A primer to scaffolded DNA origami

Molecular self-assembly with scaffolded DNA origami enables building custom-shaped nanometer-scale objects with molecular weights in the megadalton regime. Here we provide a practical guide for design and assembly of scaffolded DNA origami objects. We also introduce a computational tool for predicting the structure of DNA origami objects and provide information on the conditions under which DNA origami objects can be expected to maintain their structure.     

Polyelectrolyte surface interface for single-molecule fluorescence studies of DNA polymerase

We report the use of polyelectrolyte multilayers in a stable robust surface chemistry for specific anchoring of DNA to glass. The nonspecific binding of fluorescently tagged nucleotides is suppressed down to the single-molecule level, and DNA polymerase is active on the anchored DNA template. This surface-chemistry platform can be used for single-molecule studies of DNA and DNA polymerase and may be more broadly applicable for other situations in which it is important to have specific biomolecular surface chemistry with extremely low nonspecific binding.     

Comparative single-molecule and ensemble myosin enzymology: sulfoindocyanine ATP and ADP derivatives

Single-molecule and macroscopic reactions of fluorescent nucleotides with myosin have been compared. The single-molecule studies serve as paradigms for enzyme-catalyzed reactions and ligand-receptor interactions analyzed as individual stochastic processes. Fluorescent nucleotides, called Cy3-EDA-ATP and Cy5-EDA-ATP, were derived by coupling the dyes Cy3.29.OH and Cy5.29.OH (compounds XI and XIV, respectively, in, Bioconjug. Chem. 4:105-111)) with 2'(3')-O-[N-(2-aminoethyl)carbamoyl]ATP (EDA-ATP). The ATP(ADP) analogs were separated into their respective 2'- and 3'-O-isomers, the interconversion rate of which was 30[OH(-)] s(-1) (0.016 h(-1) at pH 7.1) at 22 degrees C. Macroscopic studies showed that 2'(3')-O-substituted nucleotides had properties similar to those of ATP and ADP in their interactions with myosin, actomyosin, and muscle fibers, although the ATP analogs did not relax muscle as well as ATP did. Significant differences in the fluorescence intensity of Cy3-nucleotide 2'- and 3'-O-isomers in free solution and when they interacted with myosin were evident. Single-molecule studies using total internal reflection fluorescence microscopy showed that reciprocal mean lifetimes of the nucleotide analogs interacting with myosin filaments were one- to severalfold greater than predicted from macroscopic data. Kinetic and equilibrium data of nucleotide-(acto)myosin interactions derived from single-molecule microscopy now have a biochemical and physiological framework. This is important for single-molecule mechanical studies of motor proteins.     

Energy transfer in reconstituted peridinin-chlorophyll-protein complexes: ensemble and single-molecule spectroscopy studies

We combine ensemble and single-molecule spectroscopy to gain insight into the energy transfer between chlorophylls (Chls) in peridinin-chlorophyll-protein (PCP) complexes reconstituted with Chl a, Chl b, as well as both Chl a and Chl b. The main focus is the heterochlorophyllous system (Chl a/b-N-PCP), and reference information essential to interpret experimental observations is obtained from homochlorophyllous complexes. Energy transfer between Chls in Chl a/b-N-PCP takes place from Chl b to Chl a and also from Chl a to Chl b with comparable Förster energy transfer rates of 0.0324 and 0.0215 ps⁻¹, respectively. Monte Carlo simulations yield the ratio of 39:61 for the excitation distribution between Chl a and Chl b, which is larger than the equilibrium distribution of 34:66. An average Chl a/Chl b fluorescence intensity ratio of 66:34 is measured, however, for single Chl a/b-N-PCP complexes excited into the peridinin (Per) absorption. This difference is attributed to almost three times more efficient energy transfer from Per to Chl a than to Chl b. The results indicate also that due to bilateral energy transfer, the Chl system equilibrates only partially during the excited state lifetimes.     

