dsdna_ewlc_odijk_distance

lumicks.pylake.dsdna_ewlc_odijk_distance

dsdna_ewlc_odijk_distance(name, dna_length_kbp, um_per_kbp=0.34, temperature=24.53608821)

Model for dsDNA with distance as the dependent variable.

Odijk’s Extensible Worm-Like Chain model [1] [2] with distance as the dependent variable using user-specified kilobase-pairs (useful for 10 pN < F < 30 pN). Default model parameters were obtained from [3] [4] and [5].

Parameters:

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

• dna_length_kbp (integer) – The length of the dna in tether/construct measured in kilobase-pairs

• um_per_kbp (float) – The number of kilobase pairs evaluating to 1 um. This is used to convert the length in kbp to um as applied in the fit function [6].

• temperature (float) – The temperature in celsius. This is used to calculate the boltzmann * temperature (kT) value

References

[1]

20. Odijk, Stiff Chains and Filaments under Tension, Macromolecules 28, 7016-7018 (1995).

[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]

Manning, G. S. (2006). The persistence length of DNA is reached from the persistence length of its null isomer through an internal electrostatic stretching force. Biophysical journal, 91(10), 3607-3616.

[4]

Liu, J. H., Xi, K., Zhang, X., Bao, L., Zhang, X., & Tan, Z. J. (2019). Structural flexibility of DNA-RNA hybrid duplex: stretching and twist-stretch coupling. Biophysical journal, 117(1), 74-86.

[5]

Herrero-Galán, E., Fuentes-Perez, M. E., Carrasco, C., Valpuesta, J. M., Carrascosa, J. L., Moreno-Herrero, F., & Arias-Gonzalez, J. R. (2013). Mechanical identities of RNA and DNA double helices unveiled at the single-molecule level. Journal of the American Chemical Society, 135(1), 122-131.

[6]

Saenger, W. (1984). Principles of Nucleic Acid Structure. Springer. New York, Berlin, Heidelberg.