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Special Issue "Advances in Single Molecule Spectroscopy"

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry, Theoretical and Computational Chemistry".

Deadline for manuscript submissions: closed (30 June 2012)

Special Issue Editor

Guest Editor
Prof. Dr. Jeanne L. McHale

Department of Chemistry, Washington State University, PO Box 644630, Pullman, WA 99164-4630, USA
E-Mail
Fax: +1 509 335 8867

Special Issue Information

Dear Colleagues,

Since the first reports of single-molecule spectroscopy in the mid 1980s, single-molecule techniques have greatly expanded to include the study of photophysics and photochemistry of individual molecules, biomolecules, living cells, and nanomaterials.  The powerful application of absorption, fluorescence, and Raman spectroscopy to individual chromophores, be they molecules, proteins, or nanoparticles, has provided tremendous insight into the structure and dynamics of heterogeneous systems.  Applications of single-chromophore spectroscopy include imaging and microfluidics as well as studies of energy and charge transfer.

Prof. Dr. Jeanne L. McHale
Guest Editor

Keywords

  • Single-molecule absorption
  • Single-molecule fluorescence
  • Single-molecule Raman
  • Biomolecules
  • Microfluidics
  • Energy transfer
  • Electron transfer
  • Photochemistry
  • Photophysics
  • Nanomaterials

Published Papers (9 papers)

