. Author manuscript; available in PMC: 2013 Aug 8.

Published in final edited form as: Biochemistry. 2005 Oct 11;44(40):13225–13234. doi: 10.1021/bi051236o

Table 3.

Free-Energy Increments (kcal/mol at 37 °C) for Symmetric 2 × 2 Purine Loops (88)^a

closing base pairs

loops

\begin{matrix} GA \\ AG \end{matrix}

\begin{matrix} AG \\ GA \end{matrix}

\begin{matrix} AA \\ AA \end{matrix}

\begin{matrix} 5^{'} G \\ 3^{'} C \end{matrix}

−2.6

−1.3

1.5

\begin{matrix} 5^{'} C \\ 3^{'} G \end{matrix}

−0.7

1.3

\begin{matrix} 5^{'} A \\ 3^{'} U \end{matrix}

0.3

1.7

2.8

\begin{matrix} 5^{'} U \\ 3^{'} A \end{matrix}

0.7

0.9

2.8

\begin{matrix} 5^{'} G \\ 3^{'} U \end{matrix}

1.8

2.6

4.1

\begin{matrix} 5^{'} U \\ 3^{'} G \end{matrix}

0.1

3.4

2.1

All motifs are symmetric. Thus, a closing base pair of $\begin{matrix} 5^{'} G \\ 3^{'} C \end{matrix}$ and a loop of $\begin{matrix} GA \\ AG \end{matrix}$ represent the motif $\begin{matrix} 5^{'} G \underline{GA} C 3^{'} \\ 3^{'} C AG G 5^{'} \end{matrix}$ . Values are from refs 26 and 88, and based on the experimental data from refs 88–92.