Difference between revisions of "Shear Unzipping of DNA"

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Original entry:  Naveen Sinha,  APPHY 226,  Spring 2009
 
Original entry:  Naveen Sinha,  APPHY 226,  Spring 2009
  
Second Entry: Nick Chisholm, AP 225, Fall 2009 (In Progress)
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Second Entry: Nick Chisholm, AP 225, Fall 2009
  
 
===Shear Unzipping of DNA===
 
===Shear Unzipping of DNA===
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==Soft Matter Keywords==
 
==Soft Matter Keywords==
[http://soft-matter.seas.harvard.edu/index.php/DNA DNA], [http://soft-matter.seas.harvard.edu/index.php/Homopolymer Homopolymer] [http://soft-matter.seas.harvard.edu/index.php/Polymer Polymer], [http://soft-matter.seas.harvard.edu/index.php/Shear Shear]
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[http://soft-matter.seas.harvard.edu/index.php/DNA DNA], [http://soft-matter.seas.harvard.edu/index.php/Homopolymer Homopolymer], [http://soft-matter.seas.harvard.edu/index.php/Polymer Polymer], [http://soft-matter.seas.harvard.edu/index.php/Shear Shear]
  
 
==Summary==
 
==Summary==
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More specifically, the authors model the sugar phosphate backbone of the DNA by Hookean springs and expand in the displacements of the nearest neighbor interactions of complementary base pairs on opposite rungs of the ladder, and the next nearest neighbor interactions on different rungs of the ladder (this is a simple model of stacking interactions). Both are expanded to quadratic order, and then the eigenmode corresponding to shear deformation is projected out, thus leading to a nonlinear Hamiltonian.
+
More specifically, the authors model the sugar phosphate backbone of the DNA by Hookean springs and expand in the displacements of the nearest neighbor interactions of complementary base pairs on opposite rungs of the ladder, and the next-nearest neighbor interactions on different rungs of the ladder (this is a simple model of stacking interactions). Both are expanded to quadratic order, and then the eigenmode corresponding to shear deformation is projected out, thus leading to a nonlinear Hamiltonian.
  
 
==Soft Matter Discussion==
 
==Soft Matter Discussion==
 
Instead of delving into the mathematics in great detail (which, at times, to the unfamiliar spectator, this could seem overwhelming), I will present a more conceptual approach to this paper with some rather mild mathematics for support.
 
Instead of delving into the mathematics in great detail (which, at times, to the unfamiliar spectator, this could seem overwhelming), I will present a more conceptual approach to this paper with some rather mild mathematics for support.
 +
  
 
Briefly examining Figure 1(b), one notices that in the tensile unzipping that is occurring, the bases are sequentially stretched by forces that are exerted on the same end of the duplex. However, for shear unzipping (as in Figure 1(a)), one notices that the forces act on opposite ends of the duplex, and the stretching that occurs is spread out over many base pairs.
 
Briefly examining Figure 1(b), one notices that in the tensile unzipping that is occurring, the bases are sequentially stretched by forces that are exerted on the same end of the duplex. However, for shear unzipping (as in Figure 1(a)), one notices that the forces act on opposite ends of the duplex, and the stretching that occurs is spread out over many base pairs.
  
In order to account for these parameters, the authors introduce a Hamiltonian which describes the interactions between nearest neighbors on the same strand, along with the interactions between the nearest neighbor nucleotides of opposite strands. The interactions between nearest neighbors on the same strand are modeled by Hookean springs with spring constant Q, and a being the equilibrium unstretched separation between adjacent nucleotides. The interactions between nearest neighbor nucleotides of opposite strands are modeled by a Lennard-Jones potential (which, traditionally, models the interaction between a pair of neutral atoms or molecules). Mathematically, this is shown below (see Figure 1(c) for clarification on location of the vectors and forces).
+
 
 +
In order to account for these parameters, the authors introduce a Hamiltonian which describes the interactions between nearest neighbors on the same strand, along with the interactions between the nearest and next nearest-neighbor nucleotides of opposite strands. The interactions between nearest neighbors on the same strand are modeled by Hookean springs with spring constant <math>Q</math>, <math>a</math> is the equilibrium unstretched separation between adjacent nucleotides, and <math>L</math> is the hybridized length, or the number of nucleotides on each strand. The interactions between nearest and next-nearest neighbor nucleotides of opposite strands are modeled by a Lennard-Jones potential (which, traditionally, models the interaction between a pair of neutral atoms or molecules). Mathematically, this is shown below (see Figure 1(c) for clarification on location of the vectors and forces).
  
