@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 {392, title = {Sulfur-Containing Foldamer-Based Artificial Lithium Channels}, journal = {Angewandte Chemie International Edition}, volume = {62}, year = {2023}, pages = {e202305623}, abstract = {

Abstract Unlike many other biologically relevant ions (Na+, K+, Ca2+, Cl-, etc) and protons, whose cellular concentrations are closely regulated by highly selective channel proteins, Li+ ion is unusual in that its concentration is well tolerated over many orders of magnitude and that no lithium-specific channel proteins have so far been identified. While one naturally evolved primary pathway for Li+ ions to traverse across the cell membrane is through sodium channels by competing with Na+ ions, highly sought-after artificial lithium-transporting channels remain a major challenge to develop. Here we show that sulfur-containing organic nanotubes derived from intramolecularly H-bonded helically folded aromatic foldamers of 3.6\ {\r A}\ in hollow cavity diameter could facilitate highly selective and efficient transmembrane transport of Li+ ions, with high transport selectivity factors of 15.3 and 19.9 over Na+ and K+ ions, respectively.

}, keywords = {Foldamers, H-Bonds, Lithium Channels, Organic Nanotubes, Supramolecular Chemistry}, doi = {https://doi.org/10.1002/anie.202305623}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.202305623}, author = {Shen, Jie and R, Deepa and Li, Zhongyan and Oh, Hyeonji and Behera, Harekrushna and Joshi, Himanshu and Kumar, Manish and Aksimentiev, Aleksei and Zeng, Huaqiang} } @article {370, title = {Fluorofoldamer-Based Salt- and Proton-Rejecting Artificial Water Channels for Ultrafast Water Transport.}, journal = {Nano Lett}, volume = {22}, year = {2022}, month = {2022 06 22}, pages = {4831-4838}, abstract = {

Here, we report on a novel class of fluorofoldamer-based artificial water channels (AWCs) that combines excellent water transport rate and selectivity with structural simplicity and robustness. Produced by a facile one-pot copolymerization reaction under mild conditions, the best-performing channel (AWC ) is an n-CH-decorated foldamer nanotube with an average channel length of 2.8 nm and a pore diameter of 5.2 {\r A}. AWC demonstrates an ultrafast water conduction rate of 1.4 {\texttimes} 10 HO/s per channel, outperforming the archetypal biological water channel, aquaporin 1, while excluding salts (i.e., NaCl and KCl) and protons. Unique to this class of channels, the inwardly facing C(sp2)-F atoms being the most electronegative in the periodic table are proposed as being critical to enabling the ultrafast and superselective water transport properties by decreasing the channel{\textquoteright}s cavity and enhancing the channel wall smoothness via reducing intermolecular forces with water molecules or hydrated ions.

}, keywords = {Aquaporins, Biological Transport, Protons, Sodium Chloride, Water}, issn = {1530-6992}, doi = {10.1021/acs.nanolett.2c01137}, author = {Shen, Jie and Roy, Arundhati and Joshi, Himanshu and Samineni, Laxmicharan and Ye, Ruijuan and Tu, Yu-Ming and Song, Woochul and Skiles, Matthew and Kumar, Manish and Aleksei Aksimentiev and Zeng, Huaqiang} } @article {351, title = {Foldamer-Based Ultrapermeable and Highly Selective Artificial Water Channels that Exclude Protons}, journal = {Nature Nanotechnology}, volume = {16}, year = {2021}, month = {08/2021}, pages = {911-917}, chapter = {911}, abstract = {

The outstanding capacity of aquaporins (AQPs) for mediating highly selective superfast water transport has inspired the recent development of supramolecular monovalent ion-excluding artificial water channels (AWCs). AWC-based bioinspired membranes are proposed for desalination, water purification, and other separation applications. While some recent progress has been made in synthesizing AWCs that approach the water permeability and ion selectivity of AQPs, a hallmark feature of AQPs{\textemdash}high water transport while excluding protons-has not been reproduced. We report a class of biomimetic, helically folded pore-forming polymeric foldamers that can serve as long-sought-after highly selective ultrafast water-conducting channels with performance exceeding those of AQPs (1.1 {\texttimes} 1010 water molecules per second for AQP1, with high water-over- monovalent-ion transport selectivity (~108 water molecules over Cl-\ ion) conferred by the modularly tunable hydrophobicity of the interior pore surface. The best-performing AWC reported here delivers water transport at an exceptionally high rate, namely, 2.5 times that of AQP1, while concurrently rejecting salts (NaCl and KCl) and even protons.