Quantification and correction of systematic errors due to detector time-averaging in single-molecule tracking experiments

Single-molecule tracking is a powerful way to look at the dynamic organization of plasma membranes. However, there are some limitations to its use. For example, it was recently observed, using numerical simulation, that time-averaging effects inherent to the exposure time of detectors are likely to bias the apparent motion of molecules confined in microdomains. Here, we solve this apparently limiting issue analytically. We explore this phenomenon by calculating its effects on the observed diffusion coefficients and domain sizes. We demonstrate that the real parameters can be easily recovered from the measured apparent ones. Interestingly, we find that single-molecule tracking can be used to explore events occurring at a timescale smaller than the exposure time.     

A metal-chelating microscopy tip as a new toolbox for single-molecule experiments by atomic force microscopy

In recent years, the atomic force microscope (AFM) has contributed much to our understanding of the molecular forces involved in various high-affinity receptor-ligand systems. However, a universal anchor system for such measurements is still required. This would open up new possibilities for the study of biological recognition processes and for the establishment of high-throughput screening applications. One such candidate is the N-nitrilo-triacetic acid (NTA)/His-tag system, which is widely used in molecular biology to isolate and purify histidine-tagged fusion proteins. Here the histidine tag acts as a high-affinity recognition site for the NTA chelator. Accordingly, we have investigated the possibility of using this approach in single-molecule force measurements. Using a histidine-peptide as a model system, we have determined the binding force for various metal ions. At a loading rate of 0.5 microm/s, the determined forces varied from 22 +/- 4 to 58 +/- 5 pN. Most importantly, no interaction was detected for Ca(2+) and Mg(2+) up to concentrations of 10 mM. Furthermore, EDTA and a metal ion reloading step demonstrated the reversibility of the approach. Here the molecular interactions were turned off (EDTA) and on (metal reloading) in a switch-like fashion. Our results show that the NTA/His-tag system will expand the "molecular toolboxes" with which receptor-ligand systems can be investigated at the single-molecule level.     

DNA translocation by type III restriction enzymes: a comparison of current models of their operation derived from ensemble and single-molecule measurements

Much insight into the interactions of DNA and enzymes has been obtained using a number of single-molecule techniques. However, recent results generated using two of these techniques-atomic force microscopy (AFM) and magnetic tweezers (MT)-have produced apparently contradictory results when applied to the action of the ATP-dependent type III restriction endonucleases on DNA. The AFM images show extensive looping of the DNA brought about by the existence of multiple DNA binding sites on each enzyme and enzyme dimerisation. The MT experiments show no evidence for looping being a requirement for DNA cleavage, but instead support a diffusive sliding of the enzyme on the DNA until an enzyme-enzyme collision occurs, leading to cleavage. Not only do these two methods appear to disagree, but also the models derived from them have difficulty explaining some ensemble biochemical results on DNA cleavage. In this 'Survey and Summary', we describe several different models put forward for the action of type III restriction enzymes and their inadequacies. We also attempt to reconcile the different models and indicate areas for further experimentation to elucidate the mechanism of these enzymes.     

The properties and applications of single-molecule DNA sequencing

Single-molecule sequencing enables DNA or RNA to be sequenced directly from biological samples, making it well-suited for diagnostic and clinical applications. Here we review the properties and applications of this rapidly evolving and promising technology.     

Fluorescence resonance energy transfer (FRET) and competing processes in donor-acceptor substituted DNA strands: a comparative study of ensemble and single-molecule data

