Effect of the DNA End of Tethering to Electrodes on Electron Transfer in Methylene Blue-Labeled DNA Duplexes

Abstract

Electron transfer (ET) in redox-labeled double-stranded (ds) DNA tethered to electrodes through the alkanethiol linker at either the 3' or 5' DNA end and bearing methylene blue (MB) conjugated to the opposite end of DNA is shown to depend on the DNA end of tethering to electrodes. For 3' tethering, a nanoscale diffusion of the positively charged MB redox probe (and thus of the individual DNA molecules) to the negatively charged electrode surface provided the highest apparent diffusion and ET rates as a result of the tilting of 3'-tethered DNA (as compared to 5'-tethered DNA) versus the normal to the surface. Dynamic values of the tilting angle varied between 57 and 45° for 16-mer and 22-mer 3'-tethered DNA, and 5'-tethering was correlated with an upright orientation of DNA at the electrode surface. The values of the diffusion coefficient D(MB) corrected for tilting angles were similar for 5'- and 3'-tethered DNA and ranged between 5.4 × 10(-12) and 2.5 × 10(-12) cm(2) s(-1), whereas the ET rate constant k(ET)(dif) fit the 4.7 × 10(-6)-10.3 × 10(-6) cm s(-1) range for 22-mer and 16-mer dsDNA, respectively. Those values, when related to the nanometer (10(-7) cm) diffusion distances (the length of the studied DNA), allow relatively fast diffusion-limited ET at an apparent rate that may exceed the rate of the corresponding surface-confined ET process. This phenomenon is of particular importance for molecular electronics and electrochemical genosensor development.