Optoelectronic Properties of Diamondoid-DNA Complexes

Abstract

DNA sensing with engineered nanomaterials can bestow a new platform for single nucleotide identification and sequencing. Nevertheless, understanding the relevant nano-bio interfaces can provide a wealth of information on structures, energetics, and dynamics with a great potential in molecular nanotechnology. Herein, we explore the sensitivity of DNA units, the nucleotides, with a tiny probe, the diamond-like structures known as diamondoids. The probe diamondoid and the target nucleotides interact via hydrogen bonding, forming nano-bio complexes. The binding strengths for these complexes lie between the physisorption and chemisorption, allowing a suitable probe to sense the DNA nucleotides. Besides electronic properties, herein we investigate the optical properties of the nucleotides interacting with a functional diamondoid for the first time by assessing the absorption spectra and the charge dynamics within these complexes. The relative arrangements and bonding characteristics of the diamondoid with the nucleotides strongly influence these properties. Interestingly, we observe charge transfer oscillations between the diamondoid and few nucleotides, while one-way transfer or no charge transfer is observed in other cases. Our results provide a deeper understanding of the inherent electron dynamics of these complexes and can be utilized to design functionalized devices for optical detection. The presented approach can be proven essential in determining the properties of molecular complexes targeted for novel applications in sensing and nanoelectronics.

Functionalized electrodes embedded in nanopores: read‐out enhancement?

“…The electronic energy gap on the x-axis is given in units of eV. charge transfer behavior between the diamondoid and the nucleotides was found to correlate to the nature of the hydrogen bonding in the complex and the location of the frontier molecular orbitals Sarap et al ( 2018) 72 . In order to visualize the charge dynamics within the diamondoid-nucleotides, in Figure 4(a), representative results for the two configurations in the case of T and C are with memS are shown.…”

“…Independent of the type of diamondoid or nucleotide used, hydrogen binding energies in the range �5-15 kcal/ mol were calculated and lie between physisorption and chemisorption. The hydrogen bonding is formed by one up to three hydrogen bonds, depending on the binding arrangements Sarap et al (2018) 72 . The charge dynamics in the complexes can be observed in the femtosecond scale and depend on the relative arrangement of the molecules and the nucleotide identity.…”

“…Continuous efforts attempt to improve these and more critical aspects in nanopore sensing and sequencing. The strength of the hydrogen bond can be tuned through a proper choice of functionalizing molecules Sarap et al (2018) 72 . In addition, processing of nanopore data using Machine Learning algorithms is a big step towards enhancing the readability of the nanopore signals for DNA Im et al (2018) 32 , Díaz Carral et al (2021) 11 , as well as amino acids Taniguchi et al (2021) 88 and refers to a very active field.…”

Nanotechnology of diamondoids for the fabrication of nanostructured systems

“…In addition, it was found that the size of the diamondoids can affect the melting temperature of the DNA [161]. These findings have initiated a number of theoretical studies [162][163][164][165][166][167][168][169] on exploring the possibility of using diamondoid-based 3D nanoarchitectures in the field of bionanotechnology [170], such as new biosensors with high sensitivity [162].…”

Synthesis and self-assembly of cytidine- and guanosine-based copolymers

“…The integration of hydrogen bond interactions in polymeric materials results in supramolecular programmable, stimuli responsive architectures with captivating optoelectronic, 1,2 mechanical, 3,4 self-assembled 5–7 and thermal properties, 6,8 which is inspired by nature. These noncovalent interactions are crucial in biological systems, for example for stability reasons of secondary, tertiary and quaternary structures of proteins or for the molecular self-assembly of nucleic acids based on the complementary base pairing property.…”