@article {385, title = {Trapping of protein cargo molecules inside DNA origami nanocages}, journal = {Nanoscale}, volume = {14}, year = {2022}, month = {11/2022}, pages = {18041{\textendash}18050}, abstract = {

The development of the DNA origami technique has directly inspired the idea of using three-dimensional DNA cages for the encapsulation and targeted delivery of drug or cargo molecules. The cages would be filled with molecules that would be released at a site of interest upon cage opening triggered by an external stimulus. Though different cage variants have been developed, efficient loading of DNA cages with freely-diffusing cargo molecules that are not attached to the DNA nanostructure and their efficient retention within the cages has not been presented. Here we address these challenges using DNA origami nanotubes formed by a double-layer of DNA helices that can be sealed with tight DNA lids at their ends. In a first step we attach DNA-conjugated cargo proteins to complementary target strands inside the DNA tubes. After tube sealing, the cargo molecules are released inside the cavity using toehold-mediated strand displacement by externally added invader strands. We show that DNA invaders are rapidly entering the cages through their DNA walls. Retention of \~{}70 kDa protein cargo molecules inside the cages was, however, poor. Guided by coarse-grained simulations of the DNA cage dynamics, a tighter sealing of the DNA tubes was developed which greatly reduced the undesired escape of cargo proteins. These improved DNA nanocages allow for efficient encapsulation of medium-sized cargo molecules while remaining accessible to small molecules that can be used to trigger reactions, including a controlled release of the cargo via nanocage opening.

}, doi = {10.1039/d2nr05356j}, author = {Merle Scherf and Florian Scheffler and Christopher Maffeo and Ulrich Kemper and Jingjing Ye and Aleksei Aksimentiev and Ralf Seidel and Uta Reibetanz} } @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 {331, title = {Tailoring interleaflet lipid transfer with a DNA-based synthetic enzyme}, journal = {Nano Letters}, volume = {20}, year = {2020}, month = {05/2020}, pages = {4306-4311}, chapter = {4306}, abstract = {

Lipid membranes, enveloping all living systems, are of crucial importance, and control over their structure and composition is a highly desirable functionality of artificial structures. However, the rational design of protein-inspired systems is still challenging. Here we have developed a highly functional nucleic acid construct that self-assembles and inserts into membranes, enabling lipid transfer between inner and outer leaflets. By designing the structure to account for interactions between the DNA, its hydrophobic modifications, and the lipids, we successfully exerted control over the rate of interleaflet lipid transfer induced by our DNA-based enzyme. Furthermore, we can regulate the level of lipid transfer by altering the concentration of divalent ions, similar to stimuli-responsive lipid-flipping proteins.

}, keywords = {DNA Nanotechnology, dodecane, lipid flipping, lipid membranes, Molecular dynamics, synthetic ion channel}, doi = {10.1021/acs.nanolett.0c00990}, author = {Sobota, Diana and Joshi, Himanshu and Ohmann, Alexander and Aleksei Aksimentiev and Keyser, Ulrich F} } @article {119, title = {Two Structural Scenarios for Protein Stabilization by PEG.}, journal = {J Phys Chem B}, volume = {118}, year = {2014}, month = {05/2014}, pages = {8388{\textendash}8395}, abstract = {

PEGylation, or addition of poly(ethylene glycol) chains to proteins, is widely used to improve delivery in pharmaceutical applications. Recent studies suggest that stabilization of a protein by PEG, and hence its proteolytic degradability, are sequence-dependent and require only short PEG chains. Here we connect stabilization by short PEG chains directly to the structural dynamics of the protein and PEG chain. We measured the stability of human Pin1 WW domain with PEG-4 at asparagine 19 for a full mutant cycle at two positions thought to influence PEG-protein interaction: Ser16Ala and Tyr23Phe. We then performed explicit solvent molecular dynamics simulations on all PEGylated and PEG-free mutants. The mutant cycle yields a non-additive stabilization effect where the pseudo wild type and double mutant are more stabilized relative to unPEGylated proteins than are the two single mutants. The simulation reveals why: the double mutant suffers loss of beta sheet structure, which PEGylation restores even though the PEG extends as a coil into the solvent. In contrast, in one of the single mutants PEG preferentially interacts with the protein surface while disrupting the interactions of its asparagine host with a nearby methionine side chain. Thus PEG attachment can stabilize a protein differentially depending on the local sequence, and either by interacting with the surface, or by extending into the solvent. A simulation with PEG-45 attached to asparagine 19 shows that PEG even can do both in the same context.

