• International Journal of Oral Biology
• /
• v.43 no.2
• /
• pp.53-59
• /
• 2018

In order to understand biological phenomena accurately, single molecule techniques using a physical research approach to molecular interactions have been developed, and are now widely being used to study complex biological processes. In this review, we discuss some of the single molecule methods which are composed of two major parts: single molecule spectroscopy and manipulation. In particular, we explain how these techniques work and introduce the current research which uses them. Finally, we present the oral biology research using the single molecule methods.

• Journal of the Optical Society of Korea
• /
• v.12 no.2
• /
• pp.107-111
• /
• 2008

We demonstrated single-molecule fluorescence resonance energy transfer (FRET) from single donor-acceptor dye pair attached to a DNA with a setup based on a confocal microscope. Singlestrand DNAs were immobilized on a glass surface with suitable inter-dye distance. Energy transfer efficiency between the donor and the acceptor dyes attached to the DNA was measured with different lengths of DNA. Photobleaching of single dye molecule was observed and used as a sign of single-molecule detection. We could achieve high enough signal-to-noise ratio to detect the fluorescence from a single-molecule, which allows real-time observation of the distance change between single dye pairs in nanometer scale.

• BMB Reports
• /
• v.52 no.10
• /
• pp.589-594
• /
• 2019

Single-molecule techniques have been used successfully to visualize real-time enzymatic activities, revealing transient complex properties and heterogeneity of various biological events. Especially, conventional force spectroscopy including optical tweezers and magnetic tweezers has been widely used to monitor change in DNA length by enzymes with high spatiotemporal resolutions of ~nanometers and ~milliseconds. However, DNA metabolism results from coordination of a number of components during the processes, requiring efficient monitoring of a complex of proteins catalyzing DNA substrates. In this min-review, we will introduce a simple and multiplexed single-molecule assay to detect DNA substrates catalyzed by enzymes with high-throughput data collection. We conclude with a perspective of possible directions that enhance capability of the assay to reveal complex biological events with higher resolution.

• Molecules and Cells
• /
• v.45 no.1
• /
• pp.33-40
• /
• 2022

The various DNA-protein interactions associated with the expression of genetic information involve double-stranded DNA (dsDNA) bending. Due to the importance of the formation of the dsDNA bending structure, dsDNA bending properties have long been investigated in the biophysics field. Conventionally, DNA bendability is characterized by innate averaging data from bulk experiments. The advent of single-molecule methods, such as atomic force microscopy, optical and magnetic tweezers, tethered particle motion, and single-molecule fluorescence resonance energy transfer measurement, has provided valuable tools to investigate not only the static structures but also the dynamic properties of bent dsDNA. Here, we reviewed the single-molecule methods that have been used for investigating dsDNA bendability and new findings related to dsDNA bending. Single-molecule approaches are promising tools for revealing the unknown properties of dsDNA related to its bending, particularly in cells.

• Bulletin of the Korean Chemical Society
• /
• v.33 no.3
• /
• pp.980-986
• /
• 2012

In this paper we develop a minimalist model of single molecule spectroscopy in a dynamic environment. Our model is based upon a lattice system consisting of a probe molecule embedded in an Ising-model like environment. We assume that the probe molecule interacts with the Ising spins via a dipole-dipole potential, and calculate free energy curves and lineshapes of the system. To investigate fluctuation behavior of the system we exploit the metadynamics sampling method. In particular, using the method, we calculate the free energy curve of magnetization of the lattice and that of the transition energy of the probe molecule. Furthermore, we compare efficiencies of three different sampling methods used; unbiased, umbrella, and metadynamics sampling methods. Finally, we explore the lineshape behavior of the probe molecule as the system undergoes a phase transition from a sub-critical and to a super-critical temperature. We show that the transition energy of a probe molecule is broadly distributed due to the heterogeneous, local environments.

• Bulletin of the Korean Chemical Society
• /
• v.32 no.6
• /
• pp.1849-1850
• /
• 2011

• Bulletin of the Korean Chemical Society
• /
• v.33 no.3
• /
• pp.958-962
• /
• 2012

In single-molecule fluorescence experiment, the oxygen scavenging system is indispensable for avoiding photo-bleaching of fluorescent dyes. Here we report that the gloxy-based oxygen scavenging system commonly used in single molecule fluorescence experiments can disturb the solution pH considerably. To track in situ pH change, we utilized the pH-sensitive conformational transition of i-motif and examined the transition with ensemble and single-molecule FRET measurements. Based on our results, we also suggested several practical remedies for the stability of the solution pH.

• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
• /
• 2003.05c
• /
• pp.120-123
• /
• 2003

To investigate the characteristics of the single dendrimer molecule, we attempt to measure morphology and electrical properties of the self-assembled dendrimer on Au (111)substrate with SPM(scanning probe microscopy). The same self-assembly procedure was used for two different concentrations, $10{\mu}mol/ml$ and $100{\mu}mol/ml$. The case of lower concentration, we can measure the diameter and the height of the single molecule with the tapping mode AFM image. The imaged single molecules were dome shaped and the average diameter and height were 15.6 nm, 1.2 nm respectively. From these sizes, we can calculate the volume of the single molecule. The volume of the single molecule was estimated about $116nm^3$. However, that of higher concentration, it is difficult to obtain obvious image of the single molecule. To add to, I-V characteristics were investigated using STM, on which the phenomenon of negative differential resistance (NDR)was observed between 0.14 V and 0.24 V reproductively.

• Proceedings of the Korean Vacuum Society Conference
• /
• 2013.02a
• /
• pp.654-654
• /
• 2013

One of the most important yet unresolved problems in molecular electronics is the controversy over the number and nature of multiple conductance peaks in single-molecule junctions. Currently, there are three competing explanations of this observation: (1) manifestation of different molecule-electrode contact geometries, (2) formation of gauche defects within the molecular core, (3) involvement of different electrode surface orientations [1]. However, the exact origin of multiple conductance peaks is not yet fully understood, which indicates our incomplete understanding of the scientifically as well as techno-logically important organic-metal contacts. To theoretically resolve this problem, we previously applied a multiscale computational approach that combines force fields molecular dynamics (FF MD), density functional theory (DFT), and matrix Green's function (MGF) calculations [2] to a thermally fluctuating haxanedithiol (C6DT) molecule stretched between flat Au(111) electrodes, but could observe only a single conductance peak [3]. In this presentation, using DFT geometry optimizations and MGF calculations, we consider molecular junctions with more realistic molecule-metal contact conformations and Au(111) electrode surface directions. We also conduct DFT-based molecular dynamics for the highly stretched junction models to confirm our conclusion. We conclude that the S-Au coordination number should be the more dominant factor than the electrode surface orientation.

• Journal of Photoscience
• /
• v.11 no.32
• /
• pp.47-53
• /
• 2004

A laser scanning fluorescence microscope system has been fabricated for single molecule detection (SMD). Problems associated with the system set-up have been discussed along with proper suggestions. Based on the SMD results obtained by using the apparatus, a statistical method has been suggested to determine the minimum number of required molecules to form a group of uniform average in a selected error range.