We studied the fluorescence resonance energy transfer (FRET) efficiency of different donor-acceptor labeled model DNA systems in aqueous solution from ensemble measurements and at the single molecule level. The donor dyes: tetramethylrhodamine (TMR); rhodamine 6G (R6G); and a carbocyanine dye (Cy3) were covalently attached to the 5'-end of a 40-mer model oligonucleotide. The acceptor dyes, a carbocyanine dye (Cy5), and a rhodamine derivative (JA133) were attached at modified thymidine bases in the complementary DNA strand with donor-acceptor distances of 5, 15, 25 and 35 DNA-bases, respectively. Anisotropy measurements demonstrate that none of the dyes can be observed as a free rotor; especially in the 5-bp constructs the dyes exhibit relatively high anisotropy values. Nevertheless, the dyes change their conformation with respect to the oligonucleotide on a slower time scale in the millisecond range. This results in a dynamic inhomogeneous distribution of donor/acceptor (D/A) distances and orientations. FRET efficiencies have been calculated from donor and acceptor fluorescence intensity as well as from time-resolved fluorescence measurements of the donor fluorescence decay. Dependent on the D/A pair and distance, additional strong fluorescence quenching of the donor is observed, which simulates lower FRET efficiencies at short distances and higher efficiencies at longer distances. On the other hand, spFRET measurements revealed subpopulations that exhibit the expected FRET efficiency, even at short D/A distances. In addition, the measured acceptor fluorescence intensities and lifetimes also partly show fluorescence quenching effects independent of the excitation wavelength, i.e. either directly excited or via FRET. These effects strongly depend on the D/A distance and the dyes used, respectively. The obtained data demonstrate that besides dimerization at short D/A distances, an electron transfer process between the acceptor Cy5 and rhodamine donors has to be taken into account. To explain deviations from FRET theory even at larger D/A distances, we suggest that the pi-stack of the DNA double helix mediates electron transfer from the donor to the acceptor, even over distances as long as 35 base pairs. Our data show that FRET experiments at the single molecule level are rather suited to resolve fluorescent subpopulations in heterogeneous mixture, information about strongly quenched subpopulations gets lost.     

Disentangling subpopulations in single-molecule FRET and ALEX experiments with photon distribution analysis

Among the advantages of the single-molecule approach when used to study biomolecular structural dynamics and interaction is its ability to distinguish between and independently observe minor subpopulations. In a single-molecule Förster resonance energy transfer (FRET) and alternating laser excitation diffusion experiment, the various populations are apparent in the resultant histograms. However, because histograms are calculated based on the per-burst mean FRET and stoichiometry ratio and not on the internal photon distribution, much of the acquired information is lost, thereby reducing the capabilities of the method. Here we suggest what to our knowledge is a novel statistical analysis tool that significantly enhances these capabilities, and we use it to identify and isolate static and dynamic subpopulations. Based on a kernel density estimator and a proper photon distribution analysis, for each individual burst, we calculate scores that reflect properties of interest. Specifically, we determine the FRET efficiency and brightness ratio distributions and use them to reveal 1), the underlying structure of a two-state DNA-hairpin and a DNA hairpin that is bound to DNA origami; 2), a minor doubly labeled dsDNA subpopulation concealed in a larger singly labeled dsDNA; and 3), functioning DNA origami motors concealed within a larger subpopulation of defective motors. Altogether, these findings demonstrate the usefulness of the proposed approach. The method was developed and tested using simulations, its rationality is described, and a computer algorithm is provided.     

Beyond origami: using behavioural observations as a strategy to improve trap design

In contrast to ad hoc methods of developing traps for pest monitoring systems, a systematic approach using direct observation of animals allowed a greater understanding of the reasons why trap catch was significantly different in traps of basically similar design. The information gained using this approach could then be used to guide the further development of the trap. The same feature on two related designs of cockroach trap was varied: the slope of the ramp leading into the trap was either 60°, 30°, or 0°. The 30° ramp version of both traps caught significantly more Blattella germanica (L.) (Dictyoptera: Blattellidae). The 60° and 0° ramp versions both caught equal, lower, numbers but observation showed that these net catches were achieved by quite different means; few insects entered over the 60° ramps but none escaped, whereas all entered over the 0° ramps but half escaped. Similar approaches could be applied to other insect-trap systems.     

