Distinction of nucleobases – a tip-enhanced Raman approach

Abstract

SummaryThe development of novel DNA sequencing methods is one of the ongoing challenges in various fields of research seeking to address the demand for sequence information. However, many of these techniques rely on some kind of labeling or amplification steps. Here we investigate the intrinsic properties of tip-enhanced Raman scattering (TERS) towards the development of a novel, label-free, direct sequencing method. It is known that TERS allows the acquisition of spectral information with high lateral resolution and single-molecule sensitivity. In the presented experiments, single stranded adenine and uracil homopolymers were immobilized on different kinds of substrates (mica and gold nanoplates) and TERS experiments were conducted, which demonstrated the reproducibility of the technique. To elucidate the signal contributions from the specific nucleobases, TERS spectra were collected on single stranded calf thymus DNA with arbitrary sequence. The results show that, while the Raman signals with respect to the four nucleobases differ remarkably, specific markers can be determined for each respective base. The combination of sensitivity and reproducibility shows that the crucial demands for a sequencing procedure are met.

Tip-enhanced Raman scattering—Targeting structure-specific surface characterization for biomedical samples

“…Such measurement pushed the detection limit of TERS to give straightforward access to all four nucleobases-a crucial requirement for DNA structure analysis with TERS. Numerous studies on pure nucleobases have been performed on nm-sized crystals of thymine and cytosine, adenine, and uracil homopolymers immobilized on mica and gold islands substrates [95]. A valuable report focused on the detection of hydrogen bonding between the single crystalline DNA base pairs (adenine (A) and thymine (T)) on a gold surface [96].…”

Raman spectroscopy: techniques and applications in the life sciences

“…One of the first biological demonstrations of this type of TERS measurement was on a single RNA strand measured using AFM-TERS in ambient conditions [364]. Here it was suggested the spatial evolution of the spectra along the strand could be used as a direct indicator of the base-pair sequence see Figure 29(a) and was later also demonstrated for DNA strands [365].…”

Tip enhanced Raman scattering: plasmonic enhancements for nanoscale chemical analysis

“…The hydrogen bonding between adenine and thymine bases was detected by spectral changes [127]. Changes in modes observed in nucleic acids have also Unauthenticated Download Date | 5/10/18 11:40 AM been attributed to the orientation of the molecules on the surface [128].…”