Nanosecond to submillisecond dynamics in dye-labeled single-stranded DNA, as revealed by ensemble measurements and photon statistics at single-molecule level

Choice of fluorophore affects dynamic DNA nanostructures

The ability to dynamically remodel DNA origami structures or functional nanodevices is highly desired in the field of DNA nanotechnology. Concomitantly, the use of fluorophores to track and validate the dynamics of such DNA-based architectures is commonplace and often unavoidable. It is therefore crucial to be aware of the side effects of popular fluorophores, which are often exchanged without considering the potential impact on the system. Here, we show that the choice of fluorophore can strongly affect the reconfiguration of DNA nanostructures. To this end, we encapsulate a triple-stranded DNA (tsDNA) into water-in-oil compartments and functionalize their periphery with a single-stranded DNA handle (ssDNA). Thus, the tsDNA can bind and unbind from the periphery by reversible opening of the triplex and subsequent strand displacement. Using a combination of experiments, molecular dynamics (MD) simulations, and reaction-diffusion modelling, we demonstrate for 12 different fluorophore combinations that it is possible to alter or even inhibit the DNA nanostructure formation-without changing the DNA sequence. Besides its immediate importance for the design of pH-responsive switches and fluorophore labelling, our work presents a strategy to precisely tune the energy landscape of dynamic DNA nanodevices.

Structure and dynamics of poly(methacrylic acid) and its interpolymer complex probed by covalently bound rhodamine-123

The dynamics and structural characteristics of polymethacrylic acid bound rhodamine-123 (PMAA-R123) and its interpolymer complex formed through hydrogen bonding between the monomeric units with poly(vinylpyrrolidone) were investigated using single molecular fluorescence studies. The time resolved fluorescence anisotropy decay of PMAA-R123 under acidic pH exhibits an associated anisotropy decay behavior characteristic of two different environments experienced by the fluorophore with one shorter and another longer rotational correlation time. The anisotropy decay retains normal bi-exponential behavior under neutral pH. Fluorescence correlation spectroscopic investigation reveals that the attached fluorophore undergoes hydrolysis under basic condition which results in the release of the fluorophore from the polymer backbone. Shrinkage in the hydrodynamic radius of PMAA is observed on addition of the complementary polymer PVP which is attributed to the formation compact solubilized nanoparticle like aggregates. The size of particle further decreases on the addition of NaCl. The detailed results show that these complexes have potential for use as drug-delivery system under physiological conditions.

Single-Molecule Study of Redox Reaction Kinetics by Observing Fluorescence Blinking

Recent advances in fluorescence microscopy allow us to track chemical reactions at the single-molecule level. Single-molecule measurements make it possible to minimize the amount of sample needed for analysis and diagnosis. Signal amplification is often applied to ultralow-level biomarker detection. Polymerase chain reaction (PCR) is used to detect DNA/RNA, and enzyme-linked immunosorbent assay (ELISA) can sensitively probe antigen-antibody interactions. While these techniques are brilliant and will continue to be used in the future, single-molecule-level measurements would allow us to reduce the time and cost needed to amplify signals.The kinetics of chemical reactions have been studied mainly using ensemble-averaged methods. However, they can hardly distinguish time-dependent fluctuations and static heterogeneity of the kinetics. The information hidden in ensemble-averaged measurements would be extractable from a single-molecule experiment. Thus, single-molecule measurement would provide unique opportunities to investigate unrevealed phenomena and to elucidate the questions in chemistry, physics, and life sciences. Redox reaction, which is triggered by electron transfer, is among the most fundamental and ubiquitous chemical reactions. The redox reaction of a fluorescent molecule results in the formation of radical ions, which are normally nonemissive. In single-molecule-level measurements, the redox reaction causes the fluctuation of fluorescence signals between the bright ON-state and the dark OFF-state, in a phenomenon called blinking. The duration of the OFF-state (τ_OFF) corresponds to the lifetime of the radical ion state, and its reaction kinetics can be measured as 1/τ_OFF. Thus, the kinetics of redox reactions of fluorescent molecules can be accessed at the single-molecule level by monitoring fluorescence blinking. One of the key aspects of single-molecule analysis based on blinking is its robustness. A blinking signal with a certain regular pattern enables single fluorescent molecules to be distinguished and resolved from the random background signal.In this Account, we summarize the recent studies on the single-molecule measurement of redox reaction kinetics, with a focus on our group's recent progress. We first introduce the control of redox blinking to increase the photostability of fluorescent molecules. We then demonstrate the control of redox blinking, which allows us to detect target DNA by monitoring the function of a molecular beacon-type probe, and we investigate antigen-antibody interactions at the single-molecule level. By tracing the time-dependent changes in blinking patterns, redox blinking is shown to be adaptable to tracking the structural switching dynamics of RNA, the preQ₁ riboswitch. This Account ends with a discussion of our ongoing work on the control of fluorescent blinking. We also discuss the development of devices that allow single-molecule-level analysis in a high-throughput fashion.

