DNA confined by surfaces

DNA 受表面限制

• 批准号: 8593300
• 负责人: Bernard MONTGOMERY PETTITT
• 金额: $ 26.78万
• 依托单位: UNIVERSITY OF TEXAS MED BR GALVESTON
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-04-01 至 2016-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8593300
• 关键词: Antibiotics; Bacteriophages; Biochemical Process; Biological Process; Capsid; Cells; Cereals; Charge; Communicable Diseases; Coupling; Cryoelectron Microscopy; DNA; DNA Packaging; Data; Disease; Elasticity; Electrostatics; Free Energy; Genome; Geometry; Goals; Grant; Hand; Hydrostatic Pressure; Infection; Integral Equation; Ions; Lead; Left; Length; Literature; Maps; Measurement; Measures; Methods; Modeling; Molecular; Molecular Conformation; Motor; Nature; Nucleic Acids; Osmotic Pressure; Polymers; Property; Proteins; Saline; Sampling; Series; Simulate; Solutions; Stress; Structure; Surface; System; Techniques; Testing; Theoretical model; Therapeutic; Thermodynamics; Validation; Viral Genome; Work; base; density; driving force; insight; intermolecular interaction; kinked DNA; multi-scale modeling; planetary Atmosphere; pressure; public health relevance; reconstruction; research study; screening; simulation; single molecule; success; theories

DESCRIPTION (provided by applicant): 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.

描述（由申请人提供）：更好地理解将病毒基因组转移到感染细胞的生物过程的生物物理基础对许多相关疾病都很重要