Quantifying force-dependent and zero-force DNA intercalation by single-molecule stretching

We used single DNA molecule stretching to investigate DNA intercalation by ethidium and three ruthenium complexes. By measuring ligand-induced DNA elongation at different ligand concentrations, we determined the binding constant and site size as a function of force. Both quantities depend strongly on force and, in the limit of zero force, converge to the known bulk solution values, when available. This approach allowed us to distinguish the intercalative mode of ligand binding from other binding modes and allowed characterization of intercalation with binding constants ranging over almost six orders of magnitude, including ligands that do not intercalate under experimentally accessible solution conditions. As ligand concentration increased, the DNA stretching curves saturated at the maximum amount of ligand intercalation. The results showed that the applied force partially relieves normal intercalation constraints. We also characterized the flexibility of intercalator-saturated dsDNA for the first time.     

Molecular dynamics study of thrombin capture by aptamers TBA26 and TBA29 coupled to a DNA origami

The fabrication of DNA origamis is one of the very few possibilities to create nanostructures with precise atomistic-tailored geometries in a variety of shapes. In addition, these origamis can be functionalized or be impregnated with specialised aptamers in order to convert them into nanosensors or to tune them with pre-specified properties simply by impregnating single-stranded DNA or RNA chains (aptamers) via the precise features of DNA pairing. We performed molecular dynamics simulations to determine the relative energetics associated with the capture of thrombin by two aptamers TBA26 and TBA29 attached to a rectangular DNA origami. The molecular simulations provided detailed structural information of aptamer–enzyme interactions which are crucial for the efficient design of aptamer-based biosensors. In addition, the simulations showed a remarkable selectivity of the biosensor assembly for thrombin. The detection, capture, and sensing of enzymes is of great significance in biomedicine. In particular, the detection of thrombin is a major task in cardiovascular diagnostics and therapeutics. On the other hand, our simulations can be extended to detect biotoxins or any other chemical or biological agent by simply choosing proper aptamers. Finally, the problems due to the large number of atoms involved as well as the quality of the approximations are also discussed.     

Folding transition into a loosely collapsed state in plasmid DNA as revealed by single-molecule observation

The conformational transition of a plasmid DNA, pGEG.GL3 (12.5 kbp, circular), induced by spermine(4+) was studied through the observation of individual DNA by fluorescence microscopy. We deduced the change in the hydrodynamic radius R(H) from an analysis of the Brownian motion of single DNA molecules. R(H) decreases in a continuous manner with an increase in spermine(4+), in contrast to the large discrete on/off change for long linear DNA. Just after the transition to the collapsed state, a small number of DNA molecules tend to form an assembly, which disperses in the bulk solution without precipitation.     

Meltable dextran esters as biocompatible and functional coating materials

The conversion of dextran with in situ synthesized iminium chlorides of long chain carboxylic acids was used to obtain pure and defined melting dextran esters in an efficient one-pot synthesis. The melting point of these esters can be tailored by the degree of substitutions (DS), the molecular weight of the starting polymer, and the chain length of the ester moiety. The dextran esters give homogeneous and completely transparent melts, which form stable films on a broad variety of materials. Even complex geometries, such as implants, can be evenly coated by multiple melting steps. The films do not display any inhomogeneity and have a very low surface roughness. Therefore, no unspecific protein binding is observed. Moreover, the dextran esters are biocompatible as demonstrated for the interaction with three types of cells namely human brain microvascular endothelial cell, primary human fibroblasts, and mouse myoblast cells.     

Type-3 copper proteins as biocompatible and reusable oxygen sensors

Fluorescently labeled type-3 copper proteins have been proposed previously as solution oxygen sensors by using a FRET mechanism. Herein, we describe how this principle can be adapted to sense O₂ by means of proteins immobilized in optically transparent silica matrices. Specifically, the protein, hemocyanin from Octopus vulgaris N-terminally labeled with Cy5, is immobilized in two different kinds of optically transparent silica matrices, which appear to be a promising platform for enzyme encapsulation. The presented results provide proof of principle that fluorescently labeled proteins immobilized in a silica matrix can be implemented in a reusable, biocompatible and stable oxygen measuring device that might lead to new developments in the field of optical biosensing.