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Research

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Open AccessArticle A Simple Bioconjugate Attachment Protocol for Use in Single Molecule Force Spectroscopy Experiments Based on Mixed Self-Assembled Monolayers
Int. J. Mol. Sci. 2012, 13(10), 13521-13541; doi:10.3390/ijms131013521
Received: 22 August 2012 / Revised: 9 September 2012 / Accepted: 29 September 2012 / Published: 19 October 2012
Cited by 3 | PDF Full-text (4127 KB) | HTML Full-text | XML Full-text
Abstract
Single molecule force spectroscopy is a technique that can be used to probe the interaction force between individual biomolecular species. We focus our attention on the tip and sample coupling chemistry, which is crucial to these experiments. We utilised a novel approach of
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Single molecule force spectroscopy is a technique that can be used to probe the interaction force between individual biomolecular species. We focus our attention on the tip and sample coupling chemistry, which is crucial to these experiments. We utilised a novel approach of mixed self-assembled monolayers of alkanethiols in conjunction with a heterobifunctional crosslinker. The effectiveness of the protocol is demonstrated by probing the biotin-avidin interaction. We measured unbinding forces comparable to previously reported values measured at similar loading rates. Specificity tests also demonstrated a significant decrease in recognition after blocking with free avidin. Full article
(This article belongs to the Special Issue Advances in Single Molecule Spectroscopy)
Open AccessArticle Photophysical Behaviors of Single Fluorophores Localized on Zinc Oxide Nanostructures
Int. J. Mol. Sci. 2012, 13(9), 12100-12112; doi:10.3390/ijms130912100
Received: 16 July 2012 / Revised: 6 September 2012 / Accepted: 12 September 2012 / Published: 24 September 2012
Cited by 2 | PDF Full-text (454 KB) | HTML Full-text | XML Full-text
Abstract
Single-molecule fluorescence spectroscopy has now been widely used to investigate complex dynamic processes which would normally be obscured in an ensemble-averaged measurement. In this report we studied photophysical behaviors of single fluorophores in proximity to zinc oxide nanostructures by single-molecule fluorescence spectroscopy and
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Single-molecule fluorescence spectroscopy has now been widely used to investigate complex dynamic processes which would normally be obscured in an ensemble-averaged measurement. In this report we studied photophysical behaviors of single fluorophores in proximity to zinc oxide nanostructures by single-molecule fluorescence spectroscopy and time-correlated single-photon counting (TCSPC). Single fluorophores on ZnO surfaces showed enhanced fluorescence brightness to various extents compared with those on glass; the single-molecule time trajectories also illustrated pronounced fluctuations of emission intensities, with time periods distributed from milliseconds to seconds. We attribute fluorescence fluctuations to the interfacial electron transfer (ET) events. The fluorescence fluctuation dynamics were found to be inhomogeneous from molecule to molecule and from time to time, showing significant static and dynamic disorders in the interfacial electron transfer reaction processes. Full article
(This article belongs to the Special Issue Advances in Single Molecule Spectroscopy)
Open AccessArticle Electric Field Induced Fluorescence Modulation of Single Molecules in PMMA Based on Electron Transfer
Int. J. Mol. Sci. 2012, 13(9), 11130-11140; doi:10.3390/ijms130911130
Received: 12 July 2012 / Revised: 24 August 2012 / Accepted: 24 August 2012 / Published: 6 September 2012
Cited by 8 | PDF Full-text (2308 KB) | HTML Full-text | XML Full-text
Abstract
We present a method to modulate the fluorescence of non-polar single squaraine-derived rotaxanes molecules embedded in a polar poly(methyl methacrylate) (PMMA) matrix under an external electric field. The electron transfer between single molecules and the electron acceptors in a PMMA matrix contributes to
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We present a method to modulate the fluorescence of non-polar single squaraine-derived rotaxanes molecules embedded in a polar poly(methyl methacrylate) (PMMA) matrix under an external electric field. The electron transfer between single molecules and the electron acceptors in a PMMA matrix contributes to the diverse responses of fluorescence intensities to the electric field. The observed instantaneous and non-instantaneous electric field dependence of single-molecule fluorescence reflects the redistribution of electron acceptors in PMMA induced by electronic polarization and orientation polarization of polar polymer chains in an electric field. Full article
