Mori-Zwanzig memory analysis in single-molecule spectroscopy

We study the dynamical behavior of the Rhodospirillum molischianum LH2 complex based on intensity time series obtained from single-molecule spectroscopy experiments. This is achieved by reconstructing the memory function describing the time-dependent fluctuations of the excited states. We conclude that the apparent stochastic evolution of the dynamics is controlled by at least two different non-Markovian main processes.     

Origins of blinking in single-molecule Raman spectroscopy

We observe spectral and intensity fluctuations in Raman scattering from single molecules of 4-mercaptopyridine (4-Mpy) adsorbed on textured silver surfaces. We present evidence that the root cause of these fluctuations is thermal. Analysis of the spectra shows that in some cases the spectral changes are associated with molecular reorientation and in others with chemical reactions of the 4-Mpy. Analogous surfaces fully covered with 4-Mpy exhibit similar behavior, indicating that monolayer Raman spectra are dominated by a few molecules at most.     

Sampling unfolding intermediates in calmodulin by single-molecule spectroscopy

We used single-pair fluorescence resonance energy transfer (spFRET) measurements to characterize denatured and partially denatured states of the multidomain calcium signaling protein calmodulin (CaM) in both its apo and Ca(2+)-bound forms. The results demonstrate the existence of an unfolding intermediate. A CaM mutant (CaM-T34C-T110C) was doubly labeled with fluorescent probes AlexaFlour 488 and Texas Red at opposing globular domains. Single-molecule distributions of the distance between fluorophores were obtained by spFRET at varying levels of the denaturant urea. Multiple conformational states of CaM were observed, and the amplitude of each conformation was dependent on urea concentration, with the amplitude of an extended conformation increasing upon denaturation. The distributions at intermediate urea concentrations could not be adequately described as a combination of native and denatured conformations, showing that CaM does not denature via a two-state process and demonstrating that at least one intermediate is present. The intermediate conformations formed upon addition of urea were different for Ca(2+)-CaM and apoCaM. An increase in the amplitude of a compact conformation in CaM was observed for apoCaM but not for Ca(2+)-CAM upon the addition of urea. The changes in the single-molecule distributions of CaM upon denaturation can be described by either a range of intermediate structures or by the presence of a single unfolding intermediate that grows in amplitude upon denaturation. A model for stepwise unfolding of CaM is suggested in which the domains of CaM unfold sequentially.     

Identification of sugar isomers by single-molecule force spectroscopy

The nanomechanical properties of beta-galactan, a 1 --> 4 linked beta-d-galactose polysaccharide, were investigated with AFM-based single-molecule force spectroscopy. AFM captured a unique plateau at 640 pN in the force spectrogram of beta-galactan, which is significantly different than the plateau at 280 pN in the force spectrogram of amylose. Thus, our results demonstrate that force spectroscopy is able to discriminate between sugar isomers in which axial and equatorial bonds at C1 and C4 are swapped.     

TOTO binding affinity analysis using single-molecule fluorescence spectroscopy

The sequence dependence of the double-stranded DNA (dsDNA)-binding affinity of TOTO, a thiazole orange dimer that functions as a DNA-intercalating fluorophore, was measured using single-molecule methods. An analysis was performed of the distribution of excited-state lifetimes of single molecules of TOTO intercalated into dsDNA fragments containing four-base pair sequences shown previously to have high affinity for TOTO under conditions used in nuclear magnetic resonance (NMR) spectroscopy. For the current studies, the putative binding sites were located centrally in 30-base pair-long dsDNA fragments in which the remaining sequence was either all poly-AT or poly-GC. The lifetime of TOTO fluorescence when bound to these fragments was entirely determined by the background sequence, i.e. DNA fragments with a poly-AT background predominantly gave a fluorescence lifetime of 1.7 ns, whereas DNA fragments with a poly-GC background gave a lifetime of 2.0 ns, independent of the presence or absence of the putative binding sequence. By performing competitive binding experiments in which these DNA fragments competed for TOTO binding with pure poly-AT fragments and using single-molecule fluorescence methods to determine the number of each type of DNA fragment having a TOTO bound in an equilibrium mixture, the relative binding affinity of each putative binding site was determined. The results of these experiments showed clearly that TOTO has no preference for binding to the putative binding sites over binding poly-AT or poly-GC under the conditions of these measurements. This suggests that there is very little sequence dependence of TOTO binding under conditions that would likely predominate in most biological applications of this intercalating dye.     

