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Hohng, Sungchul,Lee, Sanghwa,Lee, Jinwoo,Jo, Myung Hyun The Royal Society of Chemistry 2014 Chemical Society reviews Vol.43 No.4
<P>Since its first demonstration about twenty years ago, single-molecule fluorescence resonance energy transfer (FRET) has undergone remarkable technical advances. In this tutorial review, we will discuss two technical advances that increase the information content of the single-molecule FRET measurements: single-molecule multi-color FRET and single-molecule FRET combined with force or torque. Our expectations for future developments will be briefly discussed at the end.</P> <P>Graphic Abstract</P><P>Single-molecule multi-color FRET and single-molecule FRET combined with force or torque. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c3cs60184f'> </P>
An Optical Trap Combined with Three-Color FRET
Lee, Sanghwa,Hohng, Sungchul American Chemical Society 2013 JOURNAL OF THE AMERICAN CHEMICAL SOCIETY - Vol.135 No.49
<P>We developed a hybrid technique combining optical tweezers and single-molecule three-color fluorescence resonance energy transfer (FRET). In demonstrative experiments, we observed the force-sensitive correlated motion of three helical arms of a Holliday junction and identified the independent unfolding/folding dynamics of two DNA hairpins of the same length. With 3 times the number of observable elements of single-molecule FRET, this new instrument will enable the measurement of the complex, multidimensional effects of mechanical forces in various biomolecular systems, such as RNA and proteins.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/2013/jacsat.2013.135.issue-49/ja408767p/production/images/medium/ja-2013-08767p_0004.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/ja408767p'>ACS Electronic Supporting Info</A></P>
Arluison, Vé,ronique,Hohng, Sungchul,Roy, Rahul,Pellegrini, Olivier,Ré,gnier, Philippe,Ha, Taekjip Oxford University Press 2007 Nucleic acids research Vol.35 No.3
<P>Hfq protein is vital for the function of many non-coding small (s)RNAs in bacteria but the mechanism by which Hfq facilitates the function of sRNA is still debated. We developed a fluorescence resonance energy transfer assay to probe how Hfq modulates the interaction between a sRNA, DsrA, and its regulatory target mRNA, <I>rpoS</I>. The relevant RNA fragments were labelled so that changes in intra- and intermolecular RNA structures can be monitored in real time. Our data show that Hfq promotes the strand exchange reaction in which the internal structure of <I>rpoS</I> is replaced by pairing with DsrA such that the Shine-Dalgarno sequence of the mRNA becomes exposed. Hfq appears to carry out strand exchange by inducing rapid association of DsrA and a premelted <I>rpoS</I> and by aiding in the slow disruption of the <I>rpoS</I> secondary structure. Unexpectedly, Hfq also disrupts a preformed complex between <I>rpoS</I> and DsrA. While it may not be a frequent event <I>in vivo</I>, this melting activity may have implications in the reversal of sRNA-based regulation. Overall, our data suggests that Hfq not only promotes strand exchange by binding rapidly to both DsrA and <I>rpoS</I> but also possesses RNA chaperoning properties that facilitates dynamic RNA–RNA interactions.</P>
Autofocusing system based on optical astigmatism analysis of single-molecule images.
