Table 2 Numerical values reporting on the association rate constant, kon, and the dissociation rate constant, koff, quantifying the interaction between different oligonucleotides and BsCspB obtained under dilute conditions and in crowded environments determined by kinetic stopped-flow fluorescence spectroscopy.

From: Impact of crowded environments on binding between protein and single-stranded DNA

Ligand

Condition

kon (107/s/M)

koff (/s)

koffeq (/s)

dT5

Dilute

34 ± 1

100 ± 10

260

dT6

Dilute

32 ± 1

n.d

18

dT7

Dilute

35 ± 4

n.d

4

dT5

100 g/L EG

25 ± 2

120 ± 10

n.d.

dT5

200 g/L EG

15 ± 1

160 ± 10

n.d.

dT5

300 g/L EG

10 ± 3

230 ± 10

510

dT5

100 g/L PEG1

23 ± 1

100 ± 10

n.d.

dT5

200 g/L PEG1

13 ± 1

100 ± 10

n.d.

dT5

300 g/L PEG1

7 ± 1

110 ± 5

270

dT5

100 g/L glucose

29 ± 1

40 ± 10

n.d.

dT5

200 g/L glucose

18 ± 1

40 ± 10

n.d.

dT5

300 g/L glucose

10 ± 3

40 ± 5

130

dT5

100 g/L Dex20

27 ± 2

70 ± 20

190

dT5

200 g/L Dex20

8 ± 1

85 ± 5

50

dT5

300 g/L PEG1

7 ± 1

110 ± 5

266

dT6

300 g/L PEG1

7.8 ± 0.1

10 ± 1

40

dT7

300 g/L PEG1

7.5 ± 0.1

3.1 ± 0.3

13

  1. The value of koffeq has been calculated by applying koffeq = KD*kon (see Table 1 reporting on KD values). The concentration of BsCspB was set to 60 nM in all experiments except in presence of 300 g/L EG (cBsCspB = 300 nM). A 5- to 20-fold stoichiometric excess of ligand concerning BsCspB has been used in all kinetic stopped-flow fluorescence experiments which have been performed at T = 288 K. n.d.: not determined. Associated data are shown in Figs. 3A–D, S7A,B, and S8A–C.