User:Justinhlo

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Here are a few models worth investigating:
Here are a few models worth investigating:
The very basic equation used for very short sequences: Tm= (wA+xT) * 2 + (yG+zC) * 4.
The very basic equation used for very short sequences: Tm= (wA+xT) * 2 + (yG+zC) * 4.
 +
The standard G-C content equation: Tm= 64.9 +41*(yG+zC-16.4)/(wA+xT+yG+zC).
The standard G-C content equation: Tm= 64.9 +41*(yG+zC-16.4)/(wA+xT+yG+zC).
 +
The modified G-C content equation, with more length-dependent consideration: Tm = 100.5 + 41*(yG+zC-836.4)/(wA+xT+yG+zC).
The modified G-C content equation, with more length-dependent consideration: Tm = 100.5 + 41*(yG+zC-836.4)/(wA+xT+yG+zC).
 +
The NN model:   
The NN model:   
It seems that the last one here is probably the only one that actually tries to include entropic and enthalpic conditions.  That means we have limited options for the fitting of the actual curve.
It seems that the last one here is probably the only one that actually tries to include entropic and enthalpic conditions.  That means we have limited options for the fitting of the actual curve.

Revision as of 14:43, 8 January 2007

Contents

DNA Melting Project: IAP 2007

Ionic Strength

Using either NaCl or KCl (is there an advantage to one over the other? Does Na+ or K+ interact more with O-?). Original 19-bp sequence is fine ..

Goal: show how the set-up can be used to investigate the significant effects of ionic particle concentrations on DNA melting parameters.

Control and Experimental Groups: 0 mM (control), 1 mM, 10 mM (original module condition), 150 mM (physiological conditions, see http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=2703503&dopt=Abstract), 1000 mM (SantaLucia paper’s conditions – I’m curious to see if we get similar results).

These conditions form an approximately logarithmic distribution between 0 M and 1 M. This is justified because the projected dependence of ΔS and ΔH on ionic concentration is also logarithmic. The 150 mM may be replaced by 100 mM if it is deemed more desirable.

It may be worth looking into the 50 mM concentration, because this is what PCRs are run at, and it is also what many of the models have actually been designed for.

Mismatches

C, T are pyrimidines (small) A, G are purines (large) [...]

Length

[...]

Potential Models for DNA modeling

This interesting paper actually lists a good number of methods (including the one we used in the module). http://bioinformatics.oxfordjournals.org/cgi/content/full/21/6/711. However, while it compares the methods thoroughly, it does not run the empirical experiments in order to see which one is actually right.

Here are a few models worth investigating: The very basic equation used for very short sequences: Tm= (wA+xT) * 2 + (yG+zC) * 4.

The standard G-C content equation: Tm= 64.9 +41*(yG+zC-16.4)/(wA+xT+yG+zC).

The modified G-C content equation, with more length-dependent consideration: Tm = 100.5 + 41*(yG+zC-836.4)/(wA+xT+yG+zC).

The NN model: It seems that the last one here is probably the only one that actually tries to include entropic and enthalpic conditions. That means we have limited options for the fitting of the actual curve.

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