Structural Features of DNA G-Quadruplexes Revealed by Surface-Enhanced Raman Spectroscopy

Abstract

Surface-enhanced Raman spectroscopy (SERS) has been successfully used for the label-free detection of single-stranded oligonucleotides. However, the detection of complex DNA secondary structures remains a challenge. Structural features of diverse DNA G-quadruplexes were investigated via a novel SERS method. As a result, a series of highly reproducible and sensitive SERS signatures featuring the structures of G-quadruplexes were obtained. For the first time, we reported remarkably enhanced SERS bands corresponding to purine ring breathing vibrations. Moreover, we observed that by measuring the intensity of the bands corresponding to intramolecular hydrogen bonds, we could quantitatively assess the stability of the G-quadruplexes. Because no labels on DNA strands were present as the experiments were carried out in the solution, the fingerprint peaks reflect the native, internal structure of the G-quadruplexes accurately. The method here detailed provides new insights into the promising applications of diverse DNA structural studies.

Infrared Spectroscopy Reveals the Preferred Motif Size and Local Disorder in Parallel Stranded DNA G‐Quadruplexes

“…Assuming idealized structures, each additional guanine in the sequence would result in one additional G‐quartet layer in the stack (Figure 1b). However, because polyguanine tracts can fold into G‐quadruplexes with diverse conformations, [1c,11,18] the formation of ideal tetramers is not guaranteed.…”

“…Although vibrational spectra provide lower resolution information than NMR or X‐ray crystallography, they are largely insensitive to sample morphology and are thus useful probes of local structures in complex samples [15] . In recent studies of G‐quadruplexes, FTIR, [16] vibrational circular dichroism (VCD), [17] and surface‐enhanced Raman spectroscopy (SERS) [18] have used shifts in the guanine C6=O6 carbonyl stretch, near 1700 cm −1 , to monitor their formation. These shifts have been alternately attributed to C=O bond lengthening upon metal coordination and Hoogsteen hydrogen‐bonding, along with generalized base “stacking” effects [14b,16–18] .…”

“…In recent studies of G‐quadruplexes, FTIR, [16] vibrational circular dichroism (VCD), [17] and surface‐enhanced Raman spectroscopy (SERS) [18] have used shifts in the guanine C6=O6 carbonyl stretch, near 1700 cm −1 , to monitor their formation. These shifts have been alternately attributed to C=O bond lengthening upon metal coordination and Hoogsteen hydrogen‐bonding, along with generalized base “stacking” effects [14b,16–18] . These interpretations invoke local interactions of individual bases but ignore coupling effects that delocalize vibrations among multiple bases within ordered arrays.…”

Raman Scattering: From Structural Biology to Medical Applications

“…In addition, SERS enhanced sensitivity was used not only to study ss-and dsDNA, but also such DNA complexes as quadruplexes. The authors of recent work [170] claimed the availability of quantitative assessment of the stability of G-quadruplexes. Qian et al [171] developed in situ DNA-metallization, while using a glass slide to fasten a peptide nucleic acid as a recognition probe to be used in the detection procedure.…”

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

“…This enabled the application of SERS as an ultrasensitive analytical approach for the structural characterization of (bio)molecular species as well as sensing tool for their detection and quantification [11][12][13]. However, while the use of SERS in indirect approaches for nucleic acids sensing has been extensively dealt with in the literature, its wider use as an ultrasensitive analytical tool for this class of biomolecules via the acquisition of their intrinsic SERS vibrational fingerprinting (i.e., direct SERS) has been traditionally far less explored, until relatively recently [14][15][16][17][18][19][20][21][22]. Our group devised a novel approach based on the use of positively charged silver colloids as plasmonic-enhancers which successfully tackled prior issues associated with the reproducible acquisition of reliable SERS spectra of nucleic acids at low concentrations [19,23,24].…”