ssdna_efjc_distance

lumicks.pylake.ssdna_efjc_distance

ssdna_efjc_distance(name, dna_length_kb, um_per_kb=0.56, temperature=24.53608821)

Model of ssDNA with distance as the dependent variable.

Extensible Freely-Jointed Chain model [1] [2] using user-specified kilobases with default parameters obtained from [3].

Parameters:

• name (str) – Name for the model. This name will be prefixed to the model parameter names.

• dna_length_kb (integer) – The length of the dna in the sample measured in kilobases

• um_per_kb (float) – The number of kilobases evaluating to 1 um. This is used to convert the length in kb to um as applied in the fit function.

• temperature (float) – The temperature in celsius. This is used to calculate the Boltzmann’s constant * temperature value

References

[1]

S. B. Smith, Y. Cui, C. Bustamante, Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules, Science 271, 795-799 (1996).

[2]

M. D. Wang, H. Yin, R. Landick, J. Gelles, S. M. Block, Stretching DNA with optical tweezers., Biophysical journal 72, 1335-46 (1997).

[3]

Bosco, A., Camunas-Soler, J., & Ritort, F. (2014). Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions. Nucleic acids research, 42(3), 2064-2074.