Table IV.
Atomic charges estimated by Merz-Kollman analysis [18] of atoms contributing to the hydrogen bonds between the two single-strands for B-form double-strands. The average value means the average for all oxygen, nitrogen or hydrogen atoms contributing the hydrogen bonds between single-strands. It is noted that the results for A-form double-strand are listed for RNA-RNA, because A-form is more stable than B-form for only RNA-RNA.
| PNA-RNA | LNA-LNA | RNA-DNA | LNA-DNA | PNA-DNA | |
|---|---|---|---|---|---|
| O(C)…H-N(G) | −0.71, 0.55, −1.06 | −0.61, 0.50, −1.02 | −0.59, 0.46, −0.91 | −0.61, 0.53, −1.05 | −0.59, 0.46, −0.99 |
| N(C)…H-N(G) | −0.70, 0.42, −0.76 | −0.64, 0.38, −0.72 | −0.69, 0.37, −0.66 | −0.65, 0.43, −0.78 | −0.69, 0.47, −0.82 |
| N-H(C)…O(G) | −0.94, 0.51, −0.57 | −0.86, 0.45, −0.54 | −0.90, 0.47, −0.54 | −0.94, 0.49, −0.56 | −0.90, 0.47, −0.55 |
| N(A)…H-N(T) | −0.96, 0.51, −0.87 | −1.01, 0.42, −0.55 | −0.52, 0.31, −0.39 | −0.92, 0.56, −0.76 | −1.65, 0.93, −1.23 |
| N-H(A)…O(T) | −0.85, 0.46, −0.57 | −0.91, 0.44, −0.51 | −0.64, 0.32, −0.47 | −0.77, 0.40, −0.51 | −0.87, 0.45, −0.52 |
| N-H(G)…O(C) | −0.99, 0.47, −0.61 | −1.02, 0.50, −0.57 | −0.97, 0.47, −0.57 | −1.02, 0.48, −0.62 | −0.95, 0.43, −0.57 |
| N-H(G)…N(C) | −0.81, 0.51, −0.83 | −0.89, 0.47, −0.63 | −0.75, 0.43, −0.66 | −0.84, 0.53, −0.82 | −0.85, 0.49, −0.70 |
| O(G)…H-N(C) | −0.55, 0.49, −0.93 | −0.56, 0.45, −0.85 | −0.53, 0.41, −0.78 | −0.58, 0.49, −0.91 | −0.56, 0.45, −0.82 |
| average | −0.81, 0.49, −0.78 | −0.81, 0.45, −0.67 | −0.70, 0.41, −0.62 | −0.79, 0.49, −0.75 | −0.88, 0.52, −0.78 |
| LNA-RNA | PNA-LNA | PNA-PNA | DNA-DNA | RNA-RNA | |
| O(C)…H-N(G) | −0.61, 0.51, −1.02 | −0.69, 0.50, −1.02 | −0.61, 0.48, −0.98 | −0.54, 0.45, −0.86 | −0.58, 0.50, −1.06 |
| N(C)…H-N(G) | −0.66, 0.44, −0.81 | −0.72, 0.47, −0.80 | −0.65, 0.40, −0.74 | −0.56, 0.34, −0.59 | −0.65, 0.47, −0.92 |
| N-H(C)…O(G) | −0.91, 0.48, −0.59 | −0.88, 0.47, −0.54 | −0.93, 0.51, −0.57 | −0.83, 0.44, −0.54 | −0.96, 0.50, −0.60 |
| N(A)…H-N(T) | −1.59, 1.03, −1.31 | −0.87, 0.23, −0.30 | −1.28, 0.57, −0.64 | −0.98, 0.66, −0.55 | −1.02, 0.41, −0.33 |
| N-H(A)…O(T) | −0.94, 0.51, −0.63 | −0.93, 0.44, −0.49 | −0.82, 0.42, −0.54 | −0.49, 0.29, −0.54 | −0.43, 0.29, −0.43 |
| N-H(G)…O(C) | −1.03, 0.49, −0.60 | −1.01, 0.50, −0.66 | −1.14, 0.58, −0.67 | −0.90, 0.43, −0.55 | −1.05, 0.50, −0.56 |
| N-H(G)…N(C) | −0.92, 0.56, −0.83 | −0.81, 0.47, −0.73 | −0.97, 0.54, −0.75 | −0.72, 0.46, −0.68 | −0.76, 0.38, −0.55 |
| O(G)…H-N(C) | −0.60, 0.51, −0.94 | −0.58, 0.46, −0.87 | −0.58, 0.49, −0.90 | −0.55, 0.45, −0.85 | −0.57, 0.51, −0.95 |
| average | −0.91, 0.57, −0.84 | −0.81, 0.44, −0.68 | −0.87, 0.50, −0.72 | −0.70, 0.44, −0.65 | −0.75, 0.45, −0.68 |