Intermolecular intersystem crossing in single-molecule spectroscopy: Terrylene in anthracene crystal

We present a spectroscopic study of terrylene in anthracene crystals at the ensemble and single-molecule levels. In this matrix, single-molecule fluorescence is reduced by three orders of magnitude. Correlation measurements allow us to identify a new relaxation channel, matrix-enhanced intersystem crossing. This process starts with a singlet-to-triplet energy transfer from guest to host, after which the triplet exciton is transferred back to the guest. The intermolecular intersystem crossing is expected whenever the lowest triplet state of the host is located between the lowest singlet S(1) and lowest triplet T(1) excited states of the guest. It must be considered when searching for new host-guest systems for single-molecule spectroscopy.     

Concentration modulated absorption spectroscopy

A new Concentration Modulation technique has been developed at the University College of Wales, Aberystwyth, U.K., capable of markedly extending the sensitivity limits in Absorption Spectroscopy. By relating Gain and Transmittance values direct measurement of spectroscopic concentrations become possible for the first time. The use of picosecond lasers enables lifetime determinations down to ∼ 20 ps. Some of the applications for this highly sensitive technique will be presented.     

Using single-molecule fluorescence spectroscopy to study electron transfer.

Techniques in single-molecule fluorescence spectroscopy now allow sophisticated studies of photophysical processes in single molecules. As interest grows in the possibilities of molecular electronics, researchers have begun to turn these techniques to the study of electron transfer. Electron-transfer reactions have now been detected and measured at the single-molecule level in a variety of systems and on a variety of timescales by adapting techniques from previous single-molecule fluorescence studies.     

Interaction between dendrons directly studied by single-molecule force spectroscopy

In this article, we have investigated the interaction between two poly(benzyl ether) dendrons directly by single-molecule force spectroscopy. For this purpose, one dendron was immobilized on an AFM tip through a poly(ethylene glycol) (PEG) spacer, and the other dendron was anchored on a gold substrate as a self-assembled monolayer. Two dendrons approached and then interacted with each other when the AFM tip and the substrate moved close together. The rupture force between dendrons was measured while the AFM tip and the substrate separated. PEG as a flexible spacer can function as a length window for recognizing the force signals and avoiding the disturbance of the interaction between the AFM tip and the substrate. The interaction between two first-generation dendrons is measured to be about 224 pN at a force loading rate of 40 nN/s. The interaction between second- and first-generation dendrons rises to 315 pN at the same loading rate. Such interactions depend on the force loading rate in the range of several to hundreds of nanonewtons per second, indicating that the rupture between dendrons is a dynamic process. The study of the interaction between surface-bound dendrons of different generations provides a model system for understanding the surface adhesion of molecules with multiple branches. In addition, this multiple-branch molecule may be used to mimic the sticky feet of geckos as a man-made adhesive.     

Revealing two-state protein-protein interactions of calmodulin by single-molecule spectroscopy

We report a single-molecule fluorescence resonance energy transfer (FRET) and polarization study of conformational dynamics of calmodulin (CaM) interacting with a target peptide, C28W of a 28 amino acid oligomer. The C28W peptide represents the essential binding sequence domain of the Ca-ATPase protein interacting with CaM, which is important in cellular signaling for the regulation of energy in metabolism. However, the mechanism of the CaM/C28W recognition complex formation is still unclear. The amino-terminal (N-terminal) domain of the CaM was labeled with a fluorescein-based arsenical hairpin binder (FlAsH) that enables our unambiguous probing of the CaM N-terminal target-binding domain motions on a millisecond time scale without convolution of the probe-dye random motions. By analyzing the distribution of FRET efficiency between FlAsH labeled CaM and Texas Red labeled C28W and the polarization fluctuation dynamics and distributions of the CaM N-terminal domain, we reveal binding-unbinding motions of the N-terminal domain of the CaM in CaM/C28W complexes, which is strong evidence of a two-state binding interaction of CaM-mediated cell signaling.     