 
<math> H = \frac{1}{2} Q \sum_{n=1}^L([|\vec{r_{n+1}} - \vec{r_{n}}| - a]^{2} + [|\vec{s_{n+1}} - \vec{s_{n}}| - a]^{2}) + \sum_{n=1}^L[V_{LJ}(|\vec{r_{n}} - \vec{s_{n}}|) + V_{LJ}'(|\vec{r_{n+1}} - \vec{s_{n}}|) + V_{LJ}'(|\vec{s_{n+1}} - \vec{r_{n}}|)] </math>
 
<math> H = \frac{1}{2} Q \sum_{n=1}^L([|\vec{r_{n+1}} - \vec{r_{n}}| - a]^{2} + [|\vec{s_{n+1}} - \vec{s_{n}}| - a]^{2}) + \sum_{n=1}^L[V_{LJ}(|\vec{r_{n}} - \vec{s_{n}}|) + V_{LJ}'(|\vec{r_{n+1}} - \vec{s_{n}}|) + V_{LJ}'(|\vec{s_{n+1}} - \vec{r_{n}}|)] </math>
  
 
The direct nucleotide pairing is decribed by the Lennard-Jones pair potential:
 
The direct nucleotide pairing is decribed by the Lennard-Jones pair potential:
 +
 
<math> V_{LJ}(|\vec{r_{n}} - \vec{s_{n}}|) = 4\epsilon [(\frac{\sigma}{|\vec{r_{n}} - \vec{s_{n}}|})^{12} - (\frac{\sigma}{|\vec{r_{n}} - \vec{s_{n}}|})^6] </math>
 
<math> V_{LJ}(|\vec{r_{n}} - \vec{s_{n}}|) = 4\epsilon [(\frac{\sigma}{|\vec{r_{n}} - \vec{s_{n}}|})^{12} - (\frac{\sigma}{|\vec{r_{n}} - \vec{s_{n}}|})^6] </math>
  
 
whereas the interactions between the next nearest neighbors of opposite strands is given by the Lennard-Jones potential:
 
whereas the interactions between the next nearest neighbors of opposite strands is given by the Lennard-Jones potential:
<math>V_{LJ}(|\vec{r_{n}} - \vec{s_{n}}|) = 4\epsilon [(\frac{\sigma}{|\vec{r_{n}} - \vec{s_{n}}|})^{12} - (\frac{\sigma}{|\vec{r_{n}} - \vec{s_{n}}|})^6</math>
+
 
where <math>\epsilon \approx 1.6k_{B}T</math> and  
+
<math>V_{LJ}'(|\vec{r_{n}} - \vec{s_{n}}|) = 4\epsilon' [(\frac{\sigma'}{|\vec{r_{n}} - \vec{s_{n}}|})^{12} - (\frac{\sigma'}{|\vec{r_{n}} - \vec{s_{n}}|})^6</math>
 +
where <math>\epsilon' \approx 1.6k_{B}T</math> and <math>\sigma' = 2^{\frac{-1}{6}} \sqrt{2^{\frac{1}{3}}\sigma^{2} + a^{2}}</math>.
 +
 
 +
Adding in the force terms (see Figure 1(a)), we find the total energy to be:
 +
 
 +
<math> H' = H - \vec{F} \cdot (\vec{r_{1}} - \vec{s_{L}}) </math>.
 +
 
 +
 
 +
Of particular interest is the calculation of the rupture force (<math>F_{c}</math>, the force required to unzip the DNA); for small segments, they find that <math>F_{c} = f_{0} L</math> (where <math>f_{0}</math> is the rupture force of a single bond), and for long segments, they find that <math>F_{c} \approx \frac{2f_{0}}{\kappa a} = constant</math> (where <math>\kappa</math> is the elastic screening length, i.e. <math>\kappa^{-1}</math> is the distance over which the strain relaxes over). This can be explained by the fact that for short segments, each bond is stressed during the shear unzipping (i.e. one adds all the spring constants of the strand, and thus all the individual forces <math>f_{0}</math>), whereas for long segments only those interactions within <math>\kappa^{-1}</math> (to first order) of the strand are included (this turns out to be approximately <math>\frac{2}{\kappa a}</math> "springs").
 +
 
 +
 
 +
The most interesting part of this article, in my opinion, was seeing the involvement of both solid-state physics and soft matter physics. It's interesting to see that DNA is constructed of both solid-state and soft matter, and that in order to describe the shear unzipping of DNA, both needed to be taken into account. [Note: The sugar-phosphate backbone of DNA is treated like a solid-state system, i.e. by springs, and in further detail in the article they discuss phonons. Perhaps the backbone can't entirely be described by solid-state physics, but that is what this paper seems to attempt to do.] Often in experiment, we attempt to isolate one such form of matter in order to achieve certain goals in one field. However, perhaps the more appropriate way to go about research is to try and make connections between different fields, utilizing the best features of each for a particular application (much like nature seems to do on its own). This is something we should perhaps keep in mind! [Actually, I vaguely recall an article written by two leaders of the AMO (atomic, molecular, and optical) physics field stating that the next big step in the field is to combine solid-state and AMO physics, in order to enhance the feasibility of practical quantum computing. It really does seem that the combination of fields that we consider to be separate, when done appropriately, can lead to significant innovations.]
  
