Following hybridization on sensor/array platforms by using SPR, elipsometer and MALDI-MS

Nucleosides Nucleotides Nucleic Acids. 2020;39(7):1057-1072. doi: 10.1080/15257770.2020.1750635. Epub 2020 May 13.

Abstract

The aim of this study is to develop a methodology in which Surface Plasmon Resonance (SPR), Ellipsometer (EM) and Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry (MALDI-MS) will be used together for detection of single-strand oligodeoxynucleotides (ssODNs) targets. A selected target-ssODNs, and its complementary, the probe-ssODNs carrying a -SH end group, a spacer arm (HS-(CH2)6-(T)15, and a non-complementary ssODNs were used. Silicone based stamps with 16 regions were prepared and used for micro-contact printing (µCP) of the probe-ssODNs on the gold coated surfaces homogeneously. A modulator-spacer molecule (6-mercapto-1-hexanol) was co-immobilized to control surface probe density, to orientate the probe-ssODNs, and to eliminate the nonspecific interactions. SPR was used successfully to follow the hybridization of the target-ssODNs with the immobilized probe-ssODNs on the platform surfaces. Complete hybridizations were achieved in 100 min. It was obtained that there was a linear relationship between relative change in delta and target concentration below 1 µm. Using imaging version of ellipsometer (IEM) allowed imaging of the surfaces and supported extra datum for the SPR results. After a very simple dehybridization protocol, MALDI-MS analysis allowed detection of the target-ssODNs hybridized on the sensor/array platforms.

Keywords: Hybridization sensors/arrays; ellipsometer; matrix-assisted laser desorption/ıonization-mass spectrometry; micro-contact printing; self-assembling; surface plasmon resonance.

MeSH terms

  • Biosensing Techniques* / instrumentation
  • DNA, Single-Stranded / analysis*
  • Nucleic Acid Hybridization*
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / instrumentation
  • Surface Plasmon Resonance* / instrumentation

Substances

  • DNA, Single-Stranded