Fluorescence quenching by photoinduced electron transfer between 7-methoxycoumarin and guanine base facilitated by hydrogen bonds: an in silico study

In this study, the effects of hydrogen bond (H-bond) formation on fluorescence quenching of 7-methoxycoumarin (7MC) via photo-induced electron transfer from a guanine base (Gua) are investigated using a combined quantum mechanics/molecular mechanics simulation. The electronic structure is calculated by the floating occupation molecular orbital complete active space configuration interaction modification on a semiempirical method. Then the full multiple spawning method is employed for the dynamics simulations on multiple electronic states. The methods employed here are validated by simulating direct dynamics of 7MC (without Gua) and compared with available experimental results. Our computational results are in good agreement with the previously reported experimental results in terms of spectroscopic properties of 7MC. In the case of a H-bonded 7MC-Gua complex, the results from constrained dynamics simulations and single-point calculations suggest that the electron transfer occurs on the second excited state and it depends not only on the H-bond length but also on the intermolecular planarity between 7MC and Gua. Moreover, a proton coupled electron transfer can occur at ≈1 Å of H-bond length, where a proton from Gua is also transferred together with the electron to 7MC. The obtained simulations are expected to be greatly beneficial for designing effective fluorescently labeled nucleotide probes as well as providing information for precise fluorescence signal interpretation.

Single-Molecule Monitoring of the Structural Switching Dynamics of Nucleic Acids through Controlling Fluorescence Blinking

Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful tool to investigate the dynamics of biomolecular events in real time. However, it requires two fluorophores and can be applied only to dynamics that accompany large changes in distance between the molecules. Herein, we introduce a method for kinetic analysis based on control of fluorescence blinking (KACB), a general approach to investigate the dynamics of biomolecules by using a single fluorophore. By controlling the kinetics of the redox reaction the blinking kinetics or pattern can be controlled to be affected by microenvironmental changes around a fluorophore (rKACB), thereby enabling real-time single-molecule measurement of the structure-changing dynamics of nucleic acids.

Dynamics of single-stranded DNA tethered to a solid

Tethering is used to deliver specific biological and industrial functions. For example, single-stranded DNA (ssDNA) is tethered to polymerases and long sequences of double-stranded DNA (dsDNA) during replication, and to solids in DNA microarrays. However, tethering ssDNA to a large object limits not only the available ssDNA conformations, but also the range of time-scales over which the mechanical responses of ssDNA are important. In this work we examine the effect of tethering by measurement of the mechanical response of ssDNA that is tethered at each end to two separate atomic force microscope cantilevers in aqueous solution. Thermal motion of the cantilevers drives the ends of the ssDNA chain at frequencies near 2 kHz. The presence of a tethered molecule makes a large difference to the asymmetric cross-correlation of two cantilevers, which enables resolution of the mechanical properties in our experiments. By analysis of the correlated motion of the cantilevers we extract the friction and stiffness of the ssDNA. We find that the measured friction is much larger than the friction that is usually associated with the unencumbered motion of ssDNA. We also find that the measured relaxation time, ∼30 μs, is much greater than prior measurements of the free-molecule relaxation time. We attribute the difference to the loss of conformational possibilities as a result of constraining the ends of the ssDNA.