  
The most interesting part of this article, in my opinion, was seeing the connection between solid-state physics and soft matter physics.
+
It should be noted that these calculations were done for low temperatures, i.e. temperatures such that thermal noise in each strand can be ignored.
  
 
==Reference==
 
==Reference==
 
[1] B. Chakrabarti, and D. R. Nelson, "Shear Unzipping of DNA," The Journal of Physical Chemistry B '''113''' (12), 3831-3836 (2009).
 
[1] B. Chakrabarti, and D. R. Nelson, "Shear Unzipping of DNA," The Journal of Physical Chemistry B '''113''' (12), 3831-3836 (2009).

Latest revision as of 02:10, 30 October 2009

Original entry: Naveen Sinha, APPHY 226, Spring 2009

Second Entry: Nick Chisholm, AP 225, Fall 2009

Shear Unzipping of DNA

Buddhapriya Chakrabarti, David R. Nelson

The Journal of Physical Chemistry B 113 (12), 3831-3836 (2009).

Soft matter keywords:

deGennes, polymer, shear

Summary

Biologists have already investigated the helical unzipping of DNA, which occurs during DNA replication and other biological processes (see Fig. 1b). However, the problem of shear-induced unzipping in such systems (see Fig. 1a) has yet to be investigated. Although not as prevalent in biological systems, it is directly relevant to artificially constructed nanostructures that are bound together with DNA duplexes. The shear situation is different from the helical one because the stress is distributed throughout the length of the DNA, rather than at just the bond nearest the end.

NelsonUnzipDNAfig1.png

Soft Matter Aspects

When studying an analogous system, deGennes used the model of a ladder connected by harmonic springs. This led to the prediction of a linear increase in the minimal force needed to unzip the DNA as a function of overlap length (<math>\beta \gamma</math> and <math>\delta \epsilon</math> in Fig. 1). The model also predicted a saturation in this force above a critical DNA length. A physical version of this system has been realized by the Prentiss group, in which a double-stranded DNA is trapped between a glass capillary and a magnetic bead, which can be pulled away from the surface to stretch the DNA (i.e. the force, F, would be applied at <math>\alpha</math> and <math>\omega</math> in Fig. 1). To more accurately model this situation, the authors look at both complementary base-pair interactions on opposite strands of the DNA and next-nearest neighbor interactions, also on opposite strands. In addition, the authors look at the case of a heteropolymer, with both A-T and G-C pairs.

The authors find that most of the bond breakages occur near the endpoints, with a frequency that occurs with a characteristic length scale. The unzipping process advances in jumps and plateaus, rather than uniformly. In future work, the model could be modified to take into account the helical twist of the DNA. It would also be interesting to investigate how these findings could be applied to other heteropolymers.

written by: Naveen N. Sinha




General Information

Authors: B. Chakrabarti, and D. R. Nelson

Publication: The Journal of Physical Chemistry B 113 (12), 3831-3836 (2009)

Soft Matter Keywords

DNA, Homopolymer, Polymer, Shear

Summary

This paper is a theoretical study of shear denaturation (unzipping) of DNA. Using a microscopic Hamiltonian, the authors derive a nonlinear generalization of a ladder model of shear unzipping proposed by deGennes. Previously studied is the physics behind single molecule DNA unzipping, which is the helicase-mediated unzipping that occurs during DNA replication (see Figure 1(b)). Although the case of shear unzipping (see Figure 1(a)) is less biologically relevant, its study leads to interesting materials science applications; the authors note that these include determining the strength of DNA or gold nanoparticle assemblies.

Figure 1, taken from [1].


More specifically, the authors model the sugar phosphate backbone of the DNA by Hookean springs and expand in the displacements of the nearest neighbor interactions of complementary base pairs on opposite rungs of the ladder, and the next-nearest neighbor interactions on different rungs of the ladder (this is a simple model of stacking interactions). Both are expanded to quadratic order, and then the eigenmode corresponding to shear deformation is projected out, thus leading to a nonlinear Hamiltonian.

Soft Matter Discussion

Instead of delving into the mathematics in great detail (which, at times, to the unfamiliar spectator, this could seem overwhelming), I will present a more conceptual approach to this paper with some rather mild mathematics for support.


Briefly examining Figure 1(b), one notices that in the tensile unzipping that is occurring, the bases are sequentially stretched by forces that are exerted on the same end of the duplex. However, for shear unzipping (as in Figure 1(a)), one notices that the forces act on opposite ends of the duplex, and the stretching that occurs is spread out over many base pairs.