}, doi = {10.1038/s41565-021-00915-2}, author = {Roy, Arundhati and Shen, Jie and Joshi, Himanshu and Song, Woochul and Tu, Yu-Ming and Chowdhury, Ratul and Ruijuan, Ye and Li, Ning and Ren, Changliang and Kumar, Manish and Aleksei Aksimentiev and Zeng, Huaqiang} } @article {360, title = {Synthetic Macrocycle Nanopore for Potassium-Selective Transmembrane Transport}, journal = {Journal of the American Chemical Society}, volume = {143}, year = {2021}, month = {08/2021}, pages = {15975-15983}, chapter = {15975}, abstract = {

Reproducing the structure and function of biological membrane channels, synthetic nanopores have been developed for applications in membrane filtration technologies and biomolecular sensing. Stable stand-alone synthetic nanopores have been created from a variety of materials, including peptides, nucleic acids, synthetic polymers, and solid-state membranes. In contrast to biological nanopores, however, furnishing such synthetic nanopores with an atomically defined shape, including deliberate placement of each and every chemical group, remains a major challenge. Here, we introduce a chemosynthetic macromolecule,\ extended pillararene macrocycle (EPM) as a chemically defined transmembrane nanopore that exhibits selective transmembrane transport. Our ionic current measurements reveal stable insertion of individual EPM nanopores into a lipid bilayer membrane and remarkable cation type-selective transport, with up to a 21-fold selectivity for potassium over sodium ions. Taken together, direct chemical synthesis offers a path to de novo design of a new class of synthetic nanopores with custom transport functionality imprinted in their atomically defined chemical structure.\ 

}, keywords = {Electrical conductivity, MD Simulations, Nanopores, Potassium Ions Selectivity}, doi = {10.1021/jacs.1c04910}, author = {Qiao, Dan and Joshi, Himanshu and Zhu, Huangtianzhi and Wang, Fushi and Xu, Yang and Gao, Jia and Huang, Feihe and Aleksei Aksimentiev and Feng, Jiandong} } @article {320, title = {Polyhydrazide-based organic nanotubes as extremely efficient and highly selective artificial iodide channels}, journal = {Angewandte Chemie International Edition}, volume = {12}, year = {2020}, month = {02/2020}, pages = {4806-4813}, chapter = {4806}, abstract = {

We report herein a series of pore-containing polymeric nanotubes based on an H-bonded hydrazide backbone. Nanotubes of suitable lengths, possessing a hollow cavity of ~ 6.5 {\r A} in diameter, are found to mediate highly efficient transport of diverse types of anions, rather than cations, across the lipid membrane. Polymer channel 1a, having an averaged molecular weight of 18.2 KDa and 3.6 nm in helical height, exhibits the highest anion transport activities with iodide (EC50 = 0.042 micromolar\ or 0.028 mol \% relative to lipid) being transported 10 times more efficiently than chlorides (EC50 = 0.47 micromolar). Notably, even in the cholesterol-rich environment, iodide transport activity still remains high with EC50\ \ of 0.37 micromolar. Molecular dynamics simulation studies confirm that the channel is highly selective for anions and that such anion selectivity arises from a positive electrostatic potential of the central lumen rendered by the interior-pointing methyl groups.

}, doi = { https://doi.org/10.1002/anie.201916287}, author = {Roy, Arundhati and Joshi, Himanshu and Ye, Ruijuan and Shen, Jie and Chen, Feng and Aleksei Aksimentiev and Zeng, Huaqiang} } @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 {297, title = {Effect of temperature and hydrophilic ratio on the structure of poly(N-vinylcaprolactam)-block-poly(dimethylsiloxane)-block-poly(N-vinylcaprolactam) polymersomes}, journal = {ACS Applied Polymer Materials}, volume = {1}, year = {2019}, month = {04/2019}, pages = {722--736}, chapter = {722}, abstract = {

