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.

Electronic analysis of hydrogen-bonded molecular complexes: the case of DNA sensed in a functionalized nanogap

“…Note, that previous studies focusing on the isolated molecule, that is no electrodes were present, have evaluated the exact influence of the molecular binding on the electronic properties of the isolated molecules, as well as the charge dynamics across different molecular donor or acceptor configurations. 28,40 These can provide a direct comparison to the results of the current work. For example, in the isolated molecules, the HOMO and LUMO levels are mainly associated with the nucleotide, while in the nanogap these are less localized on the molecules.…”

Functionalized electrodes embedded in nanopores: read‐out enhancement?

“…As evident from this figure, the range of the electronic band gaps for each nucleotide-nucleobase do differ underlying the different electronic and nucleobase-specific characteristics of the hydrogen bonded complexes. The distinct features are based on the underlying molecular orbitals Maier and Fyta (2014) 46 , Sivaraman and Fyta (2014) 77 . These trends suggest a possible electronic detection of the nucleobase identity that will be further investigated.…”

Derivatization of diamondoids for functional applications

“…[88][89][90][91] When the diamondoids bind with a DNA unit (such as nucleobase), the electronic band gaps will be significantly affected even with weak interaction energies. [88][89][90][91] When the diamondoids bind with a DNA unit (such as nucleobase), the electronic band gaps will be significantly affected even with weak interaction energies.…”

“…Very recently, diamondoids and their derivatives were explored as probes and biosensors for DNA due to the strong hydrogen bonds between the diamondoids and DNA units. [88][89][90][91] When the diamondoids bind with a DNA unit (such as nucleobase), the electronic band gaps will be significantly affected even with weak interaction energies. As such, diamondoids can clearly distinguish the regular nucleobase from the modified nucleobase.…”