Single-molecule mechanical identification and sequencing

Fangyuan Ding, Maria Manosas, Michelle M Spiering, Stephen J Benkovic, David Bensimon, Jean-François Allemand, and Vincent Croquette



High-throughput, low-cost DNA sequencing has emerged as one of the challenges of the postgenomic era. Here we present the proof of concept for a single-molecule platform that allows DNA identification and sequencing. In contrast to most present methods, our scheme is not based on the detection of the fluorescent nucleotides but on DNA hairpin length. By pulling on magnetic beads tethered by a DNA hairpin to the surface, the molecule can be unzipped. In this open state it can hybridize with complementary oligonucleotides, which transiently block the hairpin rezipping when the pulling force is reduced. By measuring from the surface to the bead of a blocked hairpin, one can determine the position of the hybrid along the molecule with nearly single-base precision. Our approach can be used to identify a DNA fragment of known sequence in a mix of various fragments and to sequence an unknown DNA fragment by hybridization or ligation.

DOI

Journal: Nature Methods

Imaging the charge distribution within a single molecule

Fabian Mohn, Leo Gross, Nikolaj Moll, and Gerhard Meyer


Scanning tunnelling microscopy and atomic force microscopy can be used to study the electronic and structural properties of surfaces, as well as molecules and nanostructures adsorbed on surfaces, with atomic precision, but they cannot directly probe the distribution of charge in these systems. However, another form of scanning probe microscopy, Kelvin probe force microscopy, can be used to measure the local contact potential difference between the scanning probe tip and the surface, a quantity that is closely related to the charge distribution on the surface. Here, we use a combination of scanning tunnelling microscopy, atomic force microscopy and Kelvin probe force microscopy to examine naphthalocyanine molecules (which have been used as molecular switches) on a thin insulating layer of NaCl on Cu(111). We show that Kelvin probe force microscopy can map the local contact potential difference of this system with submolecular resolution, and we use density functional theory calculations to verify that these maps reflect the intramolecular distribution of charge. This approach could help to provide fundamental insights into single-molecule switching and bond formation, processes that are usually accompanied by the redistribution of charge within or between molecules 


DOI


Journal: Nature Nanotechnology

Piezo proteins are pore-forming subunits of mechanically activated channels

Bertrand Coste, Bailong Xiao, Jose S. Santos, Ruhma Syeda, Jörg Grandl, Kathryn S. Spencer, Sung Eun Kim, Manuela Schmidt, Jayanti Mathur, Adrienne E. Dubin, Mauricio Montal, and Ardem Patapoutian


Mechanotransduction has an important role in physiology. Biological processes including sensing touch and sound waves require as-yet-unidentified cation channels that detect pressure. Mouse Piezo1 (MmPiezo1) and MmPiezo2 (also called Fam38a and Fam38b, respectively) induce mechanically activated cationic currents in cells; however, it is unknown whether Piezo proteins are pore-forming ion channels or modulate ion channels. Here we show that Drosophila melanogaster Piezo (DmPiezo, also called CG8486) also induces mechanically activated currents in cells, but through channels with remarkably distinct pore properties including sensitivity to the pore blocker ruthenium red and single channel conductances. MmPiezo1 assembles as a ~1.2-million-dalton homo-oligomer, with no evidence of other proteins in this complex. Purified MmPiezo1 reconstituted into asymmetric lipid bilayers and liposomes forms ruthenium-red-sensitive ion channels. These data demonstrate that Piezo proteins are an evolutionarily conserved ion channel family involved in mechanotransduction.