Triple helix conformation-specific blinking of Cy3 in DNA

We report that Cy3 undergoes triple helix conformation-specific blinking in DNA. Blinking patterns were affected by the stabilization of the Hoogsteen base-pair, suggesting that not only the presence but also the fluctuating behaviour of the triple helix can be monitored by the changes in the Cy3 blinking patterns.

Molecular dynamics simulation of a single-stranded DNA with heterogeneous distribution of nucleobases in aqueous medium

The DNA metabolic processes often involve single-stranded DNA (ss-DNA) molecules as important intermediates. In the absence of base complementarity, ss-DNAs are more flexible and interact strongly with water in aqueous media. Ss-DNA-water interactions are expected to control the conformational flexibility of the DNA strand, which in turn should influence the properties of the surrounding water molecules. We have performed room temperature molecular dynamics simulation of an aqueous solution containing the ss-DNA dodecamer, 5'-CGCGAATTCGCG-3'. The conformational flexibility of the DNA strand and the microscopic structure and ordering of water molecules around it have been explored. The simulation reveals transformation of the initial base-stacked form of the ss-DNA to a fluctuating collapsed coil-like conformation with the formation of a few non-sequentially stacked base pairs. A preliminary analysis shows further collapse of the DNA conformation in presence of additional salt (NaCl) due to screening of negative charges along the backbone by excess cations. Additionally, higher packing of water molecules within a short distance from the DNA strand is found to be associated with realignment of water molecules by breaking their regular tetrahedral ordering.

Blinking triggered by the change in the solvent accessibility of a fluorescent molecule

The more a fluorescent molecule is exposed to a solvent, the faster its triplet excited state is quenched by molecular oxygen.

Detection of single-nucleotide variations by monitoring the blinking of fluorescence induced by charge transfer in DNA

Charge transfer dynamics in DNA: Photo-induced charge separation and charge-recombination dynamics in DNA was assessed by monitoring the blinking of fluorescence. Single nucleotide variations, mismatch and one base deletion, were differentiated based on the length of the off-time of the blinking, which corresponds to the lifetime of the charge-separated state.

PNA-peptide assembly in a 3D DNA nanocage at room temperature

Proteins and peptides fold into dynamic structures that access a broad functional landscape; however, designing artificial polypeptide systems is still a great challenge. Conversely, DNA engineering is now routinely used to build a wide variety of 2D and 3D nanostructures from hybridization based rules, and their functional diversity can be significantly expanded through site specific incorporation of the appropriate guest molecules. Here we demonstrate a new approach to rationally design 3D nucleic acid-amino acid complexes using peptide nucleic acid (PNA) to assemble peptides inside a 3D DNA nanocage. The PNA-peptides were found to bind to the preassembled DNA nanocage in 5-10 min at room temperature, and assembly could be performed in a stepwise fashion. Biophysical characterization of the DNA-PNA-peptide complex was performed using gel electrophoresis as well as steady state and time-resolved fluorescence spectroscopy. Based on these results we have developed a model for the arrangement of the PNA-peptides inside the DNA nanocage. This work demonstrates a flexible new approach to leverage rationally designed nucleic acid (DNA-PNA) nanoscaffolds to guide polypeptide engineering.

Advances in quantitative FRET-based methods for studying nucleic acids

Förster resonance energy transfer (FRET) is a powerful tool for monitoring molecular distances and interactions at the nanoscale level. The strong dependence of transfer efficiency on probe separation makes FRET perfectly suited for "on/off" experiments. To use FRET to obtain quantitative distances and three-dimensional structures, however, is more challenging. This review summarises recent studies and technological advances that have improved FRET as a quantitative molecular ruler in nucleic acid systems, both at the ensemble and at the single-molecule levels.

