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. Author manuscript; available in PMC: 2008 Sep 3.
Published in final edited form as: Biochemistry. 2007 Jan 9;46(1):192–199. doi: 10.1021/bi061706u

Table 1.

Kinetic and thermodynamic parameters for variable length vTopo substrates with guanine base substitutions and deletionsa

DNA Sequence KD
(nM)		 kcl kcl
(S−1)		 kr
(S−1)		 kcl/KDb
(107 M−1s−1)		 kcl/KDb
(107 M−1)
32/32 GGGAA 118 ± 20 1.6 ± 0.3 2.2 ± 0.2 1.4 ± 0.2 1.9 1.4
N5 NGGAA 148 ± 30 0.5 ± 0.05 2.3 ± 0.1 4.8 ± 0.1 1.6 0.34
N4 GNGAA 171 ± 20 0.5 ± 0.03 2.4 ± 0.1 5.1 ± 0.1 1.4 0.3
N3 GGNAA 55 ± 10 1 ± 0.2 3.2 ± 0.2 3.1 ± 0.2 5.8 1.8
H5 HGGAA 75 ± 20 0.4 ± 0.03 1.5 ± 0.1 4.2 ± 0.1 2.0 0.53
H4 GHGAA 59 ± 10 0.5 ± 0.03 1.6 ± 0.1 3.4 ± 0.1 2.7 0.85
H3 GGHAA 77 ± 20 0.7 ± 0.03 3.2 ± 0.2 4.4 ± 0.2 4.2 0.91
N5N4 NNGAA 87 ± 10 0.1 ± 0.01 0.2 ± 0.1 2.5 ± 0.3 0.2 0.11
N5N3 NGNAA 48 ± 10 0.2 ± 0.02 1.1 ± 0.2 4.8 ± 0.2 2.2 0.42
H5H4 HHGAA 67 ± 20 0.5 ± 0.06 2.7 ± 0.1 5.8 ± 0.1 4.0 0.75
H5H3 HGHAA 110 ± 20 0.3 ± 0.02 0.9 ± 0.1 3.1 ± 0.2 0.8 0.27
ϕ3 ϕGGAA 64 ± 20 0.015 ± 0.002 0.02
ϕ4 GϕGAA 55 ± 20 0.01 ± 0.002 0.07 ± 0.04 73 ± 45 0.13 0.018
ϕ5 GGϕAA 98 ± 20 0.019 ± 0.003 0.019
24/32 GGGAA 20 ± 5 1.5 ± 0.1 5.6 ± 0.1 3.7 ± 0.1 28 7.5
N5 NGGAA 105 ± 20 0.6 ± 0.1 3.5 ± 0.2 5.9 ± 0.2 3.3 0.57
N4 GNGAA 150 ± 30 0.5 ± 0.05 3.1 ± 0.1 6.4 ± 0.1 2.1 0.33
N3 GGNAA 44 ± 7 2.1 ± 0.2 1.9 ± 0.1 0.9 ± 0.1 4.3 4.8
H5 HGGAA 62 ± 10 0.5 ± 0.03 1.7 ± 0.1 3.8 ± 0.1 2.7 0.8
H4 GHGAA 34 ± 8 0.7 ± 0.05 2.1 ± 0.1 3.3 ± 0.1 6.1 2.0
H3 GGHAA 87 ± 20 1 ± 0.1 2.7 ± 0.1 2.7 ± 0.1 3.1 1.1
N5N4 NNGAA 110 ± 20 0.08 ± 0.01 0.8 ± 0.4 9.4 ± 0.5 0.73 0.073
N5N3 NGNAA 192 ± 20 0.21 ± 0.03 1.6 ± 0.1 7.9 ± 0.1 0.83 0.11
H5H4 HHGAA 54 ± 10 0.25 ± 0.02 1.8 ± 0.1 7.2 ± 0.1 3.3 0.46
H5H3 HGHAA 113 ± 20 0.23 ± 0.03 1.2 ± 0.2 5.1 ± 0.2 1.1 0.2
ϕ3 ϕGGAA 84 ± 20 0.011 ± 0.001 0.012
ϕ4 GϕGAA 7 ± 2 0.007 ± 0.001 0.1
ϕ5 GGϕAA 64 ± 15 0.014 ± 0.003 0.02
18/32 GGGAA 95 ± 20 2.1 ± 0.03 2.2
N5 NGGAA 380 ± 50 0.59 ± 0.05 0.15
N4 GNGAA 95 ± 20 0.65 ± 0.05 0.68
N5N4 NNGAA 167 ± 20 0.09 ± 0.02 0.054
N5N3 NGNAA 134 ± 20 0.12 ± 0.04 0.084
H5H4 HHGAA 347 ± 50 0.29 ± 0.11 0.083
H5H3 HGHAA 590 ± 70 0.24 ± 0.10 0.04
ϕ4 GϕGAA 129 ± 20 0.0003 ±
0.0001		 0.0002
a

See Fig. 2 for structures of H, N and ϕ. Except for the ϕ substitutions, the data for the 32/32mer have been previously reported and are recapitulated here for comparative purposes.

b

Propagated errors in kcl/KD and kcl/KD are less than ± 30% .