Microfluidic separation and capture of analytes for single-molecule spectroscopy

A complex mixture of fluorescently labeled biological molecules is separated electrophoretically on a chip and the constituent molecules are confined in a sub-nanolitre microchamber, which allows analysis by various single-molecule techniques.     

Influence of pulling handles and device stiffness in single-molecule force spectroscopy

In single-molecule force spectroscopy, individual molecules and complexes are often stretched by pulling devices via intervening molecular handles. Accurate interpretation of measurements from such experiments in terms of the underlying energy landscape, defined by activation barriers and intrinsic rates of transition, relies on our understanding, and proper theoretical treatment, of the effects of the pulling device and handle. Here, we present a framework based on Kramers' theory that elucidates the dependence of measured rupture forces and rates on the pulling device stiffness and attributes of the handle, contour length and persistence length. We also introduce a simple analytic model that improves prediction of activation barriers and intrinsic rates for all device stiffnesses and handle properties, thus allowing for a more reliable interpretation of experiments. Our analyses also suggests intuitive ways of displaying the measured force spectra for proper prognosis of device and handle effects and provides the range of device and handle attributes over which these effects can be neglected.     

A frequency domain existence proof of single-molecule surface-enhanced Raman spectroscopy

The existence of single-molecule surface-enhanced Raman spectroscopy (SMSERS) is proven by employing a frequency-domain approach. This is demonstrated using two isotopologues of Rhodamine 6G that offer unique vibrational signatures. When an average of one molecule was adsorbed per silver nanoparticle, only one isotopologue was typically observed under dry N2 environment. Additionally, the distribution of vibrational frequencies hidden under the ensemble average is revealed by examining the single-molecule spectra. Correlation with transmission electron microscopy reveals that SMSERS active aggregates are composed of multiple randomly sized and shaped nanoparticles. At higher coverage and in a humid environment, adsorbate interchange was detected. Using 2D cross correlation, vibrational modes from different isotopologues were anti-correlated, indicating that the dynamic behavior was from multiple molecules competing for a single hot spot. This allows hot-spot diffusion to be directly observed without analyzing the peak intensity fluctuations.     

Ensemble and single-molecule fluorescence spectroscopy of a calcium-ion indicator dye

The spectroscopic properties of Calcium Green 2 (CG-2), a dual-fluorophore Ca(2+) indicator dye, were characterized by a combination of steady state and time-resolved ensemble spectroscopic measurements, molecular mechanics calculations and single-molecule fluorescence spectroscopy. It was found that in Ca(2+) free solutions, CG-2 exists primarily as a highly quenched intramolecular dimer, but when bound to Ca(2+), the molecule adopts an extended, fluorescent conformation. The difference in emission properties of these two CG-2 conformations is explained in terms of simple exciton theory. Through single-molecule fluorescence measurements, we have shown that the bulk increase in ensemble fluorescence intensity correlates with a simple statistical increase in the number of fluorescent molecules in solution. In addition, we have also observed that the majority of CG-2 molecules photobleach in a single step, despite the molecule possessing two distinct fluorophores. A small fraction of molecules photobleach in multiple steps or show a series of transitions between emissive and nonemissive fluorescent states ("blinking"). We rationalize these photophysical phenomena using a simple model based on dipole-dipole F?rster coupling between fluorophores in conjunction with irreversible photodamage to one of the constituent chromophores.     

Facile method of constructing polyproteins for single-molecule force spectroscopy studies

Constructing polyproteins consisting of identical tandem repeats of proteins provides an unambiguous method of investigating the mechanical properties of proteins at the single-molecule level using force spectroscopy techniques. Here we report a maleimide-thiol coupling-based facile method of constructing polyproteins for single-molecule force spectroscopy studies on the mechanical properties of proteins. This method allows for the construction of polyproteins in an efficient fashion under room temperature. The resultant thioether bonds are resistant to reduction and make it possible to carry out single-molecule force spectroscopy studies under various redox conditions. This novel method complements existing polyprotein engineering methods and can be easily applied to a wide variety of proteins.