Structural Recognition of Triple-Stranded DNA by Surface-Enhanced Raman Spectroscopy

Abstract

Direct, label-free analysis of nucleic acids via surface-enhanced Raman spectroscopy (SERS) has been continuously expanding its range of applications as an intriguing and powerful analytical tool for the structural characterization of diverse DNA structures. Still, interrogation of nucleic acid tertiary structures beyond the canonical double helix often remains challenging. In this work, we report for the first time the structural identification of DNA triplex structures. This class of nucleic acids has been attracting great interest because of their intriguing biological functions and pharmacological potential in gene therapy, and the ability for precisely engineering DNA-based functional nanomaterials. Herein, structural discrimination of the triplex structure against its duplex and tertiary strand counterparts is univocally revealed by recognizing key markers bands in the intrinsic SERS fingerprint. These vibrational features are informative of the base stacking, Hoogsteen hydrogen bonding and sugar–phosphate backbone reorganization associated with the triple helix formation. This work expands the applicability of direct SERS to nucleic acids analysis, with potential impact on fields such as sensing, biology and drug design.

Artificial Intelligence‐Assisted Label‐Free Spectroscopic Quantification of Global DNA Cytosine Methylation in a Miniature Plasmonic Pickering Emulsion

“…In addition to the molecular signatures from the nucleobases, both canonical dNMPs and d 5m CMP also show two consistent SERS bands located at ≈1022 and ≈1060 cm −1 , which are assigned to the C─O stretching vibration ( v (C─O)) mode of deoxyribose and the PO 2 − stretching vibration ( v (PO 2 − )) mode of the phosphate backbone, respectively (Figure 4B and Table S2, Supporting Information). [ 38,48 ] The results from the PCA analysis obviously show different clusters for dCMP and d 5m CMP (Figure 4C); in addition to the negative 789 cm −1 SERS peak, we also observed the shifting of the v (C═N) mode from 1496 to 1454 cm −1 after C 5 ‐methylation (Figure 4B,C). The heatmap from the unsupervised HCA analysis verifies the 100% accuracy for pristine dAMP, dGMP, and dTMP, and 95% accuracy for pristine dCMP and d 5m CMP (Figure 4D).…”

“…As is well-known, the SERS spectrum of a DNA strand is enriched with spectral signatures of its deoxyribonucleotide components including deoxyribose, phosphate backbone, and the four canonical nucleobases. [38,39] In this work, we utilize the remarkable features of the SERS technique, such as ultrahigh sensitivity and molecular signatures, to spectrally identify and quantify DNA cytosine methylation. The plasmonic Pickering emulsions, comprising a DNAcontaining aqueous droplet covered with a shell of hydrophobic Au nanostars (AuSts) in the immiscible n-decane, are constructed and employed as the biosensing platform.…”

Resonance Hyper-Raman Spectroscopy of Nucleotides and Polynucleotides

“…Among biomolecules, deoxyribonucleic acid (DNA) is considered to be a suitable target for demonstrating the benefits of HR spectroscopy because (i) the 532 nm excitation matches the two-photon resonance condition to the electronic absorption of the nucleobases near 260 nm, (ii) unique HR bands may offer new markers for the structure analysis of DNA, and (iii) accumulated knowledge of DNA studies using vibrational spectroscopy is available, e.g., studies on the backbone structures of double-stranded A-, B-, and Z-DNA, triple-stranded DNA, , the quadruplex, , thermal denaturation, metal coordination, − and the enzyme–DNA interaction. , To determine if HR spectroscopy benefits DNA structure analysis, it is of interest to compare the spectral pattern of DNA obtained with HR and conventional vibrational spectroscopy. Of particular interest is the comparison with UV-resonance Raman (UVRR) spectroscopy because it can perform site-selective structure analysis with the aid of resonance enhancement.…”