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Harnessing intrinsic fluorescence for typing of secondary structures of DNA

Abstract : High-throughput investigation of structural diversity of nucleic acids is hampered by the lack of suitable label-free methods, combining fast and cheap experimental workflow with high information content. Here, we explore the use of intrinsic fluorescence emitted by nucleic acids for this scope. After a preliminary assessment of suitability of this phenomenon for tracking conformational changes of DNA, we examined steady-state emission spectra of an 89-membered set of oligonucleotides with reported conformation (G-quadruplexes (G4s), i-motifs, single-and double-strands) by means of multivariate analysis. Principal component analysis of emission spectra resulted in successful clustering of oligonucleotides into three corresponding conformational groups, without discrimination between single-and double-stranded structures. Linear discriminant analysis was exploited for the assessment of novel sequences, allowing the evaluation of their G4-forming propensity. Our method does not require any labeling agent or dye, avoiding the related bias, and can be utilized to screen novel sequences of interest in a high-throughput and cost-effective manner. In addition, we observed that left-handed (Z-) G4 structures were systematically more fluorescent than most other G4 structures, almost reaching the quantum yield of 5'-[(G3T)3G3]-3' (G3T, the most fluorescent G4 structure reported to date).
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https://hal.archives-ouvertes.fr/hal-03025247
Contributor : Anton Granzhan <>
Submitted on : Thursday, November 26, 2020 - 11:12:45 AM
Last modification on : Friday, December 4, 2020 - 8:31:56 AM

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Michela Zuffo, Aurélie Gandolfini, Brahim Heddi, Anton Granzhan. Harnessing intrinsic fluorescence for typing of secondary structures of DNA. Nucleic Acids Research, Oxford University Press, 2020, 48, pp.e61. ⟨10.1093/nar/gkaa257⟩. ⟨hal-03025247⟩

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