DOI


Journal: Nature

Proton Grease: An Acid Accelerated Molecular Rotor

Brent E. Dial, Perry J. Pellechia, Mark D. Smith, and Ken D. Shimizu

A molecular rotor was designed that rotates 7 orders of magnitude faster upon protonation. The quinoline rotor is based on a rigid N-arylimide framework that displays restricted rotation due to steric interaction between the quinoline nitrogen and imide carbonyls. At rt (23 °C), the rotor rotates slowly (t1/2 = 26 min, ΔG‡ = 22.2 kcal/mol). However, upon addition of 3.5 equiv of acid the rotor rotates rapidly (t1/2 = 2.0 × 10–4 s, ΔG‡ = 12.9 kcal/mol). Mechanistic studies show that this dramatic acid catalyzed change is due to stabilization of the planar transition state by the formation of an intramolecular hydrogen bond between the protonated quinoline nitrogen (N+—H) and an imide carbonyl (O═C). The acid catalyzed acceleration is reversible and can be stopped by addition of base.

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Journal: Journal of the American Chemical Society

Thermodynamic and Kinetic Analysis of an RNA Kissing Interaction and Its Resolution into an Extended Duplex

Nilshad Salim, Rajan Lamichhane, Rui Zhao, Tuhina Banerjee, Jane Philip, David Rueda, and Andrew L. Feig



Kissing hairpin interactions form when the loop residues of two hairpins have Watson-Crick complementarity. In a unimolecular context, kissing interactions are important for tertiary folding and pseudoknot formation, whereas in a bimolecular context, they provide a basis for molecular recognition. In some cases, kissing complexes can be a prelude to strand displacement reactions where the two hairpins resolve to form a stable extended intermolecular duplex. The kinetics and thermodynamics of kissing-complex formation and their subsequent strand-displacement reactions are poorly understood. Here, biophysical techniques including isothermal titration calorimetry, surface plasmon resonance, and single-molecule fluorescence have been employed to probe the factors that govern the stability of kissing complexes and their subsequent structural rearrangements. We show that the general understanding of RNA duplex formation can be extended to kissing complexes but that kissing complexes display an unusual level of stability relative to simple duplexes of the same sequence. These interactions form and break many times at room temperature before becoming committed to a slow, irreversible forward transition to the strand-displaced form. Furthermore, using smFRET we show that the primary difference between stable and labile kissing complexes is based almost completely on their off rates. Both stable and labile complexes form at the same rate within error, but less stable species dissociate rapidly, allowing us to understand how these complexes can help generate specificity along a folding pathway or during a gene regulation event.

DOI

Journal: Biophysical Journal

Mechanical Anisotropy of Ankyrin Repeats

Whasil Lee, Xiancheng Zeng, Kristina Rotolo, Ming Yang, Christopher J. Schofield, Vann Bennett, Weitao Yang, and Piotr E. Marszalek



Red blood cells are frequently deformed and their cytoskeletal proteins such as spectrin and ankyrin-R are repeatedly subjected to mechanical forces. While the mechanics of spectrin was thoroughly investigated in vitro and in vivo, little is known about the mechanical behavior of ankyrin-R. In this study, we combine coarse-grained steered molecular dynamics simulations and atomic force spectroscopy to examine the mechanical response of ankyrin repeats (ARs) in a model synthetic AR protein NI6C, and in the D34 fragment of native ankyrin-R when these proteins are subjected to various stretching geometry conditions. Our steered molecular dynamics results, supported by AFM measurements, reveal an unusual mechanical anisotropy of ARs: their mechanical stability is greater when their unfolding is forced to propagate from the N-terminus toward the C-terminus (repeats unfold at ∼60 pN), as compared to the unfolding in the opposite direction (unfolding force ∼ 30 pN). This anisotropy is also reflected in the complex refolding behavior of ARs. The origin of this unfolding and refolding anisotropy is in the various numbers of native contacts that are broken and formed at the interfaces between neighboring repeats depending on the unfolding/refolding propagation directions. Finally, we discuss how these complex mechanical properties of ARs in D34 may affect its behavior in vivo

DOI

Journal: Biophysical Journal

Peptide tag forming a rapid covalent bond to a protein

Bijan Zakeri, Jacob O. Fierer, Emrah Celik, Emily C. Chittock,Ulrich Schwarz-Linek, Vincent T. Moy, and Mark Howarth

