Nucleic Acids

Nucleic Acids

1. Electromagnetic Force

   • Only relevant force for this scale
   • All intermolecular forces
   • Charge mediated
     • Attractive and Repulsive
   • F(r)=-(nCm1m2)/r^(n+1)
   • Long range interactions disappear for n>3
   • Lennard- Jones type potential graphs
     • Positive energy = Repulsive force
     • Negative energy = Attractive Force
     • Lennard- Jones: V(r)= -A/r^6 + B/r^12

2. Polymers

   • Made up of monomers
     • Joined via covalent bonds
   • Degree of polymization = number of monomers = N
   • Mass of polymer= Nm(mon)
   • Types
     • Homopolymers
       • Same monomer
     • Heteropolymer
       • Different monomers
         • Random
         • Block
   • Flexibility
     • Coil
     • Rod
     • Depends on length scale
   • Isomerisation
     • Isotatic
       • Chemical group always in same position
     • Syndiotactic
       • Chemical group swaps sides
     • Atactic
       • Chemical group in random positon
   • Topology
     • Linear
     • Ring
     • Branched

3. Molecular Conformations

   • Free Jointed Chain (FJC) Model
     • Mean squared value= Cn*n*l^2
       • Cn=Flory Characteristic Ratio – average of all Ci, converging for C∞
       • l= bond length
       • n= number of bond lengths
     • No correlations between all θij, and all θij allowable
     • Equivalent FJC
       • N=L^2/(
         • L= Contour length