Diffusion, Electroporation, Materials Testing, Membranes, Artificial, Nanostructures, Paromomycin, Porosity, RNA, Semiconductors}, issn = {1936-086X}, doi = {10.1021/nn203764j}, author = {Meni Wanunu and Bhattacharya, Swati and Xie, Yun and Tor, Yitzhak and Aleksei Aksimentiev and Drndic, Marija} } @inbook {192, title = {Third Generation DNA Sequencing with a Nanopore}, booktitle = {Nanopores: Sensing fundamental biological interactions at the single molecule level}, year = {2011}, pages = {287-311}, publisher = {Springer US}, organization = {Springer US}, chapter = {12}, abstract = {

With the advent of Next-Generation-Sequencing (NGS) technologies, an enormous volume of DNA sequencing data can be generated at low cost, placing genomic science within the grasp of everyday medicine. However, mired in this voluminous data, a new problem has emerged: the assembly of the genome from the short reads. In this chapter we examine the prospects for sequencing DNA using a synthetic nanopore. Nanopore sequencing has the potential for very long reads, reducing the computational burden posed by alignment and genome assembly, while at the same time eliminating logistically challenging and error-prone amplification and library formation due to its exquisite single molecule sensitivity. On the other hand, long high fidelity reads demand stringent control over both the DNA configuration in the pore and the translocation kinetics. We examine the prospects for satisfying these specifications with a synthetic nanopore.

}, keywords = {Comparison between biological and synthetic nanopores, Hydrodynamic focusing, Molecular dynamics simulations, Sequencing DNA, Trapping DNA, λ-DNA}, isbn = {978-1-4419-8251-3}, doi = {10.1007/978-1-4419-8252-0_12}, url = {http://dx.doi.org/10.1007/978-1-4419-8252-0_12}, author = {Gregory Timp and Mirsaidov, Utkur and Timp, Winston and Shim, Jiwook and Wang, Deqiang and Valentin Dimitrov and Scrimgeour, Jan and Lin, Chunchen and Jeffrey Comer and Anthony H. Ho and Zou, Xueqing and Aleksei Aksimentiev and Klaus Schulten}, editor = {Iqbal, Samir M. and Rashid Bashir} } @article {41, title = {Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix}, journal = {Nanotechnology}, volume = {21}, year = {2010}, month = {2010 Oct 1}, pages = {395501}, abstract = {

It is now possible to slow and trap a single molecule of double-stranded DNA (dsDNA), by stretching it using a nanopore, smaller in diameter than the double helix, in a solid-state membrane. By applying an electric force larger than the threshold for stretching, dsDNA can be impelled through the pore. Once a current blockade associated with a translocating molecule is detected, the electric field in the pore is switched in an interval less than the translocation time to a value below the threshold for stretching. According to molecular dynamics (MD) simulations, this leaves the dsDNA stretched in the pore constriction with the base-pairs tilted, while the B-form canonical structure is preserved outside the pore. In this configuration, the translocation velocity is substantially reduced from 1 bp/10 ns to approximately 1 bp/2 ms in the extreme, potentially facilitating high fidelity reads for sequencing, precise sorting, and high resolution (force) spectroscopy.

}, keywords = {Bacteriophage lambda, DNA, DNA, Viral, Electrochemical Techniques, Microscopy, Electron, Transmission, Molecular Dynamics Simulation, Nanopores, Nanotechnology, Nucleic Acid Conformation, Particle Size}, issn = {1361-6528}, doi = {10.1088/0957-4484/21/39/395501}, author = {Mirsaidov, Utkur and Jeffrey Comer and Valentin Dimitrov and Aleksei Aksimentiev and Gregory Timp} } @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 {49, title = {Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore}, journal = {Nucleic Acids Res}, volume = {37}, year = {2009}, month = {2009 Jul}, pages = {4170-9}, abstract = {

Restriction endonucleases are used prevalently in recombinant DNA technology because they bind so stably to a specific target sequence and, in the presence of cofactors, cleave double-helical DNA specifically at a target sequence at a high rate. Using synthetic nanopores along with molecular dynamics (MD), we have analyzed with atomic resolution how a prototypical restriction endonuclease, EcoRI, binds to the DNA target sequence--GAATTC--in the absence of a Mg(2+) ion cofactor. We have previously shown that there is a voltage threshold for permeation of DNA bound to restriction enzymes through a nanopore that is associated with a nanonewton force required to rupture the complex. By introducing mutations in the DNA, we now show that this threshold depends on the recognition sequence and scales linearly with the dissociation energy, independent of the pore geometry. To predict the effect of mutation in a base pair on the free energy of dissociation, MD is used to qualitatively rank the stability of bonds in the EcoRI-DNA complex. We find that the second base in the target sequence exhibits the strongest binding to the protein, followed by the third and first bases, with even the flanking sequence affecting the binding, corroborating our experiments.

}, keywords = {Computer Simulation, Deoxyribonuclease EcoRI, DNA, DNA-Binding Proteins, Models, Molecular, Nanostructures, Protein Binding}, issn = {1362-4962}, doi = {10.1093/nar/gkp317}, author = {Dorvel, B and G Sigalov and Zhao, Q and Jeffrey Comer and Valentin Dimitrov and Mirsaidov, U and Aleksei Aksimentiev and Gregory Timp} } @article {50, title = {Microscopic mechanics of hairpin DNA translocation through synthetic nanopores}, journal = {Biophys J}, volume = {96}, year = {2009}, month = {2009 Jan}, pages = {593-608}, abstract = {

Nanoscale pores have proved useful as a means to assay DNA and are actively being developed as the basis of genome sequencing methods. Hairpin DNA (hpDNA), having both double-helical and overhanging coil portions, can be trapped in a nanopore, giving ample time to execute a sequence measurement. In this article, we provide a detailed account of hpDNA interaction with a synthetic nanopore obtained through extensive all-atom molecular dynamics simulations. For synthetic pores with minimum diameters from 1.3 to 2.2 nm, we find that hpDNA can translocate by three modes: unzipping of the double helix and--in two distinct orientations--stretching/distortion of the double helix. Furthermore, each of these modes can be selected by an appropriate choice of the pore size and voltage applied transverse to the membrane. We demonstrate that the presence of hpDNA can dramatically alter the distribution of ions within the pore, substantially affecting the ionic current through it. In experiments and simulations, the ionic current relative to that in the absence of DNA can drop below 10\% and rise beyond 200\%. Simulations associate the former with the double helix occupying the constriction and the latter with accumulation of DNA that has passed through the constriction.

