Table 1 Binding kinetic and associated errors for relevant datasets
From: Nucleosome unwrapping and PARP1 allostery drive affinities for chromatin and DNA breaks
DNA substrate | DNA tension | Protein | Tag | Lifetime (s) | kon (M-1s-1) | KD (nM) | N |
|---|---|---|---|---|---|---|---|
Nicked lambda DNA | 10 pN | PARP1 | HaloTag | 2.3 ± 0.04 s | 5.4 ± 0.9 ×108 | 0.8 ± 0.1 | 272 |
Nicked lambda DNA | 10 pN | PARP1-H862A /896 A /E988A | HaloTag | τ1 = 6.7 ± 0.3 s (41%) τ2 = 100.0 ± 3.9 s (59%) τavg = 61.7 ± 3.9 s | 2.0 ± 0.2 ×108 | 0.08 ± 0.01 | 105 |
Nicked lambda DNA | 10 pN | PARP1-E988Q | HaloTag | τ1 = 3.8 ± 0.1 s (68%) τ2 = 78.1 ± 6.5 s (32%) τavg = 27.5 ± 2.4 s | 2.0 ± 0.2 ×108 | 0.18 ± 0.03 | 97 |
Nicked lambda DNA | 10 pN | PARP1 + 100 μM EB-47 | HaloTag | τ1 = 23.2 ± 1.1 s (41%) τ2 = 193.5 ± 7.2 s (59%) τavg = 123.7 ± 7.6 s | 1.3 ± 0.3 ×109a | 0.01 ± 0.001 | 135 |
Nicked lambda DNA | 10 pN | PARP1 + 100 μM Olaparib | HaloTag | 2.0 ± 0.03 s | 3.4 ± 0.6 ×108 | 1.6 ± 0.1 | 420 |
Nicked lambda DNA | 10 pN | PARP1-ZnF1-2 | HaloTag | 2.1 ± 0.4 s | 3.4 ± 0.5 ×107 | 14 ± 3.5 | 253 |
Nicked lambda DNA | 10 pN | PARP2 | YFP | 16.6 ± 0.5 s | 9.1 ± 5.0 ×107 | 0.7 ± 0.4 | 79 |
NCP (undamaged) | 4 pN | PARP1 | YFP | 2.5 ± 0.1 s | 3.9 ± 0.3 ×107 | 10.2 ± 0.9 | 57 |
NCP (undamaged) | 10 pN | PARP1 | YFP | 6.9 ± 0.5 s | 1.4 ± 0.1 ×108 | 1.0 ± 0.1 | 54 |
NCP (undamaged) | 4 pN | PARP1-H862A /896 A /E988A | HaloTag | 56 ± 12 s | 4.5 ± 1.9 ×109 | 0.004 ± 0.002 | 22 |
NCP (undamaged) | 4 pN | PARP1+100 μM EB-47 | HaloTag | τ1 = 2.1 ± 0.3 s (45%) τ2 = 264 ± 31 s (55%) τavg = 146 ± 27.0 s | 6.7 ± 1.4 ×108 | 0.01 ± 0.003 | 32 |
Single nonligatable nick | 4 pN | PARP1 | YFP | 2.9 ± 0.1 s | 1.7 ± 0.1 ×108 | 2.0 ± 0.2 | 87 |
NCP with nick at SHL-4.5 | 4 pN | PARP1 | YFP | 2.3 ± 0.2 s | 1.1 ± 0.1 ×108 | 4.0 ± 0.5 | 32 |
NCP with nick at SHL-2.5 | 4 pN | PARP1 | YFP | 2.6 ± 0.1 s | 1.0 ± 0.1 ×108 | 3.9 ± 0.4 | 96 |
NCP with nick at SHL0 | 4 pN | PARP1 | YFP | 2.9 ± 0.2 s | 1.6 ± 0.2 ×108 | 2.2 ± 0.3 | 62 |
Single nonligatable nick | 10 pN | PARP1 | YFP | 3.4 ± 0.08 s | 2.7 ± 0.2 ×108 | 1.1 ± 0.1 | 89 |
NCP with nick at SHL-4.5 | 10 pN | PARP1 | YFP | 5.0 ± 0.1 s | 1.3 ± 0.1 ×108 | 1.5 ± 0.1 | 115 |
NCP with nick at SHL−2.5 | 10 pN | PARP1 | YFP | 4.7 ± 0.1 s | 1.7 ± 0.1 ×108 | 1.3 ± 0.1 | 99 |
NCP with nick at SHL0 | 10 pN | PARP1 | YFP | 4.6 ± 0.4 s | 8.3 ± 0.7 ×107 | 2.6 ± 0.3 | 112 |
Nick DNA | 10 pN | PBZ | mRuby2 | 0.6 ± 0.2 s | 6.0 ± 1.3 ×108 | 2.7 ± 0.4 | 26 |
NCP (undamaged) | 4 pN | PBZ | mRuby2 | 1.9 ± 0.03 s | 9.0 ± 0.6 ×108 | 5.8 ± 0.4 | 93 |
NCP with nick at SHL0 | 10 pN | PBZ | mRuby2 | 1.4 ± 0.1 s | 3.0 ± 0.6 ×107 | 24.3 ± 4.4 | 36 |
