Modulating Fluorescence Anisotropy of Terminally Labeled Double-Stranded DNA via the Interaction between Dye and Nucleotides for Rational Design of DNA Recognition Based Applications

Abstract

Effective signal enhancement for fluorescence anisotropy in a simple manner is most desirable for fluorescence anisotropy method development. This work aimed to provide insights into the fluorescence anisotropy of terminally labeled double-stranded DNA (dsDNA) to facilitate a facile and universal design strategy for DNA recognition based applications. We demonstrated that fluorescence anisotropy of dsDNA could be regulated by the nature of dyes, the molecular volume, and the end structure of dsDNA. Fluorescence anisotropy ascended with the increased number of base pairs up to 18 bp and leveled off thereafter, indicating the molecular volume was not the only factor responsible for fluorescence anisotropy. By choosing dyes with the positively charged center, high fluorescence anisotropy signal was obtained due to the confinement of the segmental motion of dyes through the electrostatic interaction. By properly designing the end structure of dsDNA, fluorescence anisotropy could be further improved by enlarging the effective overall rotational volume, as supported by two-dimensional (2D) (1)H-(1)H nuclear Overhauser enhancement spectroscopy (NOESY). With the successful enhancement of the fluorescence anisotropy for terminally labeled dsDNA, simple and universal designs were demonstrated by sensing of major classes of analytes from macromolecules (DNA and protein) to small molecules (cocaine).

Deoxyribonucleic Acid Photonic Wires with Three Primary Color Emissions for Information Encryption

“…In addition, the fluorescence anisotropy of 0–B–0 further identified homo‐FRET with the assembly of AO (B) on DNA scaffolds (Figure S3, Supporting Information). [ 16 ] That is, the DNA PWs could realize directional photon energy transfer and color adjustment via energy transfer on DNA.…”

DNA oligomer binding in competition exhibits cooperativity

“…The technique is useful in clinical domains for detection of drugs or toxins in food. In biology FA enables the study of molecular binding among DNA strands and/or proteins [55][56][57][58][59][60][61]. A FA measurement relies on the increase in emission polarisation anisotropy of fluorescently labeled molecules as a measure of the slowdown of Brownian rotation caused by formation of molecular complexes.…”

“…A common approach to enhance the signal-to-noise ratio if small molecules are involved is to increase the molecular volume through DNA-binding proteins or nanoparticles. However, sometimes this strategy renders the interpretation of the observed anisotropy more difficult [25,56,[62][63][64]. Moreover the influence of the particular fluorophore, the choice of an appropriate labeling site and the interaction between fluorophore and binding partner are factors that need to be considered.…”

Competitive fluorescence anisotropy/polarization assay for ATP using aptamer as affinity ligand and dye-labeled ATP as fluorescence tracer

“…Direct FA assays for small molecules using dye-labeled aptamers usually rely on the binding-induced structure change [11] or change of interaction between labeled dye and bases of aptamer [12,13]. To increase change in molecular size during affinity binding for FA signal generation and amplification, large biomolecules (e.g., proteins and oligonucleotides) or nanomaterials (e.g., silica nanoparticles and graphene) have been used in indirect aptamer-based FA assays for small molecules [9,10,[15][16][17][18].…”