Type-dependent identification of DNA nucleobases by using diamondoids

Abstract

The possibility of distinguishing between DNA nucleobases of different sizes is manifested here through quantum-mechanical simulations. By using derivatives of small, modified diamond clusters, known as diamondoids, it is possible to separate the pyrimidines (cytosine and thymine) from the larger purines (adenine and guanine), according to the collective electronic and binding properties of these DNA nucleobases and the diamondoid. The latter acts as a probe with which these properties can be examined in detail. Short single-stranded DNA is built up from single nucleobases to reveal the effect of each DNA unit on the sensing abilities of the diamondoid probe. Several ways of orienting the nucleobases, nucleosides, nucleotides, and short single-stranded DNA are investigated; these lead to quite different electronic properties and may or may not enhance the possibility of separating the DNA nucleobases. For the optimum orientation, that is, one that promotes stronger hydrogen bonding of the diamondoid to the short DNA strand, it is found that the electronic band gaps of a purine strand lie in a completely different range to the band gaps of a pyrimidine strand. This difference can be over 1 eV, which is measurable and shows the potential of using diamondoids and their derivatives in biosensing devices.

Keywords: DNA recognition; biosensing; computational chemistry; diamondoids; nucleobases.