Conformational Details of Quantum Dot-DNA Resolved by Förster Resonance Energy Transfer Lifetime Nanoruler

Abstract

DNA-nanoparticle conjugates are important tools in nanobiotechnology. Knowing the orientation, function, and length of DNA on nanoparticle surfaces at low nanomolar concentrations under physiological conditions is therefore of great interest. Here, we investigate the conformation of a 31 nucleotides (nt) long DNA attached to a semiconductor quantum dot (QD) via Forster resonance energy transfer (FRET) from Tb-DNA probes hybridized to different positions on the QD-DNA. Precise Tb-to-QD distance determination from 7 to 14 nm along 26 nt of the peptide-appended QD-DNA was realized by time-resolved FRET spectroscopy. The FRET nanoruler measured linear single-stranded (ssDNA) and double-stranded (dsDNA) extensions of ∼0.15 and ∼0.31 nm per base, reflecting the different conformations. Comparison with biomolecular modeling confirmed the denser conformation of ssDNA and a possibly more flexible orientation on the QD surface, whereas the dsDNA was fully extended with radial orientation. The temporally distinct photoluminescence decays of the different DNA-FRET configurations were used for prototypical DNA hybridization assays that demonstrated the large potential for extended temporal multiplexing. The extensive experimental and theoretical analysis of 11 different distances/configurations of the same QD-DNA conjugate provided important information on DNA conformation on nanoparticle surfaces and will be an important benchmark for the development and optimization of DNA-nanobiosensors.

Förster resonance energy transfer (FRET) paired carbon dot-based complex nanoprobes: versatile platforms for sensing and imaging applications

“…Förster resonance energy transfer (FRET) is the mechanism by which non-radiative energy is transferred between a luminescent donor and an energy acceptor within a close range of approximately 10 to 100 Å. [1][2][3] FRET can be easily measured in standard bulk fluorescence experiments. FRET can also be monitored using fluorescence microscopy techniques, including single-molecule fluorescence spectroscopy.…”

Upconversion Luminescence Sandwich Assay For Detection of Influenza H7 Subtype

“…[10,11] It is the fact that organic dyes are widely used in conventional qPCR assays via downconversion processes. [18][19][20] The excitation may induce background fluorescence and broad emission peaks, contributing to severe cross-talking problem. [14] Therefore, they were usually employed as quenchers in nanoparticle-based detection systems.…”

“…[14] Therefore, they were usually employed as quenchers in nanoparticle-based detection systems. [18][19][20] The excitation may induce background fluorescence and broad emission peaks, contributing to severe cross-talking problem. [18][19][20] The excitation may induce background fluorescence and broad emission peaks, contributing to severe cross-talking problem.…”

Distance-Dependence Study of Plasmon Resonance Energy Transfer with DNA Spacers

“…As we all know, under the premise of donor–receptor energy matching, the distance ( d ) between the donor and the acceptor is significant to the efficiency of the energy transfer, which is also the widely involved key point in most of the application designs. For instance, nanosurface energy transfer (NSET) causing quenching of the fluorescence intensity follows 1/ d 4 distance dependence. − The FRET efficiency is proportional to 1/ d 6 . , In addition, light signals exhibit high sensitivity to small changes in d in surface-enhanced Raman scattering (SERS) optical rulers. − As light–matter interactions, PRET originating from the coupling of the plasmonic resonance surface dipole of nanoparticles and the quantized electronic energy levels of molecules should also be distance dependent.…”

“…22−24 The FRET efficiency is proportional to 1/d 6 . 25,26 In addition, light signals exhibit high sensitivity to small changes in d in surface-enhanced Raman scattering (SERS) optical rulers. 27−32 As light−matter interactions, PRET originating from the coupling of the plasmonic resonance surface dipole of nanoparticles and the quantized electronic energy levels of molecules should also be distance dependent.…”