Nanosized polymeric vesicles (polymersomes) assembled from ABA triblock copolymers of poly(N-vinylcaprolactam)-poly(dimethylsiloxane)-poly(N-vinylcaprolactam) (PVCL-PDMS-PVCL) are a promising platform for biomedical applications, as the temperature-responsiveness of the PVCL blocks enables reversible vesicle shrinkage and permeability of the polymersome shell at elevated temperatures. Herein, we explore the effects of molecular weight, polymer block weight ratios, and temperature on the structure of these polymersomes via electron microscopy, dynamic light scattering, small angle neutron scattering (SANS), and all-atom molecular dynamic methods. We show that the shell structure and overall size of the polymersome can be tuned by varying the hydrophilic (PVCL) weight fraction of the polymer: at room temperature, polymers of smaller hydrophilic ratios form larger vesicles that have thinner shells, whereas polymers with higher PVCL content exhibit interchain aggregation of PVCL blocks within the polymersome shell above 50 {\textdegree}C. Model fitting and model-free analysis of the SANS data reveals that increasing the mass ratio of PVCL to the total copolymer weight from 0.3 to 0.56 reduces the temperature-induced change in vesicle diameter by a factor of 3 while simultaneously increasing the change in shell thickness by a factor of 1.5. Finally, by analysis of the shell structures and overall size of polymersomes with various PVCL weight ratios and those without temperature-dependent polymer components, we bring into focus the mechanism of temperature-triggered drug release reported in a previous study. This work provides new fundamental perspectives on temperature-responsive polymersomes and elucidates important structure-property relationships of their constituent polymers.

}, doi = {10.1021/acsapm.8b00259}, url = {https://pubs.acs.org/doi/pdf/10.1021/acsapm.8b00259}, author = {Yiming Yang and Aaron Alford and Kozlovskaya, Veronika and Zhao, Shidi and Joshi, Himanshu and Kim, Eunjung and Qian, Shuo and Urban, Volker and Cropek, Donald and Aleksei Aksimentiev and Kharlampieva, Eugenia} } @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} } @inbook {277, title = {A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems}, booktitle = {DNA Nanotechology: Methods and Protocols}, series = {Methods in Molecular Biology}, volume = {1811}, year = {2018}, pages = {209-229}, publisher = {Humana Press}, organization = {Humana Press}, edition = {2}, chapter = {A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems}, address = {New York}, abstract = {

The DNA origami method exploits the self-assembly property of nucleic acids to build diverse nanoscale systems. The all-atom molecular dynamics (MD) method has emerged as a powerful computational tool for atomic-resolution characterization of the in situ structure and physical properties of DNA origami objects. This chapter provides step-by-step instructions for building atomic-scale models of DNA origami systems, using the MD method to simulate the models, and performing basic analyses of the resulting MD trajectories.\ 

}, issn = {978-1-4939-8581-4}, doi = {10.1007/978-1-4939-8582-1_15}, url = {https://link.springer.com/protocol/10.1007/978-1-4939-8582-1_15}, author = {Jejoong Yoo and Chen-Yu Li and Scott Michael Slone and Christopher Maffeo and Aleksei Aksimentiev}, editor = {Giampaolo Zuccheri} } @article {279, title = {Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization}, journal = {ACS Nano}, volume = {11}, year = {2017}, month = {12/2017}, pages = {11931-11945}, abstract = {

Nanopore-based sensors for nucleic acid sequencing and single-molecule detection typically employ pore-forming membrane proteins with hydrophobic external surfaces, suitable for insertion into a lipid bilayer. In contrast, hydrophilic pore-containing molecules such as DNA origami, have been shown to require chemical modification to favor insertion into a lipid environment. In this work, we describe a strategy for inserting polar proteins with an inner pore into lipid membranes, focusing here on a circular 12-subunit assembly of the thermophage G20c portal protein. X-ray crystallography, electron microscopy, molecular dynamics and thermal/chaotrope denaturation experiments all find the G20c portal protein to have a highly stable structure, favorable for nanopore sensing applications. Porphyrin conjugation to a cysteine mutant in the protein facilitates the protein{\textquoteright}s insertion into lipid bilayers, allowing us to probe ion transport through the pore. Finally, we probed the portal interior size and shape using a series of cyclodextrins of varying sizes, revealing asymmetric transport that possibly originates from the portal{\textquoteright}s DNA-ratchet function.

}, doi = {10.1021/acsnano.7b06980}, url = {http://pubs.acs.org/doi/abs/10.1021/acsnano.7b06980}, author = {Cressiot*, Benjamin and Greive*, Sandra J. and Si*, Wei and Pascoa, Tomas and Mojtabavi, Mehrnaz and Chechik, Maria and Jenkins, Huw Thomas and Lu, Xueguang and Zhang, Ke and Aleksei Aksimentiev and Antson, Alfred A. and Wanunu, Meni} } @article {274, title = {Quantification of Membrane Protein-Detergent Complex Interactions}, journal = {The Journal of Physical Chemistry B}, volume = {121}, year = {2017}, month = {11/2017}, pages = {10228-10241}, chapter = {10228}, abstract = {

