Effect of short chain alkane diluents on the label free electrochemical DNA hybridization discrimination at the HS-ssDNA/diluent binary mixed monolayer in presence of cationic intercalators

Influence of short chain alkane diluents (number of carbons, n = 2, 3 and 6) on the control of non-specific DNA-gold (DNA-Au) interactions and hybridization discrimination effect has been investigated at the binary monolayer interface consisting of 6-mercapto-1-hexane labeled single stranded DNA (HS-ssDNA) and a diluent (HS-ssDNA/diluent) in presence of double stranded DNA (dsDNA) specific cationic intercalators and [Fe(CN)6]3−. The diluents used are 1-mercaptopropane (MP), 3-mercaptopropionic acid (MPA), Cystamine, 1-mercapto ethanol (MCE) and 6-mercapto-1-hexanol (MCH). Label free electrochemical DNA hybridization discrimination of the complementary hybrid (hybridized) and non-complementary (un-hybridized) surfaces has been made comparatively in presence of the [Fe(CN)6]3− and dsDNA specific intercalators, such as proflavine and methylene blue. Prior to the target hybridization, the control of non-specific DNA-Au interaction is interrogated by monitoring the integrity of the HS-ssDNA monolayer in presence of the [Fe(CN)6]3− before and after the HS-ssDNA/diluent binary interface formation. Change in the peak-to-peak separation (ΔEp), taken as a measure of the control of the non-specific DNA-Au interactions, follows the order MP < MCH < MPA. But the hybridization discrimination effect, measured as the difference in the total charge passed through the hybridized and un-hybridized layer in presence of the Fe(CN)63− and intercalator, follows the reverse order MPA < MCH < MP. These contrasting behaviors are related to the different interactions of hydrophobic and/or hydrophilic diluents with the hydrophobic HS-ssDNA while forming the binary recognition interface. Reductive desorption voltammetry of these binary interfaces in 0.5 M KOH evidences the formation of highly compact layer in presence of MP and MCH diluents and defective layer in presence of MPA diluent by the difference in their reductive desorption pattern and supports the observed phenomenon. Brain tumor sequence is used as the model system and the lowest target concentration of 100 pM is detected sensitively and selectively at these binary monolayers.