Native DNA electronics: is it a matter of nanoscale assembly?

Ultrafast excitonic dynamics in DNA: Bridging correlated quantum dynamics and sequence dependence

After photoexcitation of DNA, the excited electron (in the LUMO) and the remaining hole (in the HOMO) localized on the same DNA base form a bound pair, called the Frenkel exciton, due to their mutual Coulomb interaction. In this study, we demonstrate that a tight-binding (TB) approach, using TB parameters for electrons and holes available in the literature, allows us to correlate relaxation properties, average charge separation, and dipole moments to a large ensemble of double-stranded DNA sequences (all 16384 possible sequences with 14 nucleobases). This way, we are able to identify a relatively small subensemble of sequences responsible for long-lived excited states, high average charge separation, and high dipole moment. Further analysis shows that these sequences are particularly T rich. By systematically screening the impact of electron-hole interaction (Coulomb forces), we verify that these correlations are relatively robust against finite-size variations of the interaction parameter, not directly accessible experimentally. This methodology combines simulation methods from quantum physics and physical chemistry with statistical analysis known from genetics and epigenetics, thus representing a powerful bridge to combine information from both fields.

The Effect of Amino-Phosphate Interactions on the Biosensing Performance of Enzymatic Graphene Field-Effect Transistors

The interaction between polyamines and phosphate species is found in a wide range of biological and abiotic systems, yielding crucial consequences that range from the formation of supramolecular colloids to structure determination. In this work, the occurrence of phosphate-amino interactions is evidenced from changes in the electronic response of graphene field effect transistors (gFETs). First, the surface of the transistors is modified with poly(allylamine), and the effect of phosphate binding on the transfer characteristics is interpreted in terms of its impact on the surface charge density. The electronic response of the polyamine-functionalized gFETs is shown to be sensitive to the presence of different phosphate anions, such as orthophosphate, adenosine triphosphate, and tripolyphosphate, and a simple binding model is developed to explain the dependence of the shift of the Dirac point potential on the phosphate species concentration. Afterward, the impact of phosphate-amino interactions on the immobilization of enzymes to polyamine-modified graphene surfaces is investigated, and a decrease in the amount of anchored enzyme as the phosphate concentration increases is found. Finally, multilayer polyamine-urease biosensors are fabricated while increasing the phosphate concentration in the enzyme solution, and the sensing properties of the gFETs toward urea are evaluated. It is found that the presence of simple phosphate anions alters the nanoarchitecture of the polyelectrolyte-urease assemblies, with direct implications on urea sensing.

Caging Polycations: Effect of Increasing Confinement on the Modes of Interaction of Spermidine3+ With DNA Double Helices

Polyamines have important roles in the modulation of the cellular function and are ubiquitous in cells. The polyamines putrescine²⁺, spermidine³⁺, and spermine⁴⁺ represent the most abundant organic counterions of the negatively charged DNA in the cellular nucleus. These polyamines are known to stabilize the DNA structure and, depending on their concentration and additional salt composition, to induce DNA aggregation, which is often referred to as condensation. However, the modes of interactions of these elongated polycations with DNA and how they promote condensation are still not clear. In the present work, atomistic molecular dynamics (MD) computer simulations of two DNA fragments surrounded by spermidine³⁺ (Spd³⁺) cations were performed to study the structuring of Spd³⁺ “caged” between DNA molecules. Microsecond time scale simulations, in which the parallel DNA fragments were constrained at three different separations, but allowed to rotate axially and move naturally, provided information on the conformations and relative orientations of surrounding Spm³⁺ cations as a function of DNA-DNA separation. Novel geometric criteria allowed for the classification of DNA-Spd³⁺ interaction modes, with special attention given to Spd³⁺ conformational changes in the space between the two DNA molecules (caged Spd³⁺). This work shows how changes in the accessible space, or confinement, around DNA affect DNA-Spd³⁺ interactions, information fundamental to understanding the interactions between DNA and its counterions in environments where DNA is compacted, e.g. in the cellular nucleus.