Project

Figure 1 – Paralell DNA hexadecamer @ monoatomic graphene. DNA is represented as a van der Waals volume coloured according to the chemical nature of its nucleobases (phosphate backbone is represented as ochre lines running through the entire double-strand). Red spheres) H2O Oxygen atoms, green spheres) Na+ and Cl- ions. The grey mesh represents chemical bonds between sp2 carbon atoms, arranged in a graphene hexagonal symmetry. All atoms are atomically detailed in the calculations (Cruz et. al., Liquids 2023, 3, 168).

Figure 2 – Nucleobase detailed dsDNA model.

Representation of the coarse-grained DNA model of de Pablo and co-workers, 5'-D(*AP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*GP-GP*)-3', evidencing the nucleobase-detailed description. Lines are chemical bonds and each sphere represents a pseudoatom: brown (phosphate), yellow (deoxyribose ring), orange (A), red (G), green (T) and blue (C). Electrostatic interactions include explicit representations of ions (Na+ and Mg2+), via a solvent averaged dielectric constant. (Hinckley et al., J. Chem. Phys. 2013 139 144903).

Figure 3 – Configuration setup for the DNA@lambda-bacteriophage (T=310 K, p=1bar, [NaCl]=130–140mM). The bacteriophage capsid is spherically symmetrical, and in order to mimic a small portal terminase protein found in bacteriophage SF6 (Büttner et al Proc. Nat. Acad. Sci. 2012 109 811), an opening of 6.5 nm is introduced in the capsid. The van der Waals diameter of the barrel (1 nm), where DNA translocation occurs, corresponds to the most constricted part of the portal.

Figure 4 – Human Hepatitis B Virus, T4 empty capsid. Atomistic description of the virus capsid to be employed to probe the packaged DNA phase space. The viral tail has been omitted and colours correspond to the protein residues identification.