Detection of Human Immunodeficiency Virus Type 1 DNA Sequence Using Plasmonics Nanoprobes

Abstract

This paper describes the use of plasmonics-based nanoprobes that act as molecular sentinels for DNA diagnostics. The plasmonics nanoprobe comprises a metal nanoparticle and a stem-loop DNA molecule tagged with a Raman label. The nanoprobe utilizes the specificity and selectivity of the DNA hairpin probe sequence to detect a specific target DNA sequence of interest. In the absence of target DNA, the stem-loop configuration maintains the Raman label in proximity to the metal nanoparticle, inducing an intense surface-enhanced Raman scattering (SERS) effect that produces a strong Raman signal upon laser excitation. Upon hybridization of a complementary target DNA sequence to the nanoprobe, the stem-loop configuration is disrupted, causing the Raman label to physically separate from the metal nanoparticle, thus quenching the SERS signal. The usefulness and potential application of the plasmonics nanoprobe for diagnosis is demonstrated using the gag gene sequence of the human immunodeficiency virus type 1 (HIV-1). We successfully demonstrated the specificity and selectivity of the plasmonics nanoprobes to detect PCR amplicons of the HIV gene. The potential for combining the spectral selectivity and high sensitivity of the SERS process with inherent molecular specificity of DNA hairpins to diagnose molecular target sequences in homogeneous solutions is discussed.

Single-Molecule Studies on Fluorescently Labeled Silver Particles: Effects of Particle Size

“…17,18 The actual loading number of fluorophores per metal particle could be estimated quantitatively when dissolving the metal core with NaCN aqueous solution. 37 The released fluorophore-labeled oligonucleotide was observed to display an identical emission spectrum to the free oligonucleotide in the absence of metal, and the concentration of the released fluorophore was estimated from the emission intensity. The value was 0.3, indicating that more than half of the metal particles were not labeled, indeed as we expected.…”

Raman spectroscopy: techniques and applications in the life sciences

“…bacterial communication) metabolite see Figure 27(b) [327]. At an even smaller scale, DNA sequences from the HIV virus were identified using AgNP SERS particles conjugated with specific DNAtargeting ligands [328].…”

Existing Biosensing Platforms for the Nucleotide Markers Detection

“…In the Surface-Enhanced Raman Scattering Spectroscopy spectrum, the same dyes have narrower signals that potentially makes it possible to use a greater number of reporter groups in the system, and, hence, to identify a larger number of analytes in a multiplex assay [28]. The identification of the analyzed DNA sequence based both on the appearance of the Surface-Enhanced Raman Scattering Spectroscopy signal [29], and its disappearance [30], for example, by using hairpin DNA probes carrying the SERS-active label and immobilized on the gold nanoparticles (similar to the 'molecular beacons') is possible ( Figure 3). Increasing the sensitivity analysis of DNA detection by SERS method is implemented using gold nanoparticles, and signal gain is sought by depositing silver metal on their surface ( Figure 4) [28].…”