Packaging of DNA in bacteriophage Heads: Some considerations on energetics

Abstract

SynopsisWe have made quantitative estimates of some of the energetic factors to be considered in packaging of double-stranded DNA in virus particles. Numerical calculations were made using parameters appropriate for T4 bacteriophage. The unfavorable factors, and the Gibbs free energies per mole virus a t 20°C associated with them, are bending, 1.5 X lo3 kcal/mol; conformational restriction upon condensation, 5.1 X lo2 kcal/mol; polyelectrolyte repulsion, 2.1 X lo5 kcal/mol; and melting or kinking, 6.9 X lo3 kcal/mol. These must be counterbalanced in the assembled phage by noncovalent bonding interactions between protein subunits in the phage-head shell; by interactions between the DNA and polyvalent cations, especially putrescine and spermidine; and perhaps by repulsive excluded volume and electrostatic interactions between the DNA and acidic polypeptides. Indeed, a rough estimate of the standard free energy of interaction between T4 DNA and the putrescine and spermidine contained in the head is -2.1 X lo5 kcal/mol. In the absence of the other two sources of stabilization, each head protein subunit must contribute about 210 kcal/mol of binding energy.

Strongly correlated electrostatics of viral genome packaging

“…There exists different models to calculate the bending energy of a packaged DNA molecules in literature [5,9,[32][33][34]. In this paper, for simplicity, we employ the viral DNA packaging model used previously in [9,32,33].…”

“…In this paper, for simplicity, we employ the viral DNA packaging model used previously in [9,32,33]. In this model, the DNA viral genome are assumed to simply coil co-axially inward with the neighboring DNA helices forming a hexagonal lattice with lattice constant d (Fig.…”

Biological consequences of tightly bent DNA: The other life of a macromolecular celebrity

“…[14][15][16][17][18][19][20] The force due to bending is small during the initial stages of packing. However, as more DNA is forced into the capsid, the DNA takes up increasing amounts of available space and loops must be produced at smaller radii, increasing the force.…”

“…Alternative models of the packed DNA structure have also been proposed, 21 but the asymmetric cryoelectron microscopy structures described above strongly support the inverse spool model. In one of the original models of the energetics of viral DNA packing, 14 the DNA is assumed to be packed tightly into an inverse spool, with strands touching each other so that they are locally aligned on a square lattice, with an interstrand separation d ¼ 2 nm. Applied to bacteriophage l, this model predicts that the DNA loops in the center of the capsid have a radius as small as $10 nm.…”

Nanofluidic structures for single biomolecule fluorescent detection

“…For DNA, structural properties govern actions such as packaging into chromatin and bacteriophage heads. [30][31][32] To elucidate mechanical properties, optically trapped or magnetically responsive beads can be conjugated to a single DNA strand, enabling controlled stretching and twisting of the molecule. [33][34][35][36] By fixing one end of a fluorescently labeled DNA strand in an elongational flow, it is also possible to observe inhomogenous hydrodynamic stretching, which is a theoretically interesting phenomenon.…”