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Results: 4

1.
Figure 2

Figure 2. From: The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation.

Secondary structures of native, mutant1 and mutant2 hairpins. They differ only in the stem region. Mutant1 has the G2-C11 base pair replaced with the A2-U11, and the mutant2 has G1-C12 replaced with A1-U12 and G2-C11 with A2-U11. This diagram shows the number of hydrogen bonds in each pair.

Aleksandar Spasic, et al. J Chem Theory Comput. 2012 July 10;8(7):2497-2505.
2.
Figure 1

Figure 1. From: The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation.

Solution structure of native hairpin GGCGUAAUAGCC.42 Figure 1a shows the structure, illustrating the continuous stack of A6, A7 and U8. Figure 1b shows the sheared base pair between G4 and A9. G4 and A9 are bonded via trans Hoogsteen/sugar edge hydrogen bond.87

Aleksandar Spasic, et al. J Chem Theory Comput. 2012 July 10;8(7):2497-2505.
3.
Figure 4

Figure 4. From: The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation.

Thermodynamic cycle for transition between two hairpins. The difference in and determined by umbrella sampling, is equal to the difference between and , which can be accurately predicted using nearest neighbor parameters if the free energy changes required to stretch the hairpins from the random coil to an extended conformation ( and ) are sequence-independent, an approximation which is routinely made in single molecule stretching experiments.

Aleksandar Spasic, et al. J Chem Theory Comput. 2012 July 10;8(7):2497-2505.
4.
Figure 3

Figure 3. From: The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation.

Potential of mean force (PMF) and number of broken hydrogen bonds plotted against the end-to-end distance for native (Figure 3a), mutant1 (Figure 3b) and mutant2 sequences (Figure 3c). The PMF calculation has been run three times for the native hairpin and four times for mutant1 and mutant2 hairpins. Solid lines and the left-hand side y-axis are the PMF plots, dashed lines and the right-hand side y-axis denote data for the number of hydrogen bonds broken.

Aleksandar Spasic, et al. J Chem Theory Comput. 2012 July 10;8(7):2497-2505.

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