(This article belongs to the Special Issue Advances in Single Molecule Spectroscopy)
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Open AccessArticle Early Amyloidogenic Oligomerization Studied through Fluorescence Lifetime Correlation Spectroscopy
Int. J. Mol. Sci. 2012, 13(8), 9400-9418; doi:10.3390/ijms13089400
Received: 19 June 2012 / Revised: 13 July 2012 / Accepted: 19 July 2012 / Published: 25 July 2012
Cited by 11 | PDF Full-text (1372 KB) | HTML Full-text | XML Full-text
Abstract
Amyloidogenic protein aggregation is a persistent biomedical problem. Despite active research in disease-related aggregation, the need for multidisciplinary approaches to the problem is evident. Recent advances in single-molecule fluorescence spectroscopy are valuable for examining heterogenic biomolecular systems. In this work, we have explored
[...] Read more.
Amyloidogenic protein aggregation is a persistent biomedical problem. Despite active research in disease-related aggregation, the need for multidisciplinary approaches to the problem is evident. Recent advances in single-molecule fluorescence spectroscopy are valuable for examining heterogenic biomolecular systems. In this work, we have explored the initial stages of amyloidogenic aggregation by employing fluorescence lifetime correlation spectroscopy (FLCS), an advanced modification of conventional fluorescence correlation spectroscopy (FCS) that utilizes time-resolved information. FLCS provides size distributions and kinetics for the oligomer growth of the SH3 domain of α-spectrin, whose N47A mutant forms amyloid fibrils at pH 3.2 and 37 °C in the presence of salt. The combination of FCS with additional fluorescence lifetime information provides an exciting approach to focus on the initial aggregation stages, allowing a better understanding of the fibrillization process, by providing multidimensional information, valuable in combination with other conventional methodologies. Full article
(This article belongs to the Special Issue Advances in Single Molecule Spectroscopy)
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Open AccessArticle Identification of Intensity Ratio Break Points from Photon Arrival Trajectories in Ratiometric Single Molecule Spectroscopy
Int. J. Mol. Sci. 2012, 13(6), 7445-7465; doi:10.3390/ijms13067445
Received: 19 April 2012 / Revised: 7 June 2012 / Accepted: 12 June 2012 / Published: 18 June 2012
Cited by 2 | PDF Full-text (636 KB) | HTML Full-text | XML Full-text
Abstract
We describe a statistical method to analyze dual-channel photon arrival trajectories from single molecule spectroscopy model-free to identify break points in the intensity ratio. Photons are binned with a short bin size to calculate the logarithm of the intensity ratio for each bin. Stochastic photon counting noise
[...] Read more.
We describe a statistical method to analyze dual-channel photon arrival trajectories from single molecule spectroscopy model-free to identify break points in the intensity ratio. Photons are binned with a short bin size to calculate the logarithm of the intensity ratio for each bin. Stochastic photon counting noise leads to a near-normal distribution of this logarithm and the standard student t-test is used to find statistically significant changes in this quantity. In stochastic simulations we determine the significance threshold for the t-test’s p-value at a given level of confidence.We test the method’s sensitivity and accuracy indicating that the analysis reliably locates break points with significant changes in the intensity ratio with little or no error in realistic trajectories with large numbers of small change points, while still identifying a large fraction of the frequent break points with small intensity changes. Based on these results we present an approach to estimate confidence intervals for the identified break point locations and recommend a bin size to choose for the analysis. The method proves powerful and reliable in the analysis of simulated and actual data of single molecule reorientation in a glassy matrix. Full article
(This article belongs to the Special Issue Advances in Single Molecule Spectroscopy)

