Research on fluorescent semiconductor nanocrystals (also known as quantum dots or qdots) has evolved over the past two decades from electronic materials science to biological applications. We review current approaches to the synthesis, solubilization, and functionalization of qdots and their applications to cell and animal biology. Recent examples of their experimental use include the observation of diffusion of individual glycine receptors in living neurons and the identification of lymph nodes in live animals by near-infrared emission during surgery. The new generations of qdots have farreaching potential for the study of intracellular processes at the single-molecule level, high-resolution cellular imaging, long-term in vivo observation of cell trafficking, tumor targeting, and diagnostics.

/pdf/quantum-dots-for-live-cells-in-vivo-imaging-and-diagnostics-3y9ayecoh8.pdf

Quantum Dots for Live Cells, in Vivo Imaging, and Diagnostics

One of the fastest moving and most exciting interfaces of nanotechnology is the use of quantum dots (QDs) in biology. The unique optical properties of QDs make them appealing as in vivo and in vitro fluorophores in a variety of biological investigations, in which traditional fluorescent labels based on organic molecules fall short of providing long-term stability and simultaneous detection of multiple signals. The ability to make QDs water soluble and target them to specific biomolecules has led to promising applications in cellular labelling, deep-tissue imaging, assay labelling and as efficient fluorescence resonance energy transfer donors. Despite recent progress, much work still needs to be done to achieve reproducible and robust surface functionalization and develop flexible bioconjugation techniques. In this review, we look at current methods for preparing QD bioconjugates as well as presenting an overview of applications. The potential of QDs in biology has just begun to be realized and new avenues will arise as our ability to manipulate these materials improves.

Quantum dot bioconjugates for imaging, labelling and sensing

The term photonic crystals appears because of the analogy between electron waves in crystals and the light waves in artificial periodic dielectric structures. During the recent years the investigation of one-, two-and three-dimensional periodic structures has attracted a widespread attention of the world optics community because of great potentiality of such structures in advanced applied optical fields. The interest in periodic structures has been stimulated by the fast development of semiconductor technology that now allows the fabrication of artificial structures, whose period is comparable with the wavelength of light in the visible and infrared ranges.

http://ieeexplore.ieee.org/iel5/6354/16969/00781867.pdf

Photonic crystals

MicroRNAs (miRNAs) are a class of non-coding RNAs that play important roles in regulating gene expression. The majority of miRNAs are transcribed from DNA sequences into primary miRNAs and processed into precursor miRNAs, and finally mature miRNAs. In most cases, miRNAs interact with the 3' untranslated region (3' UTR) of target mRNAs to induce mRNA degradation and translational repression. However, interaction of miRNAs with other regions, including the 5' UTR, coding sequence, and gene promoters, have also been reported. Under certain conditions, miRNAs can also activate translation or regulate transcription. The interaction of miRNAs with their target genes is dynamic and dependent on many factors, such as subcellular location of miRNAs, the abundancy of miRNAs and target mRNAs, and the affinity of miRNA-mRNA interactions. miRNAs can be secreted into extracellular fluids and transported to target cells via vesicles, such as exosomes, or by binding to proteins, including Argonautes. Extracellular miRNAs function as chemical messengers to mediate cell-cell communication. In this review, we provide an update on canonical and non-canonical miRNA biogenesis pathways and various mechanisms underlying miRNA-mediated gene regulations. We also summarize the current knowledge of the dynamics of miRNA action and of the secretion, transfer, and uptake of extracellular miRNAs.

/pdf/overview-of-microrna-biogenesis-mechanisms-of-actions-and-2lluskbdwf.pdf

Overview of MicroRNA Biogenesis, Mechanisms of Actions, and Circulation.

Surface plasmons (SPs) are coherent oscillations of conduction electrons on a metal surface excited by electromagnetic radiation at a metal -dielectric interface. The growing field of research on such light -metal interactions is known as ‘plasmonics’. 1-3 This branch of research has attracted much attention due to its potential applications in miniaturized optical devices, sensors, and photonic circuits as well as in medical diagnostics and therapeutics. 4-8

Nanostructured plasmonic sensors.

Single-molecule fluorescence resonance energy transfer (smFRET) is one of the most general and adaptable single-molecule techniques. Despite the explosive growth in the application of smFRET to answer biological questions in the last decade, the technique has been practiced mostly by biophysicists. We provide a practical guide to using smFRET, focusing on the study of immobilized molecules that allow measurements of single-molecule reaction trajectories from 1 ms to many minutes. We discuss issues a biologist must consider to conduct successful smFRET experiments, including experimental design, sample preparation, single-molecule detection and data analysis. We also describe how a smFRET-capable instrument can be built at a reasonable cost with off-the-shelf components and operated reliably using well-established protocols and freely available software.

/pdf/a-practical-guide-to-single-molecule-fret-3blag506ll.pdf

A practical guide to single-molecule FRET

Colloidal semiconductor quantum dots are attractive fluorophores for multicolor imaging because of broad absorption and narrow emission spectra, and they are brighter and far more photostable than organic dyes. However, severe intermittence in emission (also known as blinking) has been universally observed from single dots and has been considered an intrinsic limitation difficult to overcome. This is unfortunate because growing applications in spectroscopy of single biological molecules and quantum information processing using single photon sources could greatly benefit from long-lasting and nonblinking single-molecule emitters. For instance, in a recent application of single-dot imaging, the tracking of membrane receptors was interrupted frequently due to the stroboscopic nature of recording. Blinking can also reduce the brightness in ensemble imaging via signal saturation. Here we show that the quantum dot blinking can be suppressed with the emission duty cycle approaching 100% while maintaining biocomp...

Near-complete suppression of quantum dot blinking in ambient conditions.

Functional Anatomy of the Human Microprocessor

Single-molecule three-color FRET.

Despite the recent advances in single-molecule manipulation techniques, purely mechanical approaches cannot detect subtle conformational changes in the biologically important regime of weak forces. We developed a hybrid scheme combining force and fluorescence that allowed us to examine the effect of subpiconewton forces on the nanometer scale motion of the Holliday junction (HJ) at 100-hertz bandwidth. The HJ is an exquisitely sensitive force sensor whose force response is amplified with an increase in its arm lengths, demonstrating a lever-arm effect at the nanometer-length scale. Mechanical interrogation of the HJ in three different directions helped elucidate the structures of the transient species populated during its conformational changes. This method of mapping two-dimensional reaction landscapes at low forces is readily applicable to other nucleic acid systems and their interactions with proteins and enzymes.

/pdf/fluorescence-force-spectroscopy-maps-two-dimensional-8r3jk97ths.pdf

Sungchul Hohng

Papers

A practical guide to single-molecule FRET

Near-complete suppression of quantum dot blinking in ambient conditions.

Functional Anatomy of the Human Microprocessor

Single-molecule three-color FRET.

Fluorescence-Force Spectroscopy Maps Two-Dimensional Reaction Landscape of the Holliday Junction