Person: Chong, Shasha
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Chong
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Shasha
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Chong, Shasha
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Publication Detection of Single-Molecule Optical Absorption at Room Temperature and Mechanistic Study of Transcriptional Bursting(2014-06-06) Chong, Shasha; Xie, Xiaoliang Sunney; Lieber, Charles; Zhuang, XiaoweiAdvances in optical imaging techniques have allowed quantitative studies of many biological systems. This dissertation elaborates on our efforts in both developing novel imaging modalities based on detection of optical absorption and applying high-sensitivity fluorescence microscopy to the study of biology.Publication Mechanism of Transcriptional Bursting in Bacteria(2015-08-07) Chong, Shasha; Xie, XiaoliangPublication Probing Allostery through DNA(American Association for the Advancement of Science, 2013) Kim, Sangjin; Broströmer, Erik; Jin, Jianshi; Chong, Shasha; Ge, Hao; Wang, Siyuan; Gu, Chan; Yang, Lijiang; Gao, Yi Qin; Su, Xiao-dong; Sun, Yujie; Xie, Xiaoliang; Xing, DongAllostery is well documented for proteins but less recognized for DNA-protein interactions. Here, we report that specific binding of a protein on DNA is substantially stabilized or destabilized by another protein bound nearby. The ternary complex's free energy oscillates as a function of the separation between the two proteins with a periodicity of ~10 base pairs, the helical pitch of B-form DNA, and a decay length of ~15 base pairs. The binding affinity of a protein near a DNA hairpin is similarly dependent on their separation, which—together with molecular dynamics simulations—suggests that deformation of the double-helical structure is the origin of DNA allostery. The physiological relevance of this phenomenon is illustrated by its effect on gene expression in live bacteria and on a transcription factor's affinity near nucleosomes.Publication Imaging Chromophores With Undetectable Fluorescence by Stimulated Emission Microscopy(Nature Publishing Group, 2009) Min, Wei; Lu, Sijia; Chong, Shasha; Roy, Rahul; Holtom, Gary; Xie, XiaoliangFluorescence, that is, spontaneous emission, is generally more sensitive than absorption measurement, and is widely used in optical imaging. However, many chromophores, such as haemoglobin and cytochromes, absorb but have undetectable fluorescence because the spontaneous emission is dominated by their fast non-radiative decay. Yet the detection of their absorption is difficult under a microscope. Here we use stimulated emission, which competes effectively with the nonradiative decay, to make the chromophores detectable, and report a new contrast mechanism for optical microscopy. In a pump-probe experiment, on photoexcitation by a pump pulse, the sample is stimulated down to the ground state by a time-delayed probe pulse, the intensity of which is concurrently increased. We extract the miniscule intensity increase with shot-noise-limited sensitivity by using a lock-in amplifier and intensity modulation of the pump beam at a high megahertz frequency. The signal is generated only at the laser foci owing to the nonlinear dependence on the input intensities, providing intrinsic three-dimensional optical sectioning capability. In contrast, conventional one-beam absorption measurement exhibits low sensitivity, lack of three-dimensional sectioning capability, and complication by linear scattering of heterogeneous samples. We demonstrate a variety of applications of stimulated emission microscopy, such as visualizing chromoproteins, non-fluorescent variants of the green fluorescent protein, monitoring lacZ gene expression with a chromogenic reporter, mapping transdermal drug distributions without histological sectioning, and label-free microvascular imaging based on endogenous contrast of haemoglobin. For all these applications, sensitivity is orders of magnitude higher than for spontaneous emission or absorption contrast, permitting nonfluorescent reporters for molecular imaging.