Single-Molecule Three-Color FRET with Both Negligible Spectral Overlap and Long Observation Time

Full understanding of complex biological interactions frequently requires multi-color detection capability in doing single-molecule fluorescence resonance energy transfer (FRET) experiments. Existing single-molecule three-color FRET techniques, however, suffer from severe photobleaching of Alexa 488, or its alternative dyes, and have been limitedly used for kinetics studies. In this work, we developed a single-molecule three-color FRET technique based on the Cy3-Cy5-Cy7 dye trio, thus providing enhanced observation time and improved data quality. Because the absorption spectra of three fluorophores are well separated, real-time monitoring of three FRET efficiencies was possible by incorporating the alternating laser excitation (ALEX) technique both in confocal microscopy and in total-internal-reflection fluorescence (TIRF) microscopy

One at a time, live tracking of NGF axonal transport using quantum dots

Retrograde axonal transport of nerve growth factor (NGF) signals is critical for the survival, differentiation, and maintenance of peripheral sympathetic and sensory neurons and basal forebrain cholinergic neurons. However, the mechanisms by which the NGF signal is propagated from the axon terminal to the cell body are yet to be fully elucidated. To gain insight into the mechanisms, we used quantum dot-labeled NGF (QD-NGF) to track the movement of NGF in real time in compartmentalized culture of rat dorsal root ganglion (DRG) neurons. Our studies showed that active transport of NGF within the axons was characterized by rapid, unidirectional movements interrupted by frequent pauses. Almost all movements were retrograde, but short-distance anterograde movements were occasionally observed. Surprisingly, quantitative analysis at the single molecule level demonstrated that the majority of NGF-containing endosomes contained only a single NGF dimer. Electron microscopic analysis of axonal vesicles carrying QD-NGF confirmed this finding. The majority of QD-NGF was found to localize in vesicles 50–150 nm in diameter with a single lumen and no visible intralumenal membranous components. Our findings point to the possibility that a single NGF dimer is sufficient to sustain signaling during retrograde axonal transport to the cell body

Efficient preparation of internally modified single-molecule constructs using nicking enzymes

Investigations of enzymes involved in DNA metabolism have strongly benefited from the establishment of single molecule techniques. These experiments frequently require elaborate DNA substrates, which carry chemical labels or nucleic acid tertiary structures. Preparing such constructs often represents a technical challenge: long modified DNA molecules are usually produced via multi-step processes, involving low efficiency intermolecular ligations of several fragments. Here, we show how long stretches of DNA (>50 bp) can be modified using nicking enzymes to produce complex DNA constructs. Multiple different chemical and structural modifications can be placed internally along DNA, in a specific and precise manner. Furthermore, the nicks created can be resealed efficiently yielding intact molecules, whose mechanical properties are preserved. Additionally, the same strategy is applied to obtain long single-strand overhangs subsequently used for efficient ligation of ss- to dsDNA molecules. This technique offers promise for a wide range of applications, in particular single-molecule experiments, where frequently multiple internal DNA modifications are required

FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices

Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current ‘state of the art’ from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of ‘soft recommendations’ about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage ‘open science’ practices

Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes

Assembly of 30S ribosomes involves the hierarchical addition of ribosomal proteins that progressively stabilize the folded 16S rRNA. Here, we use three-color single molecule FRET to show how combinations of ribosomal proteins uS4, uS17 and bS20 in the 16S 5' domain enable the recruitment of protein bS16, the next protein to join the complex. Analysis of real-time bS16 binding events shows that bS16 binds both native and non-native forms of the rRNA. The native rRNA conformation is increasingly favored after bS16 binds, explaining how bS16 drives later steps of 30S assembly. Chemical footprinting and molecular dynamics simulations show that each ribosomal protein switches the 16S conformation and dampens fluctuations at the interface between rRNA subdomains where bS16 binds. The results suggest that specific protein-induced changes in the rRNA dynamics underlie the hierarchy of 30S assembly and simplify the search for the native ribosome structure

Quantum dots coordinated with conjugated organic ligands: new nanomaterials with novel photophysics

CdSe quantum dots functionalized with oligo-(phenylene vinylene) (OPV) ligands (CdSe-OPV nanostructures) represent a new class of composite nanomaterials with significantly modified photophysics relative to bulk blends or isolated components. Single-molecule spectroscopy on these species have revealed novel photophysics such as enhanced energy transfer, spectral stability, and strongly modified excited state lifetimes and blinking statistics. Here, we review the role of ligands in quantum dot applications and summarize some of our recent efforts probing energy and charge transfer in hybrid CdSe-OPV composite nanostructures

Universal emission intermittency in quantum dots, nanorods, and nanowires

Virtually all known fluorophores, including semiconductor nanoparticles, nanorods and nanowires exhibit unexplainable episodes of intermittent emission blinking. A most remarkable feature of the fluorescence intermittency is a universal power law distribution of on- and off-times. For nanoparticles the resulting power law extends over an extraordinarily wide dynamic range: nine orders of magnitude in probability density and five to six orders of magnitude in time. The exponents hover about the ubiquitous value of -3/2. Dark states routinely last for tens of seconds, which are practically forever on quantum mechanical time scales. Despite such infinite states of darkness, the dots miraculously recover and start emitting again. Although the underlying mechanism responsible for this phenomenon remains an enduring mystery and many questions remain, we argue that substantial theoretical progress has been made.Comment: 9 pages, 2 figures, Accepted versio

Probing and controlling fluorescence blinking of single semiconductor nanoparticles

In this review we present an overview of the experimental and theoretical development on fluorescence intermittency (blinking) and the roles of electron transfer in semiconductor crystalline nanoparticles. Blinking is a very interesting phenomenon commonly observed in single molecule/particle experiments. Under continuous laser illumination, the fluorescence time trace of these single nanoparticles exhibit random light and dark periods. Since its first observation in the mid-1990s, this intriguing phenomenon has attracted wide attention among researchers from many disciplines. We will first present the historical background of the discovery and the observation of unusual inverse power-law dependence for the waiting time distributions of light and dark periods. Then, we will describe our theoretical modeling efforts to elucidate the causes for the power-law behavior, to probe the roles of electron transfer in blinking, and eventually to control blinking and to achieve complete suppression of the blinking, which is an annoying feature in many applications of quantum dots as light sources and fluorescence labels for biomedical imaging

Two-color picosecond and continuous-wave experiments on anti-Stokes and Stokes carrier-transfer phenomena in GaAslAl(x)Ga(1-x)As and InGaP2/AlxGa1-xAs heterostructures

We present direct evidence of the two-step absorption process in anti-Stokes photoluminescence in both GaAs/AlxGa1-xAs and InGaP2/AlxGa1-xAs heterostructures using two-color picosecond and continuous-wave photoluminescence experiments. We show information about the lifetime of the defect states that participate in the two-step absorption process. As a result, we conclude that the long-lived states rather than excitons play the dominant role in the two-step absorption process. We also study the possible contribution of the two-step absorption process to Stokes carrier transfer in GaAs/AlxGa1-xAs asymmetric double quantum well structuresclos