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. Author manuscript; available in PMC: 2008 Dec 8.
Published in final edited form as: Biochemistry. 2007 Mar 27;46(16):4861–4875. doi: 10.1021/bi062169g

Table 3.

Thermodynamic Contribution from the P1 Extension

Oligonucleotide Kd (μM) Δ ΔG (kcal/mol)
CCUCdTA 3.0•10−3
CCUCdTAAACC 0.4•10−6 a − 5.4
 UCGA 1050
 UCGAAACC 0.11 − 5.5

Dissociation constants from ternary complexes E•S•G and E•P•UCGA(AACC) were obtained at 30 °C. S and P had 2′-deoxyribose substitutions at position -1.

a

Calculated from the dissociation rate constant of S from E•S and the observation of 6-fold cooperativity of S and G binding with this oligonucleotide substrate (Table 2). Direct measurement was not possible because dissociation was slower than reaction to form P.