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Sub-Nanomolar Detection of Oligonucleotides Using Molecular Beacons Immobilized on Lightguiding Nanowires

Johansson, Therese B. LU ; Davtyan, Rubina LU ; Valderas-Gutiérrez, Julia LU orcid ; Gonzalez Rodriguez, Adrian LU ; Agnarsson, Björn ; Munita, Roberto LU ; Fioretos, Thoas LU ; Lilljebjörn, Henrik LU orcid ; Linke, Heiner LU orcid and Höök, Fredrik LU , et al. (2024) In Nanomaterials 14(5).
Abstract

The detection of oligonucleotides is a central step in many biomedical investigations. The most commonly used methods for detecting oligonucleotides often require concentration and amplification before detection. Therefore, developing detection methods with a direct read-out would be beneficial. Although commonly used for the detection of amplified oligonucleotides, fluorescent molecular beacons have been proposed for such direct detection. However, the reported limits of detection using molecular beacons are relatively high, ranging from 100 nM to a few µM, primarily limited by the beacon fluorescence background. In this study, we enhanced the relative signal contrast between hybridized and non-hybridized states of the beacons by... (More)

The detection of oligonucleotides is a central step in many biomedical investigations. The most commonly used methods for detecting oligonucleotides often require concentration and amplification before detection. Therefore, developing detection methods with a direct read-out would be beneficial. Although commonly used for the detection of amplified oligonucleotides, fluorescent molecular beacons have been proposed for such direct detection. However, the reported limits of detection using molecular beacons are relatively high, ranging from 100 nM to a few µM, primarily limited by the beacon fluorescence background. In this study, we enhanced the relative signal contrast between hybridized and non-hybridized states of the beacons by immobilizing them on lightguiding nanowires. Upon hybridization to a complementary oligonucleotide, the fluorescence from the surface-bound beacon becomes coupled in the lightguiding nanowire core and is re-emitted at the nanowire tip in a narrower cone of light compared with the standard 4π emission. Prior knowledge of the nanowire positions allows for the continuous monitoring of fluorescence signals from each nanowire, which effectively facilitates the discrimination of signals arising from hybridization events against background signals. This resulted in improved signal-to-background and signal-to-noise ratios, which allowed for the direct detection of oligonucleotides at a concentration as low as 0.1 nM.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
lightguiding, limit of detection, molecular beacons, nanowires, oligonucleotides
in
Nanomaterials
volume
14
issue
5
article number
453
publisher
MDPI AG
external identifiers
  • pmid:38470783
  • scopus:85187452181
ISSN
2079-4991
DOI
10.3390/nano14050453
language
English
LU publication?
yes
id
bdfb4150-7375-44ae-b820-804017a6c927
date added to LUP
2024-04-05 15:01:08
date last changed
2025-05-18 07:25:15
@article{bdfb4150-7375-44ae-b820-804017a6c927,
  abstract     = {{<p>The detection of oligonucleotides is a central step in many biomedical investigations. The most commonly used methods for detecting oligonucleotides often require concentration and amplification before detection. Therefore, developing detection methods with a direct read-out would be beneficial. Although commonly used for the detection of amplified oligonucleotides, fluorescent molecular beacons have been proposed for such direct detection. However, the reported limits of detection using molecular beacons are relatively high, ranging from 100 nM to a few µM, primarily limited by the beacon fluorescence background. In this study, we enhanced the relative signal contrast between hybridized and non-hybridized states of the beacons by immobilizing them on lightguiding nanowires. Upon hybridization to a complementary oligonucleotide, the fluorescence from the surface-bound beacon becomes coupled in the lightguiding nanowire core and is re-emitted at the nanowire tip in a narrower cone of light compared with the standard 4π emission. Prior knowledge of the nanowire positions allows for the continuous monitoring of fluorescence signals from each nanowire, which effectively facilitates the discrimination of signals arising from hybridization events against background signals. This resulted in improved signal-to-background and signal-to-noise ratios, which allowed for the direct detection of oligonucleotides at a concentration as low as 0.1 nM.</p>}},
  author       = {{Johansson, Therese B. and Davtyan, Rubina and Valderas-Gutiérrez, Julia and Gonzalez Rodriguez, Adrian and Agnarsson, Björn and Munita, Roberto and Fioretos, Thoas and Lilljebjörn, Henrik and Linke, Heiner and Höök, Fredrik and Prinz, Christelle N.}},
  issn         = {{2079-4991}},
  keywords     = {{lightguiding; limit of detection; molecular beacons; nanowires; oligonucleotides}},
  language     = {{eng}},
  number       = {{5}},
  publisher    = {{MDPI AG}},
  series       = {{Nanomaterials}},
  title        = {{Sub-Nanomolar Detection of Oligonucleotides Using Molecular Beacons Immobilized on Lightguiding Nanowires}},
  url          = {{http://dx.doi.org/10.3390/nano14050453}},
  doi          = {{10.3390/nano14050453}},
  volume       = {{14}},
  year         = {{2024}},
}