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. Author manuscript; available in PMC: 2010 May 12.
Published in final edited form as: Biochemistry. 2009 May 12;48(18):3988–3997. doi: 10.1021/bi900070f

Table 2.

Comparison of the differences in base-pair opening free energies (ΔΔGop) in the two RNA-DNA hybrids investigated to the differences in the NN free energies (ΔΔGNN) predicted by duplex melting data

Position Base pair ΔΔGop (kcal/mol)1 ΔΔGNN (kcal/mol)2
3 C-G −0.73 0
4 G-C −0.12 0
5 C-G 0.41 0
6 A-U/T −0.11 −0.5
7 G-C −1.33 −1.2
8 G-C - -
9 C-G −0.37 0.7
10 C-G 0.25 1.2
11 T/U-A 0.89 0.7
12 T/U-A 1.44 0.8
13 C-G 1.72 1.3
1

ΔΔ Gop was calculated from the values reported in Table 1, as ΔΔGop = ΔGop(Hybrid I) – ΔGop(Hybrid II).

2

ΔΔGNN was calculated as ΔΔGNN = ΔGNN(Hybrid I) – ΔGNN(Hybrid II).

The ΔGNN value for each base pair was calculated as the sum of the NN free energies for the base pair of interest and the two base pairs adjacent to it (35).