Thermodynamics of unfolding mechanisms of pseudoknotted RNA from a coarse-grained loop-entropy model and absorbance/fluorescence measurements - presented by Prof. Jie Liang

Thermodynamics of unfolding mechanisms of pseudoknotted RNA from a coarse-grained loop-entropy model and absorbance/fluorescence measurements

Prof. Jie Liang

Prof. Jie Liang
Slide at 31:48
(Tang, Roca, Ansari, and JL, J Biol Phys, 2022) Two Tms: 3-state model - TM,A=H: [Alternative]=[Hairpin] - TM, H=U: [Hairpin]~[Unfolded] Spectroscopy - Absorbance: Two Tms Florescence: One Tm 30 40 50 60 70 80 90 10 20 30 40 50 60 70 80 90 Temperature (°C) Temperature (°C) Good agreement btw model and experiments Computational Experimental - TM,H=U: excellent prediction - TM,A=H : challenging Computational model: - Can identify the nature of intermediate and alternative 10 20 30 40 50 60 70 80 90 0 1020 30 40 50 60 70 80 90 Temperature (°C) Temperature (°C) structures - No adjustable parameters. HP2-2AP HP2-PK3D Tm,AeH 57.8 I 2.0 (56.8) Tm,H#U 75.7 I 2.6 (75.6)
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References
  • 1.
    K. Tang et al. (2022) Thermodynamics of unfolding mechanisms of mouse mammary tumor virus pseudoknot from a coarse-grained loop-entropy model. Journal of Biological Physics
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Summary (AI generated)

There is very little effect on the fluorescent probe when the hairpin unfolds. Therefore, there is good agreement between models and experiments for the high temperature melting temperatures, which range from ri to unfolded degrees. However, the low temperature melting from the alternative structures are not modeled very well.

The reason for this discrepancy is believed to be due to the first melting temperature.