Although fundamentally significant in structural, chemical, and membrane biology, the interfacial protein-detergent complex (PDC) interactions have been modestly examined because of the complicated behavior of both detergents and membrane proteins in aqueous phase. Membrane proteins are prone to unproductive aggregation resulting from poor detergent solvation, but the participating forces in this phenomenon remain ambiguous. Here, we show that using rational membrane protein design, targeted chemical modification, and steady-state fluorescence polarization spectroscopy, the detergent desolvation of membrane proteins can be quantitatively evaluated. We demonstrate that depleting the detergent in the sample well produced a two-state transition of membrane proteins between a fully detergent-solvated state and a detergent-desolvated state, the nature of which depended on the interfacial PDC interactions. Using a panel of six membrane proteins of varying hydrophobic topography, structural fingerprint, and charge distribution on the solvent-accessible surface, we provide direct experimental evidence for the contributions of the electrostatic and hydrophobic interactions to the protein solvation properties. Moreover, all-atom molecular dynamics simulations report the major contribution of the hydrophobic forces exerted at the PDC interface. This semi-quantitative approach might be extended in the future to include studies of the interfacial PDC interactions of other challenging membrane protein systems of unknown structure. This would have practical importance in protein extraction, solubilization, stabilization, and crystallization.

}, doi = {10.1021/acs.jpcb.7b08045}, url = {http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b08045}, author = {Wolfe, Aaron John and Si, Wei and Zhang, Zhengqi and Blanden, Adam R and Hsueh, Yi-Ching and Gugel, Jack Fredrick and Pham, Bach and Chen, Min and Loh, Stewart N and Rozovsky, Sharon and Aleksei Aksimentiev and Movileanu, Liviu} } @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 {216, title = {The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study}, journal = {PLoS ONE}, volume = {11}, year = {2016}, month = {02/2016}, pages = {e0152002}, abstract = {

LacI is commonly used as a model to study the protein-DNA interaction and gene regulation. The headpiece of the lac-repressor (LacI) protein is an ideal system for investigation of nonspecific binding of the whole LacI protein to DNA. The hinge region of the headpiece has been known to play a key role in the specific binding of LacI to DNA, whereas its role in nonspecific binding process has not been elucidated. Here, we report the results of explicit solvent molecular dynamics simulation and continuum electrostatic calculations suggesting that the hinge region strengthens the nonspecific interaction, accounting for up to 50\% of the micro-dissociation free energy of LacI from DNA. Consequently, the rate of microscopic dissociation of LacI from DNA is reduced by 2~3 orders of magnitude in the absence of the hinge region. We find the hinge region makes an important contribution to the electrostatic energy, the salt dependence of electrostatic energy, and the number of salt ions excluded from binding of the LacI-DNA complex.

}, doi = {10.1371/journal.pone.0152002}, url = {http://journals.plos.org/plosone/article?id=10.1371\%2Fjournal.pone.0152002}, author = {Lili Sun and Marcin Tabaka and Sen Hou and Lin Li and Krzysztof Burdzy and Aleksei Aksimentiev and Christopher Maffeo and Xuzhu Zhang and Robert Holyst} } @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 {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 {34, title = {Control of Nanoscale Environment to Improve Stability of Immobilized Proteins on Diamond Surfaces}, journal = {Adv Funct Mater}, volume = {21}, year = {2011}, month = {2011 Mar 21}, pages = {1040-1050}, abstract = {

Immunoassays for detection of bacterial pathogens rely on the selectivity and stability of bio-recognition elements such as antibodies tethered to sensor surfaces. The search for novel surfaces that improve the stability of biomolecules and assay performance has been pursued for a long time. However, the anticipated improvements in stability have not been realized in practice under physiological conditions because the surface functionalization layers on commonly used substrates, silica and gold, are themselves unstable on time scales of days. In this paper, we show that covalent linking of antibodies to diamond surfaces leads to substantial improvements in biological activity of proteins as measured by the ability to selectively capture cells of the pathogenic bacterium Escherichia coli O157:H7 even after exposure to buffer solutions at 37 {\textdegree}C for extended periods of time, approaching 2 weeks. Our results from ELISA, XPS, fluorescence microscopy, and MD simulations suggest that by using highly stable surface chemistry and controlling the nanoscale organization of the antibodies on the surface, it is possible to achieve significant improvements in biological activity and stability. Our findings can be easily extended to functionalization of micro and nanodimensional sensors and structures of biomedical diagnostic and therapeutic interest.