In order to account for these parameters, the authors introduce a Hamiltonian which describes the interactions between nearest neighbors on the same strand, along with the interactions between the nearest and next nearest-neighbor nucleotides of opposite strands. The interactions between nearest neighbors on the same strand are modeled by Hookean springs with spring constant <math>Q</math>, <math>a</math> is the equilibrium unstretched separation between adjacent nucleotides, and <math>L</math> is the hybridized length, or the number of nucleotides on each strand. The interactions between nearest and next-nearest neighbor nucleotides of opposite strands are modeled by a Lennard-Jones potential (which, traditionally, models the interaction between a pair of neutral atoms or molecules). Mathematically, this is shown below (see Figure 1(c) for clarification on location of the vectors and forces).

<math> H = \frac{1}{2} Q \sum_{n=1}^L([|\vec{r_{n+1}} - \vec{r_{n}}| - a]^{2} + [|\vec{s_{n+1}} - \vec{s_{n}}| - a]^{2}) + \sum_{n=1}^L[V_{LJ}(|\vec{r_{n}} - \vec{s_{n}}|) + V_{LJ}'(|\vec{r_{n+1}} - \vec{s_{n}}|) + V_{LJ}'(|\vec{s_{n+1}} - \vec{r_{n}}|)] </math>

The direct nucleotide pairing is decribed by the Lennard-Jones pair potential:

<math> V_{LJ}(|\vec{r_{n}} - \vec{s_{n}}|) = 4\epsilon [(\frac{\sigma}{|\vec{r_{n}} - \vec{s_{n}}|})^{12} - (\frac{\sigma}{|\vec{r_{n}} - \vec{s_{n}}|})^6] </math>

whereas the interactions between the next nearest neighbors of opposite strands is given by the Lennard-Jones potential:

<math>V_{LJ}'(|\vec{r_{n}} - \vec{s_{n}}|) = 4\epsilon' [(\frac{\sigma'}{|\vec{r_{n}} - \vec{s_{n}}|})^{12} - (\frac{\sigma'}{|\vec{r_{n}} - \vec{s_{n}}|})^6</math> where <math>\epsilon' \approx 1.6k_{B}T</math> and <math>\sigma' = 2^{\frac{-1}{6}} \sqrt{2^{\frac{1}{3}}\sigma^{2} + a^{2}}</math>.

Adding in the force terms (see Figure 1(a)), we find the total energy to be:

<math> H' = H - \vec{F} \cdot (\vec{r_{1}} - \vec{s_{L}}) </math>.


Of particular interest is the calculation of the rupture force (<math>F_{c}</math>, the force required to unzip the DNA); for small segments, they find that <math>F_{c} = f_{0} L</math> (where <math>f_{0}</math> is the rupture force of a single bond), and for long segments, they find that <math>F_{c} \approx \frac{2f_{0}}{\kappa a} = constant</math> (where <math>\kappa</math> is the elastic screening length, i.e. <math>\kappa^{-1}</math> is the distance over which the strain relaxes over). This can be explained by the fact that for short segments, each bond is stressed during the shear unzipping (i.e. one adds all the spring constants of the strand, and thus all the individual forces <math>f_{0}</math>), whereas for long segments only those interactions within <math>\kappa^{-1}</math> (to first order) of the strand are included (this turns out to be approximately <math>\frac{2}{\kappa a}</math> "springs").


The most interesting part of this article, in my opinion, was seeing the involvement of both solid-state physics and soft matter physics. It's interesting to see that DNA is constructed of both solid-state and soft matter, and that in order to describe the shear unzipping of DNA, both needed to be taken into account. [Note: The sugar-phosphate backbone of DNA is treated like a solid-state system, i.e. by springs, and in further detail in the article they discuss phonons. Perhaps the backbone can't entirely be described by solid-state physics, but that is what this paper seems to attempt to do.] Often in experiment, we attempt to isolate one such form of matter in order to achieve certain goals in one field. However, perhaps the more appropriate way to go about research is to try and make connections between different fields, utilizing the best features of each for a particular application (much like nature seems to do on its own). This is something we should perhaps keep in mind! [Actually, I vaguely recall an article written by two leaders of the AMO (atomic, molecular, and optical) physics field stating that the next big step in the field is to combine solid-state and AMO physics, in order to enhance the feasibility of practical quantum computing. It really does seem that the combination of fields that we consider to be separate, when done appropriately, can lead to significant innovations.]


It should be noted that these calculations were done for low temperatures, i.e. temperatures such that thermal noise in each strand can be ignored.

Reference

[1] B. Chakrabarti, and D. R. Nelson, "Shear Unzipping of DNA," The Journal of Physical Chemistry B 113 (12), 3831-3836 (2009).