Table 2. Affinity of APE1 for hetero-deoxy ODNs and their duplexesa.
| Code | Sequence | KI(exp.) (μM)b | KI(calc.) (μM)c | KI(ss):KI(ds) | KI(specific):KI(nonspecific) |
|---|---|---|---|---|---|
| Nonspecific ss heterooligonucleotides | |||||
| ss dp(CTCCCTTCCT) | 3.1 ± 0.3 | 3.3 ± 0.3 | N/A | N/A | |
| ss dp(CTCACACACT) | 2.6 ± 0.3 | 2.9 ± 0.3 | N/A | N/A | |
| ss dp(GAAGAGAAGA) | 2.2 ± 0.4 | 1.9 ± 0.2 | N/A | N/A | |
| ss dp(CTAGTCA A CA)d | 2.6 ± 0.3 | 2.4 ± 0.3 | N/A | N/A | |
| Nonspecific and specific ss and ds homo-ODNs containing one irregular nucleotide | |||||
| 14C8 | ss d[(pT)7pC(pT)6] | 2.5 ± 0.3 | 2.6 ± 0.3 | 3.0 | |
| ds d[(pT)7pC(pT)6]·d(pA)14 | 0.83 ± 0.1 | N/D | |||
| 14G8 | ss d[(pT)7pG(pT)6] | 3.0 ± 0.3 | 2.6 ± 0.3 | 2.0 | ss/ss = 6.4–7.7 |
| ds d[(pT)7pG(pT)6]·d(pA)14 | 1.5 ± 0.2 | N/D | ds/ds = 6.4–11.5 | ||
| 14R8 | ss d[(pT)7pR(pT)6] | 0.39 ± 0.2 | 0.38 ± 0.4 | 3.0 | |
| ds d[(pT)7pR(pT)6]·d(pA)14 | 0.13 ± 0.15 | N/D | ss/ss = 5.0–6.0 | ||
| 14F8 | ss d[(pT)7pF(pT)6] | 0.5 ± 0.1 | N/D | 3.0 | ds/ds = 2.0 |
| ds d[(pT)7pF(pT)6]·d(pA)14 | 0.16 ± 0.03 | N/D | |||
| Nonspecific and specific ss and ds heterooligonucleotides | |||||
| 24A8 | ss dp(CTAGTCA A CACTGTCTGTGGATAC) | 2.1 ± 0.3 | 2.5 ± 0.3e | 4.2 | |
| ds dp(CTAGTCA A CACTGTCTGTGGATAC) | 0.5 ± 0.1 | 0.8 ± 0.2f | ss/ss = 6.0 | ||
| 24R8 | ss dp(CTAGTCA R CACTGTCTGTGGATAC) | 0.35 ± 0.3 | 0.39 ± 0.3e | 2.7 | ds/ds = 3.8 |
| ds dp(CTAGTCA R CACTGTCTGTGGATAC) | 0.13 ± 0.05 | 0.12 ± 0.2f | |||
N/A, not applicable, N/D, not determined.
aMean ± SE of three measurements are given.
bKI values shown in bold were determined directly, others were calculated from the respective IC50 values.
cCalculated KI values were estimated from Equation 1 using the following factors: Kd[Pi] = 264 μM, e = 1.51, hC = 1.01, hT = 1.05, hG = 1.07, hA = 1.10.
dThe italicized sequence of the decanucleotide corresponds to the 5′-sequence within long oligonucleotides 24A8 and 24R8 (the variable nucleotide in the eighth position is shown in bold).
eSince the DNA-binding site of APE1 contains 10 nucleotide-binding subsites, KI values for ss 24A8 and 24R8 were calculated for the decamers GTCAACACTG and GTCARCACTG, respectively.
fThe KI values for ds 24A8 and ds 24R8 were calculated by simple division of the calculated KI for ss 24A8 and ss 24R8 by an average value of a ratio of KI(ss)/KI(ds) = 3.0, calculated using six values from this table.