Quantitative enhanced raman scattering of dye-labeled phosphorothioate oligonucleotide

Abstract

For the diagnosis and treatment of genetic diseases and infections the detection of specific DNA sequences is important. New techniques are continually being designed to improve selectivity, sensitivity reliability and multiplexing of current DNA detection methodologies. One of these methods is surface-enhanced resonance Raman spectroscopy (SERRS) which has been used successfully as an ultrasensitive technique for the direct analysis of dye-labelled oligonucleotides using aggregated silver and gold nanoparticles. Key to the sensitivity and reproducibility is the affinity of the DNA towards the enhancing surface. This paper investigates the detection of phosphorothioate modified dye-labelled oligonucleotides whereby a non-bridging oxygen atom in the phosphodiester backbone is replaced by sulfur. TAMRA-labelled phosphorothioate oligonucleotides with the same base pair sequence but different number of modified phosphate units were compared to un-modified TAMRA-labelled oligonucleotides using silver nanoparticles as SERRS substrates using a 532 nm excitation wavelengths and different aggregation agents. This study demonstrates the importance of choosing the right experimental setup for DNA SERRS analysis to maximise sensitivity and reproducibility when oligonucleotides are modified for greater surface affinity.