meltR.F.model: Fit fluorescence binding isotherms to obtain thermodynamic...

In JPSieg/MeltR: Automated fitting of RNA/DNA absorbance melting curves and fluorescence binding isotherms in R

Fit fluorescence binding isotherms to obtain thermodynamic parameters

Description

Models data for a set of fluorescence binding isotherms given a enthalpy and entropy of folding. Assumes three replicates of quencher labeled strand concentration = 0, 1, 10, 50, 100, 150, 200, 250, 400, 600, 800, and 1000 nM with a constant concentration of 200 nM FAM. Generates isotherms from 20 to 80 degrees celcius with 0.5 degrees celcius steps. Models error using the rnorm function.

Usage

meltR.F.model(
  H,
  S,
  fmax = 2,
  fmin = 0.2,
  FAM_error = 1,
  BHQ1_error = 1,
  Emission_SD = 0.05
)

Arguments

H	The enthalpy of folding in kcal/mol.
S	The entropy of folding in kcal/mol/K.
fmax	The approximate fluorescence maximum of the fluorophore labeled strand in its single stranded state
fmin	The approximate fluorescence minimum for the double stranded state where the fluorophore labeled strand is base paired with the quencher labeled strand.
FAM_error	The error in FAM concentrations
BHQ1_error	The error in BHQ1 concentrations
Emission_SD	The approximate experimental error for each emission reading.

Value

A dataframe containing the modeled data. Ready to feed into meltR.F.

JPSieg/MeltR documentation built on Feb. 4, 2024, 7:10 a.m.