}, issn = {1616-301X}, doi = {10.1002/adfm.201002251}, author = {Radadia, Adarsh D and Courtney J Stavis and Carr, Rogan and Zeng, Hongjun and King, William P and Carlisle, John A and Aleksei Aksimentiev and Hamers, Robert J and Rashid Bashir} } @article {40, title = {Surface functionalization of thin-film diamond for highly stable and selective biological interfaces}, journal = {Proc Natl Acad Sci U S A}, volume = {108}, year = {2011}, month = {2011 Jan 18}, pages = {983-8}, abstract = {

Carbon is an extremely versatile family of materials with a wide range of mechanical, optical, and mechanical properties, but many similarities in surface chemistry. As one of the most chemically stable materials known, carbon provides an outstanding platform for the development of highly tunable molecular and biomolecular interfaces. Photochemical grafting of alkenes has emerged as an attractive method for functionalizing surfaces of diamond, but many aspects of the surface chemistry and impact on biological recognition processes remain unexplored. Here we report investigations of the interaction of functionalized diamond surfaces with proteins and biological cells using X-ray photoelectron spectroscopy (XPS), atomic force microscopy, and fluorescence methods. XPS data show that functionalization of diamond with short ethylene glycol oligomers reduces the nonspecific binding of fibrinogen below the detection limit of XPS, estimated as > 97\% reduction over H-terminated diamond. Measurements of different forms of diamond with different roughness are used to explore the influence of roughness on nonspecific binding onto H-terminated and ethylene glycol (EG)-terminated surfaces. Finally, we use XPS to characterize the chemical stability of Escherichia coli K12 antibodies on the surfaces of diamond and amine-functionalized glass. Our results show that antibody-modified diamond surfaces exhibit increased stability in XPS and that this is accompanied by retention of biological activity in cell-capture measurements. Our results demonstrate that surface chemistry on diamond and other carbon-based materials provides an excellent platform for biomolecular interfaces with high stability and high selectivity.

}, keywords = {Antibodies, Bacterial, Avidin, Chemistry, Physical, Diamond, Escherichia coli K12, Ethylene Glycol, Fibrinogen, Fluorescence, Microscopy, Atomic Force, Photoelectron Spectroscopy, Protein Binding, Surface Properties}, issn = {1091-6490}, doi = {10.1073/pnas.1006660107}, author = {Courtney J Stavis and Clare, Tami Lasseter and Butler, James E and Radadia, Adarsh D and Carr, Rogan and Zeng, Hongjun and King, William P and Carlisle, John A and Aleksei Aksimentiev and Rashid Bashir and Hamers, Robert J} } @inbook {35, title = {Modeling nanopores for sequencing DNA}, booktitle = {DNA Nanotechnology: Methods and Protocols}, volume = {749}, year = {2011}, month = {2011}, pages = {317-358}, abstract = {

Using nanopores to sequence DNA rapidly and at a low cost has the potential to radically transform the field of genomic research. However, despite all the exciting developments in the field, sequencing DNA using a nanopore has yet to be demonstrated. Among the many problems that hinder development of the nanopore sequencing methods is the inability of current experimental techniques to visualize DNA conformations in a nanopore and directly relate the microscopic state of the system to the measured signal. We have recently shown that such tasks could be accomplished through computation. This chapter provides step-by-step instructions of how to build atomic scale models of biological and solid-state nanopore systems, use the molecular dynamics method to simulate the electric field-driven transport of ions and DNA through the nanopores, and analyze the results of such computational experiments.

}, keywords = {Base Sequence, Computer Simulation, DNA, Hemolysin Proteins, Models, Molecular, Molecular Conformation, Molecular Dynamics Simulation, Nanopores, Nanotechnology, Sequence Analysis, DNA}, issn = {1940-6029}, doi = {10.1007/978-1-61779-142-0_22}, author = {Jeffrey Comer and David B Wells and Aleksei Aksimentiev}, editor = {Giampaolo Zuccheri and Bruno Samori} } @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 {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 {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 {77, title = {Large scale simulation of protein mechanics and function}, journal = {Adv Protein Chem}, volume = {66}, year = {2003}, month = {2003}, pages = {195-247}, keywords = {Amino Acid Motifs, Aquaporins, Catalysis, Cell Membrane, Computer Simulation, Fibronectins, Hydrogen Bonding, Models, Molecular, Protein Conformation, Protein Denaturation, Protein Folding, Protein Structure, Secondary, Proteins, Proton-Translocating ATPases, Substrate Specificity, Time Factors, Water}, issn = {0065-3233}, author = {Tajkhorshid, Emad and Aleksei Aksimentiev and Ilya A Balabin and Gao, Mu and Isralewitz, Barry and Phillips, James C and Zhu, Fangqiang and Klaus Schulten} }