}, keywords = {Cell Membrane Permeability, Computer Simulation, DNA, Ion Transport, Membrane Potentials, Membranes, Artificial, Microelectrodes, Microscopy, Electron, Transmission, Models, Molecular, Monte Carlo Method, Nanostructures, Nucleic Acid Conformation}, issn = {1542-0086}, doi = {10.1016/j.bpj.2008.09.023}, author = {Jeffrey Comer and Valentin Dimitrov and Zhao, Qian and Gregory Timp and Aleksei Aksimentiev} } @article {60, title = {Stretching and unzipping nucleic acid hairpins using a synthetic nanopore}, journal = {Nucleic Acids Res}, volume = {36}, year = {2008}, month = {2008 Mar}, pages = {1532-41}, abstract = {

We have explored the electromechanical properties of DNA by using an electric field to force single hairpin molecules to translocate through a synthetic pore in a silicon nitride membrane. We observe a threshold voltage for translocation of the hairpin through the pore that depends sensitively on the diameter and the secondary structure of the DNA. The threshold for a diameter 1.5 < d < 2.3 nm is V > 1.5 V, which corresponds to the force required to stretch the stem of the hairpin, according to molecular dynamics simulations. On the other hand, for 1.0 < d < 1.5 nm, the threshold voltage collapses to V < 0.5 V because the stem unzips with a lower force than required for stretching. The data indicate that a synthetic nanopore can be used like a molecular gate to discriminate between the secondary structures in DNA.

}, keywords = {Biological Transport, DNA, Electric Conductivity, Membranes, Artificial, Models, Molecular, Nanostructures, Nucleic Acid Conformation, Silicon Compounds}, issn = {1362-4962}, doi = {10.1093/nar/gkm1017}, author = {Zhao, Q and Jeffrey Comer and Valentin Dimitrov and Yemenicioglu, S and Aleksei Aksimentiev and Gregory Timp} } @article {61, title = {In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin}, journal = {Proteins}, volume = {71}, year = {2008}, month = {2008 Apr}, pages = {24-34}, abstract = {

OpcA is an integral outer membrane adhesin protein from Neisseria meningitidis, the causative agent of meningococcal meningitis and septicemia. It binds to sialic acid (SA)-containing polysaccharides on the surface of epithelial cells. The crystal structure of OpcA showed that the protein adopts a 10-stranded beta-barrel structure, with five extensive loop regions on the extracellular side of the membrane. These form a crevice structure, lined with basic residues, which was hypothesized to act as the binding site for polysaccharide ligands. In the current study, a distinctly different OpcA structure has been obtained using crystals grown from a lipidic mesophase. Comparison of the two structures shows that the largest loop (L2), which closes over the end of the beta-barrel in the original crystal form, adopts a much more extended structure by reaching outward and away from the protein. The difference in conformation may be attributable to the absence of zinc ions from the crystallization conditions for the in meso crystal form: in the original structure, two zinc ions were bound to the external loops. Molecular dynamics (MD) simulations performed on the two OpcA models in a lipid bilayer environment demonstrated pronounced loop mobility. These observations support the view that the loop regions of OpcA are capable of a high degree of conformational flexibility. The original binding site for polysaccharide is not present in the in meso crystal form, and is disrupted during MD simulations. Docking analysis suggests a putative alternative location for the SA ligand in the new crystal form of OpcA.

}, keywords = {Adhesins, Bacterial, Bacterial Outer Membrane Proteins, Binding Sites, Computer Simulation, Crystallography, X-Ray, Models, Molecular, Neisseria meningitidis, Protein Binding, Proteoglycans, Spectrum Analysis}, issn = {1097-0134}, doi = {10.1002/prot.21841}, author = {Cherezov, Vadim and Liu, Wei and Derrick, Jeremy P and Luan, Binquan and Aleksei Aksimentiev and Katritch, Vsevolod and Caffrey, Martin} } @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 {59, title = {Beyond the Gene Chip}, journal = {Bell Labs Tech J}, volume = {10}, year = {2005}, month = {2005}, pages = {5-22}, abstract = {

We describe a prospective strategy for reading the encyclopedic information encoded in the genome: using a nanopore in a membrane formed from an MOS-capacitor to sense the charge in DNA. In principle, as DNA permeates the capacitor-membrane through the pore, the electrostatic charge distribution characteristic of the molecule should polarize the capacitor and induce a voltage on the electrodes that can be measured. Silicon nanofabrication and molecular dynamic simulations with atomic detail are technological linchpins in the development of this detector. The sub-nanometer precision available through silicon nanotechnology facilitates the fabrication of the detector, and molecular dynamics provides us with a means to design it and analyze the experimental outcomes.

}, issn = {1089-7089}, doi = {10.1002/bltj.20102}, author = {Jiunn B Heng and Aleksei Aksimentiev and Ho, C and Valentin Dimitrov and Sorsch, T and Miner, J and Mansfield, W and Klaus Schulten and Gregory Timp} }