Review

Jump to: Research

Open AccessReview Optical Methods to Study Protein-DNA Interactions in Vitro and in Living Cells at the Single-Molecule Level
Int. J. Mol. Sci. 2013, 14(2), 3961-3992; doi:10.3390/ijms14023961
Received: 15 December 2012 / Revised: 13 January 2013 / Accepted: 4 February 2013 / Published: 18 February 2013
Cited by 30 | PDF Full-text (1363 KB) | HTML Full-text | XML Full-text
Abstract
The maintenance of intact genetic information, as well as the deployment of transcription for specific sets of genes, critically rely on a family of proteins interacting with DNA and recognizing specific sequences or features. The mechanisms by which these proteins search for target
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The maintenance of intact genetic information, as well as the deployment of transcription for specific sets of genes, critically rely on a family of proteins interacting with DNA and recognizing specific sequences or features. The mechanisms by which these proteins search for target DNA are the subject of intense investigations employing a variety of methods in biology. A large interest in these processes stems from the faster-than-diffusion association rates, explained in current models by a combination of 3D and 1D diffusion. Here, we present a review of the single-molecule approaches at the forefront of the study of protein-DNA interaction dynamics and target search in vitro and in vivo. Flow stretch, optical and magnetic manipulation, single fluorophore detection and localization as well as combinations of different methods are described and the results obtained with these techniques are discussed in the framework of the current facilitated diffusion model. Full article
(This article belongs to the Special Issue Advances in Single Molecule Spectroscopy)
Open AccessReview Single Molecule Fluorescence Detection and Tracking in Mammalian Cells: The State-of-the-Art and Future Perspectives
Int. J. Mol. Sci. 2012, 13(11), 14742-14765; doi:10.3390/ijms131114742
Received: 30 August 2012 / Revised: 10 October 2012 / Accepted: 8 November 2012 / Published: 13 November 2012
Cited by 10 | PDF Full-text (1337 KB) | HTML Full-text | XML Full-text
Abstract
Insights from single-molecule tracking in mammalian cells have the potential to greatly contribute to our understanding of the dynamic behavior of many protein families and networks which are key therapeutic targets of the pharmaceutical industry. This is particularly so at the plasma membrane,
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Insights from single-molecule tracking in mammalian cells have the potential to greatly contribute to our understanding of the dynamic behavior of many protein families and networks which are key therapeutic targets of the pharmaceutical industry. This is particularly so at the plasma membrane, where the method has begun to elucidate the mechanisms governing the molecular interactions that underpin many fundamental processes within the cell, including signal transduction, receptor recognition, cell-cell adhesion, etc. However, despite much progress, single-molecule tracking faces challenges in mammalian samples that hinder its general application in the biomedical sciences. Much work has recently focused on improving the methods for fluorescent tagging of target molecules, detection and localization of tagged molecules, which appear as diffraction-limited spots in charge-coupled device (CCD) images, and objectively establishing the correspondence between moving particles in a sequence of image frames to follow their diffusive behavior. In this review we outline the state-of-the-art in the field and discuss the advantages and limitations of the methods available in the context of specific applications, aiming at helping researchers unfamiliar with single molecules methods to plan out their experiments. Full article
(This article belongs to the Special Issue Advances in Single Molecule Spectroscopy)
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Open AccessReview Fluorescence Lifetime Correlation Spectroscopy (FLCS): Concepts, Applications and Outlook
Int. J. Mol. Sci. 2012, 13(10), 12890-12910; doi:10.3390/ijms131012890
Received: 15 August 2012 / Revised: 14 September 2012 / Accepted: 19 September 2012 / Published: 9 October 2012
Cited by 20 | PDF Full-text (400 KB) | HTML Full-text | XML Full-text
Abstract
Fluorescence Lifetime Correlation Spectroscopy (FLCS) is a variant of fluorescence correlation spectroscopy (FCS), which uses differences in fluorescence intensity decays to separate contributions of different fluorophore populations to FCS signal. Besides which, FLCS is a powerful tool to improve quality of FCS data
[...] Read more.
Fluorescence Lifetime Correlation Spectroscopy (FLCS) is a variant of fluorescence correlation spectroscopy (FCS), which uses differences in fluorescence intensity decays to separate contributions of different fluorophore populations to FCS signal. Besides which, FLCS is a powerful tool to improve quality of FCS data by removing noise and distortion caused by scattered excitation light, detector thermal noise and detector afterpulsing. We are providing an overview of, to our knowledge, all published applications of FLCS. Although these are not numerous so far, they illustrate possibilities for the technique and the research topics in which FLCS has the potential to become widespread. Furthermore, we are addressing some questions which may be asked by a beginner user of FLCS. The last part of the text reviews other techniques closely related to FLCS. The generalization of the idea of FLCS paves the way for further promising application of the principle of statistical filtering of signals. Specifically, the idea of fluorescence spectral correlation spectroscopy is here outlined. Full article
(This article belongs to the Special Issue Advances in Single Molecule Spectroscopy)
Open AccessReview Photoluminescence Intermittency from Single Quantum Dots to Organic Molecules: Emerging Themes
Int. J. Mol. Sci. 2012, 13(10), 12487-12518; doi:10.3390/ijms131012487
Received: 1 August 2012 / Revised: 11 September 2012 / Accepted: 17 September 2012 / Published: 28 September 2012
Cited by 17 | PDF Full-text (2058 KB) | HTML Full-text | XML Full-text
Abstract
Recent experimental and theoretical studies of photoluminescence intermittency (PI) or “blinking” exhibited by single core/shell quantum dots and single organic luminophores are reviewed. For quantum dots, a discussion of early models describing the origin of PI in these materials and recent challenges to
[...] Read more.
Recent experimental and theoretical studies of photoluminescence intermittency (PI) or “blinking” exhibited by single core/shell quantum dots and single organic luminophores are reviewed. For quantum dots, a discussion of early models describing the origin of PI in these materials and recent challenges to these models are presented. For organic luminophores the role of electron transfer, proton transfer and other photophysical processes in PI are discussed. Finally, new experimental and data analysis methods are outlined that promise to be instrumental in future discoveries regarding the origin(s) of PI exhibited by single emitters. Full article
(This article belongs to the Special Issue Advances in Single Molecule Spectroscopy)
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