Studying Z-DNA and B- to Z-DNA transitions using a cytosine analogue FRET-pair

Dumat, Blaise; Larsen, Anders Foller; Wilhelmsson, L. Marcus

doi:10.1093/nar/gkw114

Cited by 50 publications

(43 citation statements)

References 41 publications

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“…1–16 Recent highlights include Tor’s isomorphic RNA alphabet, 17,18 Wilhelmsson’s internucleobase FRET pair, 12,19 Sasaki’s fluorescent sensors for nucleobase damage, 20 and a number of examples of nucleobase surrogates that can report on events in the major groove, such as protein binding. 21,22 Still, significant unmet needs persist.…”

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confidence: 99%

Fluorescence Turn-On Sensing of DNA Duplex Formation by a Tricyclic Cytidine Analogue

et al. 2017

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Most fluorescent nucleoside analogues are quenched when base stacked and some maintain their brightness, but there has been little progress toward developing nucleoside analogues that markedly increase their fluorescence upon duplex formation. Here, we report on the design and synthesis of a new tricyclic cytidine analogue, 8-diethylamino-tC (8-DEA-tC), that responds to DNA duplex formation with up to a 20-fold increase in fluorescent quantum yield as compared with the free nucleoside, depending on neighboring bases. This turn-on response to duplex formation is the greatest of any reported nucleoside analogue that can participate in Watson–Crick base pairing. Measurements of the quantum yield of 8-DEA-tC mispaired with adenosine and, separately, opposite an abasic site show that there is almost no fluorescence increase without the formation of correct Watson–Crick hydrogen bonds. Kinetic isotope effects from the use of deuterated buffer show that the duplex protects 8-DEA-tC against quenching by excited state proton transfer. These results, supported by DFT calculations, suggest a rationale for the observed photophysical properties that is dependent on duplex integrity and the electronic structure of the analogue.

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confidence: 99%

Fluorescence Turn-On Sensing of DNA Duplex Formation by a Tricyclic Cytidine Analogue

et al. 2017

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“…In these two constructs the individual U and P elements were cloned in different spatial arrangements. Fis and H-NS were purified as previously described (69,70).…”

Section: Constructsmentioning

confidence: 99%

DNA sequence-directed cooperation between nucleoid-associated proteins

Japaridze

Yang

Dekker

et al. 2020

Preprint

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Nucleoid associated proteins (NAPs) are a class of highly abundant DNA binding proteins in bacteria and archaea. While the composition and relative abundance of the NAPs change during the bacterial growth cycle, surprisingly little is known about their crosstalk in mutually binding to the bacterial chromosome and stabilising higher-order nucleoprotein complexes. Here, we use atomic force microscopy and solid-state nanopores to investigate longrange nucleoprotein structures formed by the binding of two major NAPs, FIS and H-NS, to DNA molecules with distinct binding-site arrangements. We find that spatial organisation of the protein binding sites can govern the higher-order architecture of the nucleoprotein complexes. Based on sequence arrangement the complexes differed in their global shape and compaction, as well as the extent of FIS and H-NS binding. Our observations highlight the important role the DNA sequence plays in driving structural differentiations within the bacterial chromosome.

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“…[20] Comparedw ith conventionalF RET systems,i nw hich dyes rotate randomly, th dG and tC with replaceable native nucleobases can be fixed by not only stacking interactions betweenn eighboring bases, but also hydrogen bondingw ith counter bases in the complementary strand. [16,[19][20][21] As ac onsequence, the efficiencyo ft his FRET method is dependent on the distance between the donora nd the acceptor and on ar elative orientation factor,w hich leads to significant changesi nF RET efficiency in contrastw ith the previousFRET systems with randomly rotating dyes.…”

Section: Introductionmentioning

confidence: 99%

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

Han

Park

Hashiya

et al. 2018

Chemistry A European J

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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.

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Studying Z-DNA and B- to Z-DNA transitions using a cytosine analogue FRET-pair

Cited by 50 publications

References 41 publications

Fluorescence Turn-On Sensing of DNA Duplex Formation by a Tricyclic Cytidine Analogue

Fluorescence Turn-On Sensing of DNA Duplex Formation by a Tricyclic Cytidine Analogue

DNA sequence-directed cooperation between nucleoid-associated proteins

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

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Studying Z-DNA and B- to Z-DNA transitions using a cytosine analogue FRET-pair

Cited by 50 publications

References 41 publications

Fluorescence Turn-On Sensing of DNA Duplex Formation by a Tricyclic Cytidine Analogue

Fluorescence Turn-On Sensing of DNA Duplex Formation by a Tricyclic Cytidine Analogue

DNA sequence-directed cooperation between nucleoid-associated proteins

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

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