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Dynamic competition of DsrA and rpoS fragments for the proximal binding site of Hfq as a means for efficient annealing
Wonseok Hwang, Veronique Arluison, Sungchul Hohng
Abstract
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…
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Intrinsic Z-DNA Is Stabilized by the Conformational Selection Mechanism of Z-DNA-Binding Proteins
Sangsu Bae, Doyoun Kim, Kyeong Kyu Kim, Yang-Gyun Kim, Sungchul Hohng
Abstract
Z-DNA, a left-handed isoform of Watson and Crick’s B-DNA, is rarely formed without the help of high salt concentrations or negative supercoiling. However, Z-DNA-binding proteins can efficiently convert specific sequences of the B conformation into the Z conformation in relaxed DNA under physiological salt conditions. As in the case of many other specific interactions coupled…
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Single-molecule four-color FRET
Jinwoo Lee, Sanghwa Lee, Kaushik Ragunathan, Chirlmin Joo, Taekjip Ha, Sungchul Hohng
Abstract
Six interfluorophore FRET efficiencies Eij (see scheme) can be determined in real time by a single-molecule four-color FRET technique both in confocal and in total-internal-reflection fluorescence microscopy. This technique was used to probe the correlated motion of the four arms of the Holliday junction, and to assess correlation of RecA-mediated strand exchange events at both…
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Single-Molecule Three-Color FRET with Both Negligible Spectral Overlap and Long Observation Time
Sanghwa Lee, Jinwoo Lee, Sungchul Hohng
Abstract
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…
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Highly Polymorphic G-quadruplexes in the c-MYC Promoter
Jeong-Min Yoon, Hyun-Jin Kang, Jae-Ho Sung, Hyun-Ju Park, Sung-Chul Hohng
Abstract
Guanine-rich tracts are frequently found in various regions of genomic DNA such as telomeres, centromeres, and promoters of proto-oncogenes, but rarely in the promoter of tumor-suppressor genes. When a G-tract has more than four G-stretches, it can form a G-quadruplex, a non-Watson-Crick DNA structure stabilized by a successive stacking of guanine tetrads. Guanine tetrad is…
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Single-molecule FRET studies on frameshifting RNA structures of human immunodeficiency virus
Hee-Sun Hong, Yang-Gyun Kim, Sung-Chul Hohng
Abstract
Correspondence between DNA sequences and its protein product is not straightforward because the genetic information can be dynamically reprogrammed during various steps of genetic decoding process. The programmed -1 ribosomal frameshifting (-1PRF) is an example of such genetic recoding mechanisms, where the reading frame of the translation machinery is shifted toward -1 direction at a…