Transition path times for nucleic Acid folding determined from energy-landscape analysis of single-molecule trajectories

The duration of structural transitions in biopolymers is only a fraction of the time spent searching diffusively over the configurational energy landscape. We found the transition time, τ(TP), and the diffusion constant, D, for DNA and RNA folding using energy landscapes obtained from single-molecule trajectories under tension in optical traps. DNA hairpins, RNA pseudoknots, and a riboswitch all had τ(TP)~10 μs and D~10(-13-14) m(2)/s, despite widely differing unfolding rates. These results show how energy-landscape analysis can be harnessed to characterize brief but critical events during folding reactions.

Fluorescence detection of single guest molecules in ultrasmall droplets of nonpolar solvent

We have investigated emissive behaviours of individual perylenebisimide derivatives, N,N'-dipropyl-1,6,7,12-tetrakis(4-tert-butylphenoxy)-3,4,9,10-perylenetetra-carboxydiimide (BP-PDI), in single ultrasmall droplets of n-octane at room temperature by using confocal and wide-field microscopic techniques. Single BP-PDIs in the small droplets show no distinguishable blinking in the time courses of fluorescence intensity. This is attributed to small probabilities of the formation of the long-lived ionized state leading to the off-state of the fluorescence. Temporal change in the degree of polarization of fluorescence and wide-field fluorescence images indicated short-time adsorption of the fluorescent molecules at the interfaces between n-octane and watery environments. Fluorescence correlation spectroscopy revealed that the adsorption/desorption processes took place at least in two different time scales, probably due to the difference in the adsorption geometry and/or in the interaction, such as van der Waals interaction and hydrogen bonding, between the dye and the interface.

Cy3-DNA stacking interactions strongly depend on the identity of the terminal basepair

We characterized the effect of the first basepair on the conformational dynamics of the fluorescent dye Cy3 attached to the 5' end of double-stranded DNA using gaussian-mixture adaptive umbrella sampling simulations. In the simulations, the sampling of all five dihedral angles along the linker was enhanced, so that both stacked and unstacked states were sampled. The affinity of Cy3 for a T·A basepair (with the dye attached to T) was found to be significantly less than for the other basepairs. This was verified experimentally by measuring the activation energies for cis-trans isomerization of the dye. The simulation and experimental results indicate the existence of partially unstacked conformations amenable to photoisomerization. The simulations also showed that stacking of Cy3 straightens the DNA while stabilizing the first basepair. Our findings indicate that fluorescence is modulated by Cy3-DNA interactions in a sequence-dependent manner.

A fluorescein-containing, small-molecule, water-soluble receptor for cytosine free bases

In this study, we synthesized small-molecule, water-soluble, fluorescein-containing ureido compounds 6 and 8 as target receptors for cytosine free bases and then investigated the binding of cytosine free bases with the receptors using (15)N NMR spectroscopy and partially labeled cytosine-2,4-(13)C-1,3,4-(15)N-cytosine. Binding with the receptor 6a (the disodium form of 6) caused the chemical shift of the nitrogen atom of the amino group of cytosine to move downfield; binding of the receptor 8a (the disodium form of 8), which is possessing no corresponding aryl nitrogen atom, had no effect on this signal. Fluorescence spectroscopy revealed that binding of cytosine and its derivatives led to quenching of the fluorescence of receptor 6a; in contrast, the quenching of receptor 8a was only slightly affected by cytosine. Because the fluorescence of 6a was not quenched by either deoxycytidine or uracil, it appears that this receptor is a specific for cytosine among the DNA bases. We used the fluorescence of 6a to measure the apparent binding constants for various cytosine derivatives, including the anticancer prodrug 5-fluorocytosine. Receptor 6a is the first small-molecule, water-soluble fluorescent receptor for the specific binding of cytosine free bases in aqueous solution.