Limitations of Surface Enhanced Raman Scattering in Sensing DNA Hybridization Demonstrated by Label-Free DNA Oligos as Molecular Rulers of Distance-Dependent Enhancement

Abstract

This article presents a critical evaluation of silver nanorod arrays as substrates for assaying nucleic acid hybridization by surface enhanced Raman scattering (SERS). SERS spectra acquired on complementary oligos, alone or in combination, contain the known spectral signatures of the nucleotides that comprise the oligo; however, no signature bands characteristic of the hybrid were observed. Spectra acquired on an oligo with a 5'- or 3'-thiol were distinctly different from that acquired on the identical oligo without a thiol pendant group suggesting a degree of control over the orientation of the oligo on the nanorod surface. A set of oligos consisting of adenine tracts in a polycytosine chain served as molecular rulers to probe the distance dependence of the SERS enhancement. Using these, we have identified the point at which the characteristic bands for the nucleotides that comprise the oligo disappear from the spectrum. These findings suggest that the applicability of SERS for label-free detection of nucleic acid hybridization is limited to short oligos of less than nine nucleotides.

Direct Surface‐Enhanced Raman Scattering Analysis of DNA Duplexes

“…Vibrational assignment of dsDNA was based on literature references and comparative spectral analysis with homo-and bi-polymeric sequences (Section S3). In contrast with previous results on negatively charged colloids (Section S4), [13] when the individual ss units hybridize into the ds a large reshaping of their SERS spectra is observed (Figure 1 c), influencing peak position, bandwidths, and relative intensity. Notably, if ss1 and ssc spectra show small changes in relative intensity that are associated with the base composition, the stacking and pairing of the nucleobases into the hybridized native structure is revealed by several characteristic features of the Raman melting profiles.…”

DNA-functionalized gold nanoparticle assemblies for Surface Enhanced Raman Scattering

“…The orientation of the DNA molecules is known to critically affect the SERS spectral shape, mostly in the 1200-1600 cm −1 region (high-frequency side of Figure 5) and in correspondence of the adenine band at 730 cm −1 [20]. Fortunately, the use of thiolated molecules reduces this variability [31], resulting in a less pronounced spectral modification in the present case compared to Refs. [20,30].…”

Spiky gold shells on magnetic particles for DNA biosensors

“…[31,[49][50][51][52][53] To determine which future applications of the particles would be possible or ideal, it is important to characterize the distance dependence specific to the particles. Other researchers have used oligonucleotide "rulers" to characterize the distance-dependence enhancement; [49,50,53] as the actual 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 12 relationship between enhancement and distance from the surface will vary with different substrates, [51] oligonucleotide rulers were used to characterize the relationship for the spiky particle surfaces. We bound seven different thiolated oligonucleotides to the particles, each featuring three adenine bases at different positions within a series of cytosine bases (Table 1i-vii), as well as an all cytosine oligonucleotide for a baseline (Table 1viii).…”