MODELING NUCLEIC ACID SYSTEMS

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MODELING NUCLEIC ACID SYSTEMS

• Jenn Demers and Dany Floisand
• Advisor Dr. Tricia Shepherd

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WHY MODEL NUCLEIC ACIDS?

• Experimental procedures are insufficient for
  understanding nucleic acids, but combined with
  molecular dynamics (MD) simulations the
  possibilities are endless

A. SEN P. NIELSEN, BIOPHYSICAL JOURNAL, 2006,
90, 1329-1337
Although our results so far do not allow us to
identify the origin of the different stabilities
of PNA?DNA Hybrids, the evidence does point to a
significant structural component
Can our MD simulations provide helpful insight?
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NUCLEIC ACIDS REVIEW
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NUCLEIC ACIDS REVIEW
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NUCLEIC ACIDS REVIEW
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• RNA-PNA

• PNA-DNA

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• AMBER 9.1

• Other Programs

• Prepare System
• Construct Nucleic Acid
• Equilibrate System
• Minimize
• Heat
• Production Run
• Dynamics

• XLeap
• Bonds/Charges
• Adding Hydrogen Atoms
• VMD
• Visualizing Trajectories
• Curves
• Structural Analysis

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• Construct 8-mer Nucleic Acid duplexes
• Systematically change PNA from 100 Pyrimidine to
  100 Purine
• Neutralize PNA backbone

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• Adding Ions

• Adding Water

• Sodium Ions added to system to neutralize DNAs
  backbone.

• Approximately 3500 water molecules added to each
  system.

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• Vary input parameters to change minimization
  preferences
• Minimization
• 0-off, 1-on
• Minimization steps
• Steps at steepest descent
• Periodic boundary
• 0-off, 1-Volume, 2-Pressure
• Restraints on atoms
• 0-off, 1-on
• Non-bonded cutoff in Angstroms

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• Heat from 0 K to 300 K
• DNA is restrained weakly during heating
• Langevin dynamics are used to control temperature
  (ntt3)
• gamma_ln1.0 collisions per ps-1
• Average Kinetic Energy of the system is
  calculated at each time step

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• Minimization
• 0-off
• Constant pressure
• pres01.0
• Constant Temperature
• tempi300.0, temp0300.0
• Langevin dynamics to keep average kinetic energy
  constant

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• Number of MD steps
• ntslim50000
• dt0.002 ps per step
• Data recorded to output files
• Energy
• ntpr250 steps
• Trajectory
• ntwx250 steps
• Restart file
• ntwr10000 steps

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• Production runs are completed on Supercomputer -
  Jake
• Jake consists of
• 220 Processors
• 128 Gb RAM
• 4 Tb Storage
• 50,000 x 0.002 100
• 50,000 steps
• 0.002 ps per step
• 100 ps per output file

1 ns of MD 8 days on a single processor
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• Construct
• Minimize
• Heat
• Production

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• Stability varies depending on the location of
  the purine bases
• Six hybrid duplexes of varying purine content
  were studied alongside their pure counterparts
• Purine-rich PNA hybrid has a larger negative
  entropy term (entropically disfavored) than
  pyrimidine-rich PNA hybrid. However
• Purine-rich PNA hybrid has a much larger
  negative enthalpy term (enthalpy favored) than
  pyrimidine-rich PNA hybrid.

The purine-rich strand is always listed first.
Greatest Thermal Stability
Least Thermal Stability
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• A-conformations sample North sugar puckering
• B-conformations sample South sugar puckering

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• 100 DNA Purine samples a wider range of sugar
  pucker conformations
• 25 and 0 DNA Purine sample a smaller array of
  pucker angles

100 DNA Purine strand is more flexible. How does
this affect the entropy?
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• DNA Backone

• PNA Backbone

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• All four PNA strands sample three regions, but
  with varying intensity
• No clear distinction on levels of flexibility

All four strands have similar ranges. How can we
know anything about stability and entropy?
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• 100 and 0 PNA Purine strands only sample two
  regions
• 37.5 and 75 PNA Purine sample three regions

All our PNA strands have comparable flexibility.
Can we differentiate entropy values for each
strand?
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• 100 and 37.5 PNA Purine sample three regions
• 75 and 0 PNA Purine sample only two regions

We can see no clear trend between of purine,
and PNA strand flexibility. Can DNA strands tell
us more?
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• 100 and 62.5 DNA Purine strands sample two
  distinct angle ranges
• 25 and 0 DNA Purine strands sample a narrow
  range of angles

100 and 62.5 DNA Purine strands are more
flexible. Which has a larger entropy?
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• 100 and 62.5 DNA Purine strands sample a
  slightly larger range of angles than 25 and 0
  DNA Purine strands

In terms of ßthe strands are similarly
flexible. How will this affect the systems
entropy?
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• 100 and 62.5 DNA Purine sample a wider array
  of angles.
• 25 and 0 sample nearly identical angles.

100 and 62.5 DNA Purine strands show a larger
variety. Can this change the systems entropy?
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• 100 and 62.5 DNA Purine sample a slightly
  higher range of angles than the 25 and 0 DNA
  Purine strands.

100 and 62.5 DNA Purine strands show a shift in
range. Does this increase their entropy?
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• 100 and 62.5 DNA Purine sample two ranges of
  angles
• 25 and 0 DNA Purine sample a matching range of
  angles

100 and 62.5 DNA Purine strands sample more
angles. Does more angles to sample lead to more
stability?
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• 100 and 62.5 DNA Purine sample a wider range
  of angles
• 25 and 0 DNA Purine sample a smaller similar
  range of angles

100 and 62.5 DNA Purine strands take on more
conformations. Is one conformation more stable
than another?
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• 100 and 62.5 DNA Purine strands consistently
  sample wide ranges and multiple regions
• These hybrids however, lead to less stable helix
  conformations
• Flexibility in the DNA backbone does not lead to
  stable helices
• 25 and 0 DNA Purine strands often lead to a
  more narrow conformational sampling better
  binding
• Purine-rich PNA hybrids lead to the most stable
  helix conformations

Our MD simulations indicate the key structural
factor may be due to the flexibility of the DNA
backbone
The purine-rich strand is listed first, unless
otherwise specified.
Greatest Stability
Least Stability