Better understanding the biophysical basis of the biological process to transfer a viral genome to infect a cell is important to many disease related fields. Predicting the thermodynamic pressures and forces including the osmotic pressure necessary to confine DNA-a highly-negatively charged, elastic polymer-into capsids (over a 250-fold compaction) is a problem with implications not only relevant to infectious disease mechanism but in phage therapy or phage antibiotics(1) and therapeutic delivery(2). Experimental measurements of phage DNA confinement include osmotic pressure ejection-inhibition experiments(3) and single-molecule loading force measurements that provide force or pressure data for validation of theoretical models.(4, 5) Structural insight into DNA packaging is aided by cryo-electron microscopy asymmetric reconstructions done in the NCMI with our collaborator Chiu.(6, 7) Most current models of phage packing assume DNA behaves as a linearly elastic polymer that bends uniformly under stress, like the 'inverse spool'model.(8) The assumption of such spooled conformations is based primarily on interpretations of cryo-EM density maps, obtained by averaging thousands of structures(9), which show density rings, especially near the capsid surface. Recent evidence shows that during translocation packing, the DNA helix is rotated in a left-handed direction thus under twisting it.(10, 11) It Is known tha under twisting reduces persistence length by 2 orders of magnitude when strand separation occurs in sequence specific places.(12) Our hypothesis is that DNA kinking induced disorder can have a strong effect on packing and pressures. How DNA overcomes the unfavorable thermodynamic barrier to enter and pack inside a capsid depends on many different intermolecular interactions. Because phage genomes are around ten kilo-basepairs long, we will employ a multi scale technique to model the structure and consequent thermodynamics. We will refine a coarse-grained model of DNA from our previous work.(13) Preliminary simulations of unconnected DNA coarse grained polymer beads in capsid-like confinement already show ringed density distributions consistent with cryo-EM data. Connected polymer paths will be constructed consistent with data. We will produce an ensemble of entropically-driven, low free energy conformations of DNA in confinement. Ultimately, we will test hypotheses related to the amount of disorder, ion screening and the contribution of DNA-protein confinement interactions.

Public Health Relevance

Understanding the biophysical basis of the biological process which transfers a viral genome to infect a cell is important to many disease related fields. Predicting the thermodynamic pressures including the osmotic pressure necessary to confine DNA in phage capsids (over a 250-fold compaction) is a problem with implications in infection, phage therapies and therapeutic delivery. We will resolve questions of the thermodynamic mechanism of DNA ejection by phages.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Macromolecular Structure and Function D Study Section (MSFD)
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Preusch, Peter C
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University of Texas Medical Br Galveston
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Wang, Qian; Irobalieva, Rossitza N; Chiu, Wah et al. (2017) Influence of DNA sequence on the structure of minicircles under torsional stress. Nucleic Acids Res 45:7633-7642
Myers, Christopher G; Pettitt, B Montgomery (2017) Phage-like packing structures with mean field sequence dependence. J Comput Chem 38:1191-1197
Esadze, Alexandre; Chen, Chuanying; Zandarashvili, Levani et al. (2016) Changes in conformational dynamics of basic side chains upon protein-DNA association. Nucleic Acids Res 44:6961-70
Chen, Chuanying; Pettitt, B Montgomery (2016) DNA Shape versus Sequence Variations in the Protein Binding Process. Biophys J 110:534-544
Bates, David; Pettitt, B Montgomery; Buck, Gregory R et al. (2016) Importance of disentanglement and entanglement during DNA replication and segregation: Comment on: ""Disentangling DNA molecules"" by Alexander Vologodskii. Phys Life Rev 18:160-164
Wang, Qian; Pettitt, B Montgomery (2016) Sequence Affects the Cyclization of DNA Minicircles. J Phys Chem Lett 7:1042-6
Wang, Qian; Myers, Christopher G; Pettitt, B Montgomery (2015) Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density. J Phys Chem B 119:4937-43
Wang, Qian; Pettitt, B Montgomery (2014) Modeling DNA thermodynamics under torsional stress. Biophys J 106:1182-93
Myers, Christopher G; Pettitt, B Montgomery (2013) Communication: Origin of the contributions to DNA structure in phages. J Chem Phys 138:071103
Theruvathu, Jacob A; Yin, Y Whitney; Pettitt, B Montgomery et al. (2013) Comparison of the structural and dynamic effects of 5-methylcytosine and 5-chlorocytosine in a CpG dinucleotide sequence. Biochemistry 52:8590-8

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