}, issn = {1520-5207}, doi = {10.1021/jp502234s}, author = {Shu-Han Chao and Matthews, Sam S and Paxman, Ryan and Aleksei Aksimentiev and Martin Gruebele and Price, Joshua L} } @article {24, title = {Toward detection of DNA-bound proteins using solid-state nanopores: insights from computer simulations}, journal = {Electrophoresis}, volume = {33}, year = {2012}, month = {2012 Dec}, pages = {3466-79}, abstract = {

Through all-atom molecular dynamics simulations, we explore the use of nanopores in thin synthetic membranes for detection and identification of DNA binding proteins. Reproducing the setup of a typical experiment, we simulate electric field driven transport of DNA-bound proteins through nanopores smaller in diameter than the proteins. As model systems, we use restriction enzymes EcoRI and BamHI specifically and nonspecifically bound to a fragment of dsDNA, and streptavidin and NeutrAvidin proteins bound to dsDNA and ssDNA via a biotin linker. Our simulations elucidate the molecular mechanics of nanopore-induced rupture of a protein-DNA complex, the effective force applied to the DNA-protein bond by the electrophoretic force in a nanopore, and the role of DNA-surface interactions in the rupture process. We evaluate the ability of the nanopore ionic current and the local electrostatic potential measured by an embedded electrode to report capture of DNA, capture of a DNA-bound protein, and rupture of the DNA-protein bond. We find that changes in the strain on dsDNA can reveal the rupture of a protein-DNA complex by altering both the nanopore ionic current and the potential of the embedded electrode. Based on the results of our simulations, we suggest a new method for detection of DNA binding proteins that utilizes peeling of a nicked double strand under the electrophoretic force in a nanopore.

}, keywords = {Bacterial Proteins, Deoxyribonuclease BamHI, Deoxyribonuclease EcoRI, DNA, DNA-Binding Proteins, Electrochemical Techniques, Models, Chemical, Molecular Dynamics Simulation, Nanopores, Protein Binding, Spectrum Analysis, Static Electricity}, issn = {1522-2683}, doi = {10.1002/elps.201200164}, author = {Jeffrey Comer and Anthony H. Ho and Aleksei Aksimentiev} } @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} } @inbook {189, title = {Toward understanding membrane channels}, booktitle = { Bacterial ion channels and their eukaryotic homologues}, year = {2005}, pages = {153{\textendash}190}, publisher = {ASM Press}, organization = {ASM Press}, address = {Washington, DC}, abstract = {

Membrane channels play key roles in all living cells. Owing to recent advances in protein crystallography, atomic-resolution structures for a representative set of membrane channels have become available. Transport of materials through these channels, however, is a dynamic process and cannot be fully understood from static structural information alone. Molecular dynamics simulations are in a unique position to describe the dynamics of channel transport in the cases in which the structures of channel proteins are known. However, simulation of channel permeability and gating in the native environment of lipid bilayer and water involves large systems with 100,000 - 300,000 atoms.

This review article focuses on four case studies that demonstrate the power of molecular dynamics simulations in unraveling the mechanisms underlying the function of membrane channels. Simulations of AQP water channels present a prime example of the effectiveness and usefulness of molecular dynamics in simulating conduction and explaining selectivity. A detailed energetic analysis of ion permeation through chloride channels proposes a two- ion permeation mechanism that reconciles naturally structural and physiological data. The study of ion and water permeation through hemolysin exemplifies how accurately one can simulate today even very large membrane channel systems. Finally, the study of mechanical gating of MscS shows that molecular dynamics can account even for complex gating motions of channels.

}, author = {Tajkhorshid, Emad and Cohen, Jordi and Aleksei Aksimentiev and Marcos Sotomayor and Klaus Schulten}, editor = {Boris Martinac and Andrzej Kubalski} }