DNA Methylation Detection Using Resonance and Nanobowtie-Antenna-Enhanced Raman Spectroscopy

Li, Ling; Lim, Shuang Fang; Puretzky, Alexander; Riehn, Robert; Hallen, Hans D.

doi:10.1016/j.bpj.2018.04.021

Title: DNA Methylation Detection Using Resonance and Nanobowtie-Antenna-Enhanced Raman Spectroscopy

Journal Article · Thu Jun 07 00:00:00 EDT 2018 · Biophysical Journal

DOI:https://doi.org/10.1016/j.bpj.2018.04.021· OSTI ID:1468193

Li, Ling ^[1]; Lim, Shuang Fang ^[1]; Puretzky, Alexander ^[2]; Riehn, Robert ^[1]; Hallen, Hans D. ^[1]

North Carolina State Univ., Raleigh, NC (United States). Dept. of Physics
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Sciences

In this paper, we show that DNA carrying 5-methylcytosine modifications or methylated DNA (m-DNA) can be distinguished from DNA with unmodified cytosine by Raman spectroscopy enhanced by both a bowtie nanoantenna and excitation resonance. In particular, m-DNA can be identified by a peak near 1000 cm^-1 and changes in the Raman peaks in the 1200–1700 cm^-1 band that are enhanced by the ring-absorption resonance. The identification is robust to the use of resonance Raman and nanoantenna excitation used to obtain significant signal improvement. The primary differences are three additional Raman peaks with methylation at 1014, 1239, and 1639 cm^-1 and spectral intensity inversion at 1324 (C₅=C₆) and 1473 cm^-1 (C₄=N₃) in m-DNA compared to that of DNA with unmodified cytosine. We attribute this to the proximity of the methyl group to the antenna, which brings the (C₅=C₆) mode closer to experiencing a stronger near-field enhancement. We also show distinct Raman spectral features attributed to the transition of DNA from a hydrated state, when dissolved, to a dried/denatured state. We observe a general broadening of the larger lines and a transfer of spectral weight from the ~1470 cm^-1 vibration to the two higher-energy lines of the dried m-DNA solution. We attribute the new spectral characteristics to DNA softening under high salt conditions and find that the m-DNA is still distinguishable via the ~1000 cm^-1 peak and distribution of the signal in the 1200–1700 cm^-1 band. The nanoantenna gain exceeds 20,000, whereas the real signal ratio is much less because of a low average enhanced region occupancy even with these relatively high DNA concentrations. It is improved when fixed DNA in a salt crystal lies near the nanoantenna. Finally, the Raman resonance gain profile is consistent with A-term expectations, and the resonance is found at ~259 nm excitation wavelength.

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Research Organization:: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); North Carolina State University, Raleigh, NC (United States)

Sponsoring Organization:: USDOE Office of Science (SC); National Inst. of Health (NIH) (United States); National Science Foundation (NSF)

Grant/Contract Number:: AC05-00OR22725; R21CA13207; CBET 1067508

OSTI ID:: 1468193

Journal Information:: Biophysical Journal, Vol. 114, Issue 11; ISSN 0006-3495

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 15 works

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