Protein interactions with peptides generally have low thermodynamic and mechanical stability. Streptococcus pyogenes fibronectin-binding protein FbaB contains a domain with a spontaneous isopeptide bond between Lys and Asp. By splitting this domain and rational engineering of the fragments, we obtained a peptide (SpyTag) which formed an amide bond to its protein partner (SpyCatcher) in minutes. Reaction occurred in high yield simply upon mixing and amidst diverse conditions of pH, temperature, and buffer. SpyTag could be fused at either terminus or internally and reacted specifically at the mammalian cell surface. Peptide binding was not reversed by boiling or competing peptide. Single-molecule dynamic force spectroscopy showed that SpyTag did not separate from SpyCatcher until the force exceeded 1 nN, where covalent bonds snap. The robust reaction conditions and irreversible linkage of SpyTag shed light on spontaneous isopeptide bond formation and should provide a targetable lock in cells and a stable module for new protein architectures. 

DOI

Journal: Proceedings of the National Academy of Sciences

Experimental verification of Landauer’s principle linking information and thermodynamics

Antoine Berut, Artak Arakelyan, Artyom Petrosyan, Sergio Ciliberto, Raoul Dillenschneider, and Eric Lutz


In 1961, Rolf Landauer argued that the erasure of information is a dissipative process. A minimal quantity of heat, proportional to the thermal energy and called the Landauer bound, is necessarily produced when a classical bit of information is deleted. A direct consequence of this logically irreversible transformation is that the entropy of the environment increases by a finite amount. Despite its fundamental importance for information theory and computer science, the erasure principle has not been verified experimentally so far, the main obstacle being the difficulty of doing single-particle experiments in the low-dissipation regime. Here we experimentally show the existence of the Landauer bound in a generic model of a one-bit memory. Using a system of a single colloidal particle trapped in a modulated double-well potential, we establish that the mean dissipated heat saturates at the Landauer bound in the limit of long erasure cycles. This result demonstrates the intimate link between information theory and thermodynamics. It further highlights the ultimate physical limit of irreversible computation. 


DOI


Journal: Nature

The molten globule state is unusually deformable under mechanical force

Phillip J. Elms, John D. Chodera, Carlos Bustamante, and Susan Marqusee


Recently, the role of force in cellular processes has become more evident, and now with advances in force spectroscopy, the response of proteins to force can be directly studied. Such studies have found that native proteins are brittle, and thus not very deformable. Here, we examine the mechanical properties of a class of intermediates referred to as the molten globule state. Using optical trap force spectroscopy, we investigated the response to force of the native and molten globule states of apomyoglobin along different pulling axes. Unlike natively folded proteins, the molten globule state of apomyoglobin is compliant (large distance to the transition state); this large compliance means that the molten globule is more deformable and the unfolding rate is more sensitive to force (the application of force or tension will have a more dramatic effect on the unfolding rate). Our studies suggest that these are general properties of molten globules and could have important implications for mechanical processes in the cell.


DOI

Journal: Proceedings of the National Academy of Sciences

Hopping around an entropic barrier created by force

Ronen Berkovich, Sergi Garcia-Manyes, Joseph Klafter, Michael Urbakh, Julio M. Fernández


We use Langevin dynamics to investigate the role played by the recently discovered force-induced entropic energy barrier on the two-state hopping phenomena that has been observed in single RNA, DNA and protein molecules placed under a stretching force. Simple considerations about the free energy of a molecule readily show that the application of force introduces an entropic barrier separating the collapsed state of the molecule, from a force-driven extended conformation. A notable characteristic of the force induced barrier is its long distances to transition state, up to tens of nanometers, which renders the kinetics of crossing this barrier highly sensitive to an applied force. Langevin dynamics across such force induced barriers readily demonstrates the hopping behavior observed for a variety of single molecules placed under force. Such hopping is frequently interpreted as a manifestation of two-state folding/unfolding reactions observed in bulk experiments. However, given that such barriers do not exist at zero force these reactions do not take place at all in bulk.

DOI

Journal: Biochemical and Biophysical Research Communications