Hwang, Wonseok,Bae, Sangsu,Hohng, Sungchul Optical Society of America 2012 Optics express Vol.20 No.28
<P>Single-molecule fluorescence imaging has greatly contributed to our understanding of many bio-molecular systems. While reactions occurring in the range of several minutes can be readily studied using conventional single-molecule fluorescence microscopes, data acquisition for longer time scales is hindered by the focal drift of high numerical aperture objectives, which should be corrected in real time. Here, we developed a robust autofocusing system based on optical astigmatism analysis of single-molecule images. Compared to the previously developed methods, our approach has a merit of simplicity in that neither fiducial makers nor an additional laser-detector system is required. As a demonstration, we observed B-Z transition dynamics occurring for several hours.</P>
Z-DNA stabilization is dominated by the Hofmeister effect
Bae, Sangsu,Son, Heyjin,Kim, Yang-Gyun,Hohng, Sungchul The Royal Society of Chemistry 2013 Physical chemistry chemical physics Vol.15 No.38
<P>The manner in which Z-DNA is stabilized at high salt concentrations remains unclear. Here, we systematically examine the Z-DNA-stabilizing capabilities of different salts. The strong correlation between the double-stranded DNA denaturation and B-to-Z transition efficiencies indicates that Z-DNA is mainly stabilized by the Hofmeister effect.</P> <P>Graphic Abstract</P><P>Z-DNA is stabilized mainly by the Hofmeister effect of salts rather than by the electrostatic screening effects of salts. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c3cp52047a'> </P>
Hwang, Wonseok,Arluison, Vé,ronique,Hohng, Sungchul Oxford University Press 2011 Nucleic acids research Vol.39 No.12
<P>Hfq is a key regulator involved in multiple aspects of stress tolerance and virulence of bacteria. There has been an intriguing question as to how this RNA chaperone achieves two completely opposite functions—annealing and unwinding—for different RNA substrates. To address this question, we studied the Hfq-mediated interaction of fragments of a non-coding RNA, DsrA, with its mRNA target <I>rpoS</I> by using single-molecule fluorescence techniques. These experiments permitted us to observe the mechanistic steps of Hfq-mediated RNA annealing/unwinding at the single-molecule level, for the first time. Our real-time observations reveal that, even if the ring-shaped Hfq displays multiple binding sites for its interaction with RNA, the regulatory RNA and the mRNA compete for the same binding site. The competition makes the RNA-Hfq interaction dynamic and, surprisingly, increases the overall annealing efficiency by properly aligning the two RNAs. We furthermore reveal that when Hfq specifically binds to only one of the two RNAs, the unwinding process dominates over the annealing process, thus shedding a new light on the substrate selectivity for annealing or unwinding. Finally, our results demonstrate for the first time that a single Hfq hexamer is sufficient to facilitate sRNA–mRNA annealing.</P>
Kim, D. S.,Yoon, Y. C.,Hohng, S. C.,Malyarchuk, V.,Lienau, Ch.,Park, J. W.,Kim, J. H.,Park, Q. H. Optical Society of Korea 2002 Current Optics and Photonics Vol.6 No.3
Nanoscopic emission from periodic nano-hole arrays in thick metal films is studied experimentally. The experiments give direct evidence for SP excitations in such structures. We show that the symmetry of the emission is governed by polarization and its shape is defined the interference of SP waves of different diffraction orders. Near-Held pattern analysis combined with the far-Held reflection and transmission measurements suggests that the SP eigenmodes of these arrays may be understood as those of ionic plasmon molecules.
Hidden complexity in the isomerization dynamics of Holliday junctions
Hyeon, Changbong,Lee, Jinwoo,Yoon, Jeseong,Hohng, Sungchul,Thirumalai, D. Nature Publishing Group 2012 Nature chemistry Vol.4 No.11
A plausible consequence of the rugged folding energy landscapes inherent to biomolecules is that there may be more than one functionally competent folded state. Indeed, molecule-to-molecule variations in the folding dynamics of enzymes and ribozymes have recently been identified in single-molecule experiments, but without systematic quantification or an understanding of their structural origin. Here, using concepts from glass physics and complementary clustering analysis, we provide a quantitative method to analyse single-molecule fluorescence resonance energy transfer (smFRET) data, thereby probing the isomerization dynamics of Holliday junctions, which display such heterogeneous dynamics over a long observation time (T<SUB>obs</SUB>????40?s). We show that the ergodicity of Holliday junction dynamics is effectively broken and that their conformational space is partitioned into a folding network of kinetically disconnected clusters. Theory suggests that the persistent heterogeneity of Holliday junction dynamics is a consequence of internal multiloops with varying sizes and flexibilities frozen by Mg<SUP>2+</SUP> ions. An annealing experiment using Mg<SUP>2+</SUP> pulses lends support to this idea by explicitly showing that interconversions between trajectories with different patterns can be induced.