DNA as a Polymer Flashcards

1
Q

Degree of Polymerisation

Definition

A

-number of monomers, N

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2
Q

Total Mass of Population

Definition

A

M = N*m_mon

-where m_mon is the mass of a monomer unit

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3
Q

Homopolymer/Heteropolymer

Definition

A
  • a homopolymer is made up of the same monomer

- a heteropolymer is in a random or block structure

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4
Q

Polymer Flexibility

A
  • coil or rod like

- this is length scale dependent, characterised by the persistance length

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5
Q

Polymer Isomerisation

A
  • isotactic, chemical groups on the same side
  • syndiotactic, chemical groups on opposite sides
  • atactic, chemical groups randomly distributed
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6
Q

Polymer Topology

A
  • linear
  • ring/circular
  • branched
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7
Q

Polymer - Molecular Conformations

A
  • atoms and molecules in a thermal bath follow random walks
  • for a distribution of ensemble isotropic chains, every angle between steps is equally probable
  • because each angle is equally probable, over a large number of steps, the ensemble average is zero so take the means square instead
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8
Q

Polymers - Ideal Chain Model

A
-assume fixed bond length:
l = |ri| = |rj|
ri . rj = l²cos(θij)
-mean square distance :
 = l²ΣΣ
-summed over I and j from 1 to n
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9
Q

Freely Jointed Chain Model

A

-no correlations between any θij’ and θij are allowed, so:
= 0 for I not equal j
-only N non-zero terms in the double sum since cos(θij)=1 only for I=j
=> = Nl²
-individual chain distance away from start point scales with sqrt(N) steps of step length l

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10
Q

Freely Jointed Chain Model

Real Chains

A

-as there are no angular restrictions from one bond to the next, the model allows the chain to cross or go through itself which obviously isn’t possible for a real chain
-this leads to the concept of excluded volume, the chain can’t move into the space already occupied by the chain
-for real chains:
not equal 0

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11
Q

Flory-Characteristic

A

-even after removing crossing over, after many many bonds, the pointing vector will be completely decorrelated from the final vector in the chain:
Ci = Σ
-summed over j from 1 to n
= CnN
-where N is the number of bonds and l is the bond length
-Cn is the Flory characteristic ratio, the average of all Ci

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12
Q

Contour Length

A

-the total length of the polymer

L = Nl

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13
Q

Freely Rotating Chain Model

Description

A
  • bond lengths l and bond angles θ are both fixed
  • but chain segment can take any torsional angle with no correlations:
  • π < φi ≤ π
  • the only correlation between bond vectors is that transmitted down the chain by the previous bond vectors component lcosθ
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14
Q

Persistence Length

A

-the range over which correlations between bond vectors has decayed

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15
Q

Number of Bonds in a Persistence Length

A

sp = 1 / -ln(cosθ)

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16
Q

Freely Rotating Chain Model

Mean Square Distance

A

-mean square distance is now also modulated by the fixed angle between bond vectors:
= nl² [1+cosθ]/[1-cosθ]
-where
C∞ = [1+cosθ]/[1-cosθ]

17
Q

Worm Like Chain Model

Description

A

-used for very stiff polymers, such as double stranded DNA
-as the polymer is stiff, θ is very small, so we can expand:
cosθ ≈ 1 - θ²/2
-since θ is small, the correlation length is longer so sp is larger

18
Q

Worm Like Chain Model

sp

A

ln(cosθ) ≈ - θ²/2
=>
sp = - 1/ln(cosθ) ≈ 2/θ²

19
Q

Worm Like Chain Model

Persistane Length

A

lp = sp*l = 2l/θ²

20
Q

Worm Like Chain Model

Flory Ratio

A

C∞ ≈ 4/θ²

21
Q

Worm Like Chain Model

Limits

A

-two limits can be taken from the WLC model:
1) ideal chain limit for very long chains:
≈ 2lpl, L»lp, perfect coil
2) rod like limit for very short chains:
≈ L², L<

22
Q

What is a typical persistence length for double stranded DNA?

A

~50nm

-this is quite long as double stranded DNA is a double helix making it a relatively stiff polymer

23
Q

Suitable Models for Nucleic Acid Polymers

RNA and ssDNA

A
  • RNA and ssDNA may be best modelled by FJC or FRC models but we can also use a WLC model with bond length l of nucleotide repeat along the chain
  • each nucleotide acts independently ad can rotate around the sugar phosphate backbone single bond
24
Q

Suitable Models for Nucleic Acid Polymers

dsDNA

A
  • dsDNA is well modelled by the WLC model with lp~50nm

- the double helix makes dsDNA more rigid, the backbone is able to curve but is more or less fixed in place

25
Q

Bending a Rod Like Section of DNA

Continuum Model

A
-as the rod is rigid we have small bend angles:
r = l/θ
-bending rigidity:
K = YI
-moment of inertia for a rod of circular cross section, diameter d:
I = [πd^4]/64
-bending energy per unit length:
ε = YI/2r² = YIθ²/2l²
-for length l of DNA polymer
26
Q

Surface Binding Mechanisms

Mica and Metal Cations

A
  • M2+ ions in solution bind to negatively charged DNA and to the negatively charged mica surface
  • as the M2+ ions are in solution and not fixed to any surface the DNA is able to slide over the surface once attached
  • as they are mobile, the molecules tend to stretch out further
27
Q

Surface Binding Mechanisms

AP-Mica

A
  • positive charge is immobilised on the mica surface
  • negatively charged DNA is attached to this electrostatically
  • chains are less spread out and may overlap with each other
28
Q

2D Equilibration

A

-molecules diffuse to minimum energy

29
Q

Kinetic Trapping

A

-2D projection of 3D conformation

30
Q

Stretching Individual Biomolecules - AFM

A
  • ssDNA behaves as an entropic spring
  • dsDNA is more complicated
  • force vs extension graph
  • ssDNA follows an exponentially increasing curve
  • dsDNA follows this line at small and large extensions but there is a plateau in the middle
31
Q

Optical Tweezers

A

-use laser to generate force on a dielectric head through momentum transfer of photons
-usually only exert forces up to ~100pN
-then try to pull the molecule out of the trap and observe the results
F = k_trap * x

32
Q

Mechanical Stretching of Single DNA Molecules

ssDNA

A
  • obeys WLC model
  • force stretches the molecule out against entropy until it is straight
  • force rises rapidly upon bond extension until breakage
33
Q

Mechanical Stretching of Single DNA Molecules

dsDNA

A
  • obeys WLC model
  • force plateau reached just after full extension of entropic coil configuration
  • overstretch transition occurs ~~65pN
  • after overstretch transition behaves like ssDNA
34
Q

Overstretching of dsDNA

A
  • overstretching DNA melts the double helix
  • if only one of the DNA strands is attached to each surface, the double helix is not torsionally constrained so the local topology can change
  • one strand is only held to the other by intermolecular forces, stretching the molecule introduces mechanical work which melts off one strand relative to the other
  • this phase transition occurs at constant force just as thermally induced transition occur at constant temperature