Approach to the Investigation of Nucleosome Structure by Using the Highly Emissive Nucleobase ^thdG–tC FRET Pair

Abstract

A distance- and orientation-factor-dependent FRET system is a useful and attractive approach to the investigation of the conformational dynamics of nucleosomes. In this study, the application of the highly emissive nucleobase dG-tC FRET pair to 601 nucleosomes is reported. It was found that the dG-tC FRET pair was successfully incorporated to 145 bp 601 sequences, and different FRET efficiencies were obtained for the designated donor and acceptor positions in the nucleosome.

Nucleosomes and Epigenetics from a Chemical Perspective

“…b) Stepwise manner in DNA translocation mediated by RSC [121] . c) Using nucleosomal DNA containing the thdG‐tC FRET pair, the FRET efficiency can be changed by placing the donor and acceptor at different positions [122] …”

New Size‐Expanded Fluorescent Thymine Analogue: Synthesis, Characterization, and Application

“…Chemical modifications are required to retain their structuralr esemblance to natural nucleobases and allow native Watson-Crick base pairing. [18][19][20][21][22] The quinazolines tructure is also one of the most useful fluorescent cores. [14][15][16][17] We have focused on exploitingt he potential of isomorphic emissive DNA analogues based on at hieno [3,4-d]pyrimidine core.…”

“…[14][15][16][17] We have focused on exploitingt he potential of isomorphic emissive DNA analogues based on at hieno [3,4-d]pyrimidine core. [18][19][20][21][22] The quinazolines tructure is also one of the most useful fluorescent cores. Quinazoline-derived fluorescent nucleobases have been developed by fusion of the electron-rich ring into electron-deficientp yrimidine and used as fluorescent probes.…”

“…For instance, Tor and co‐workers developed isomorphic fluorescent RNA nucleosides derived from thieno[3,4‐ d ]‐pyrimidine and demonstrated their usefulness in various studies including mechanistic investigations of RNA catalysis and RNA structural analysis . We have focused on exploiting the potential of isomorphic emissive DNA analogues based on a thieno[3,4‐ d ]‐pyrimidine core . The quinazoline structure is also one of the most useful fluorescent cores.…”

Highly sensitive and selective mercury sensor based on mismatched base pairing with dioxT

“…[12][13][14][15] Fluorescent nucleobase analogues are powerful and important tools in the chemical biology of nucleic acids, and their applications have enabled a variety of investigations, [16][17][18] such as single-molecule polymorphism, 19 monitoring of structural changes, 20,21 elucidating enzyme activities, 22,23 and the development of the orientation-sensitive FRET system. 24,25 Another advantage of fluorescent nucleobase analogues compared with conventional dyes, such as Cy3, Alexa dyes, FAM, and Texas Red, is that they are particularly useful to investigate the properties of the local structures of nucleic acids. Despite these advantages, the use of fluorescent nucleobase analogues and of their specific metal-binding interactions in the generation of metal sensors is relatively uncommon.…”