The sequences (5′-GUGUCGGUGU-3′)2 and (5′-UGUGGCUGUG-3′)2 are the same nucleotides in reverse 5′ → 3′
order, but differ by 2 kcal/mol in thermodynamic stabilities(Table 1 and Figure 6). Differences in base stacking, especially
at the penultimate base step, provide a structural basis for the difference in thermodynamic stabilities. The two most stable helices (5′-UGUGGCUGUG-3′)2 and (5′-GGUGGCUGUU-3′)2 have the extra bonus for the 5′-GU-3′/3′-UG-5′ base stepin the penultimate position, while the other helix does not have this base step sequence at this helix position. The 5′-GU-3′/3′-UG-5′ base step in the penultimate position has good base stacking, while the 5′-UG-3′/3′-GU-5′ base step has a crossstrand guanine stack that leaves the uracil bases unstacked. Thus, the comparison of the two duplexes provides a structural basis for the thermodynamic bonus parameter for the 5′-UG- 3′/3′-GU-5′ base step
The sequences (5′-GUGUCGGUGU-3′)2 and (5′-UGUGGCUGUG-3′)2 are the same nucleotides in reverse 5′ → 3′order, but differ by 2 kcal/mol in thermodynamic stabilities(Table 1 and Figure 6). Differences in base stacking, especiallyat the penultimate base step, provide a structural basis for the difference in thermodynamic stabilities. The two most stable helices (5′-UGUGGCUGUG-3′)2 and (5′-GGUGGCUGUU-3′)2 have the extra bonus for the 5′-GU-3′/3′-UG-5′ base stepin the penultimate position, while the other helix does not have this base step sequence at this helix position. The 5′-GU-3′/3′-UG-5′ base step in the penultimate position has good base stacking, while the 5′-UG-3′/3′-GU-5′ base step has a crossstrand guanine stack that leaves the uracil bases unstacked. Thus, the comparison of the two duplexes provides a structural basis for the thermodynamic bonus parameter for the 5′-UG- 3′/3′-GU-5′ base step
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