Table 1 DNA bending in glycosylase-DNA complexes.

From: Automated AFM analysis of DNA bending reveals initial lesion sensing strategies of DNA glycosylases

 

DNA bend angles from AFM ± 2 σ width (relative population)

Average from AFM angles weighted by populations

EFRET ± SD

DNA bend angle ± SD from FRET

EFRET ± SD from simulations

DNA bend angle ± SD from simulations

non-specific (nsp) DNA

8° ± 53° (100%)

8°

0.191 ± 0.002

7° ± 4°

0.186 ± 0.001

6.6° ± 0.2°

nsp DNA + hTDG

30° ± 25° (51%)

41°

n.d

n.d

n.d

n.d

69° ± 25° (49%)

nsp DNA + hOGG1

0° ± 20° (36%)

50°

0.291 ± 0.007

49° ± 2°

0.235 ± 0.035

41.5° ± 5.7°

35° ± 15° (17%)

67° ± 20° (47%)

nsp DNA + MutY

15° ± 30° (46%)

34°

0.233 ± 0.019

34° ± 8°

0.224 ± 0.019

32.2° ± 2.7°

50° ± 30°(54%)

nsp DNA + hAAG

0° ± 10° (27%)

33°

0.230 ± 0.005

33° ± 2°

0.209 ± 0.011

25.9° ± 1.4°

16° ± 15°(28%)

44° ± 30° (45%)

  1. DNA bend angles from AFM were determined as the centers of Gaussian fits (± 2 σ) to automated bend angle analyses of glycosylase complexes with undamaged (non-specific) DNA (Fig. 2). Values from FRET are averages from triplicate measurements (± one standard deviation). The average EFRET from simulations and DNA bend angles calculated from this value are based on the bend angle states and corresponding populations from AFM experiments.
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