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Proteins that act at specific DNA sequences bind DNA randomly and then …


Biology Articles » Biophysics » Molecular Biophysics » Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA » Table 1

Table 1
- Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA

Processivity values

Separation, bp

30
40
45
75
NaCl, mM RIR/IRIR/IRIR/IRIR/I
0 46 ± 2 33 ± 4 1.39 44 ± 3 33 ± 1 1.33 47 ± 3 35 ± 4 1.34 40 ± 2 42 ± 2 0.95
30 36 ± 2 29 ± 3 1.24 36 ± 1 27 ± 3 1.33 38 ± 2 31 ± 1 1.23 32 ± 6 33 ± 2 0.97
60 29 ± 3 25 ± 5 1.16 25 ± 1 22 ± 1 1.14 28 ± 8 23 ± 3 1.21 23 ± 6 22 ± 1 1.05
150 15 ± 1 15 ± 1 1.0 14 ± 1 14 ± 3 1.0 13 ± 3 13 ± 2 1.0 11 ± 2 11 ± 1 1.0
The substrates were 301-bp fragments with two BbvCI sites separated by the number of bp noted, in either repeated or inverted orientations. Reactions contained 0.3 nM BbvCI endonuclease and 30 nM DNA in reaction buffer with NaCl as indicated. Processivity factors on repeated and inverted sites, R and I, were calculated from the initial rates of product formation; the ratios of the values, R/I, are noted in bold. Error margins denote standard deviations from at least four repeats.

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