@article {354, title = {Hydrophobic Interactions between DNA Duplexes and Synthetic and Biological Membranes.}, journal = {Journal of the American Chemical Society}, volume = {143}, year = {2021}, month = {05/2021}, pages = {8305-8313}, chapter = {8305}, abstract = {

Equipping DNA with hydrophobic anchors enables targeted interaction with lipid bilayers for applications in biophysics, cell biology, and synthetic biology. Understanding DNA-membrane interactions is crucial for rationally designing functional DNA. Here we study the interactions of hydrophobically tagged DNA with synthetic and cell membranes using a combination of experiments and atomistic molecular dynamics (MD) simulations. The DNA duplexes are rendered hydrophobic by conjugation to a terminal cholesterol anchor or by chemical synthesis of a charge-neutralized alkyl-phosphorothioate (PPT) belt. Cholesterol-DNA tethers to lipid vesicles of different lipid compositions and charges, while PPT DNA binding strongly depends on alkyl length, belt position, and headgroup charge. Divalent cations in the buffer can also influence binding. Our MD simulations directly reveal the complex structure and energetics of PPT DNA within a lipid membrane, demonstrating that longer alkyl-PPT chains provide the most stable membrane anchoring but may disrupt DNA base paring in solution. When tested on cells, cholesterol-DNA is homogeneously distributed on the cell surface, while alkyl-PPT DNA accumulates in clustered structures on the plasma membrane. DNA tethered to the outside of the cell membrane is distinguished from DNA spanning the membrane by nuclease and sphingomyelinase digestion assays. The gained fundamental insight on DNA-bilayer interactions will guide the rational design of membrane-targeting nanostructures.

}, issn = {1520-5126}, doi = {10.1021/jacs.0c13235}, author = {Jones, Sioned F and Joshi, Himanshu and Terry, Stephen J and Burns, Jonathan R and Aleksei Aksimentiev and Eggert, Ulrike S and Howorka, Stefan} } @article {338, title = {High-Fidelity Capture, Threading, and Infinite-Depth Sequencing of Single DNA Molecules with a Double-Nanopore System}, journal = {ACS Nano}, volume = {14}, year = {2020}, month = {11/2020}, pages = {15566-15576}, chapter = {15566}, abstract = {

Nanopore sequencing of nucleic acids has an illustrious history of innovations that eventually made commercial nanopore sequencing possible. Nevertheless, the present nanopore sequencing technology leaves much room for improvement, especially with respect to accuracy of raw reads and detection of nucleotide modifications. Double-nanopore sequencing{\textemdash}an approach where a DNA molecule is pulled back and forth by a tug-of-war of two nanopores{\textemdash}could potentially improve single-molecule read accuracy and modification detection by offering multiple reads of the same DNA fragment. One principle difficulty in realizing such a technology is threading single-stranded DNA through both nanopores. Here, we describe and demonstrate through simulations a nanofluidic system for loading and threading DNA strands through a double-nanopore setup with nearly 100\% fidelity. The high-efficiency loading is realized by using hourglass-shaped side channels that not only deliver the molecules to the nanopore but also retain molecules that missed the nanopore at the first passage to attempt the nanopore capture again. The second nanopore capture is facilitated by an orthogonal microfluidic flow that unravels the molecule captured by the first nanopore and delivers it to the capture volume of the second nanopore. We demonstrate the potential utility of our double-nanopore system for DNA sequencing by simulating repeat back-and-forth motion{\textemdash}flossing{\textemdash}of a DNA strand through the double-nanopore system. We show that repeat exposure of the same DNA fragments to the nanopore sensing volume considerably increases accuracy of the nucleotide sequence determination and that correlated displacement of ssDNA through the two nanopores may facilitate recognition of homopolymer fragments.

}, keywords = {Gene delivery, Genetics, Molecules, Monomers, Nanopores}, doi = {10.1021/acsnano.0c06191}, url = {https://doi.org/10.1021/acsnano.0c06191}, author = {Choudhary, Adnan and Joshi, Himanshu and Chou, Han-Yi and Sarthak, Kumar and Wilson, James and Maffeo, Christopher and Aleksei Aksimentiev} } @article {207, title = {Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA}, journal = {Nucleic Acids Research}, volume = {44}, year = {2016}, month = {03/2016}, pages = {2085--2092}, chapter = {2085}, abstract = {

Oxidation of a DNA thymine to 5-hydroxymethyluracil is one of several recently discovered epigenetic modifications. Here, we report the results of nanopore translocation experiments and molecular dynamics simulations that provide insight into the impact of this modification on the structure and dynamics of DNA. When transported through ultrathin solid-state nanopores, short DNA fragments containing thymine modifications were found to exhibit distinct, reproducible features in their transport characteristics that differentiate them from unmodified molecules. Molecular dynamics simulations suggest that 5-hydroxymethyluracil alters the flexibility and hydrophilicity of the DNA molecules, which may account for the differences observed in our nanopore translocation experiments. The altered physico-chemical properties of DNA produced by the thymine modifications may have implications for recognition and processing of such modifications by regulatory DNA-binding proteins.

}, doi = {10.1093/nar/gkv1199}, url = {http://nar.oxfordjournals.org/content/early/2015/11/16/nar.gkv1199.abstract}, author = {Carson, Spencer and Wilson, James and Aleksei Aksimentiev and Weigele, Peter R. and Wanunu, Meni} } @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 {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} }