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Mechanism of DNA flexibility enhancement by HMGB proteins.

Zhang J, McCauley MJ, Maher LJ, Williams MC, Israeloff NE - Nucleic Acids Res. (2009)

Bottom Line: These results are consistent with analysis of the observed global persistence length changes derived from end-to-end distance measurements, and with results of DNA-stretching experiments.The moderately broad distributions of bend angles induced by both proteins are inconsistent with either a static kink model, or a purely flexible hinge model for DNA distortion by protein binding.Therefore, the mechanism by which HMGB proteins enhance the flexibility of DNA must differ from that of the Escherichia coli HU protein, which in previous studies showed a flat angle distribution consistent with a flexible hinge model.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, Northeastern University, Boston, MA 02115, USA.

ABSTRACT
The mechanism by which sequence non-specific DNA-binding proteins enhance DNA flexibility is studied by examining complexes of double-stranded DNA with the high mobility group type B proteins HMGB2 (Box A) and HMGB1 (Box A+B) using atomic force microscopy. DNA end-to-end distances and local DNA bend angle distributions are analyzed for protein complexes deposited on a mica surface. For HMGB2 (Box A) binding we find a mean induced DNA bend angle of 78 degrees, with a standard error of 1.3 degrees and a SD of 23 degrees, while HMGB1 (Box A+B) binding gives a mean bend angle of 67 degrees, with a standard error of 1.3 degrees and a SD of 21 degrees. These results are consistent with analysis of the observed global persistence length changes derived from end-to-end distance measurements, and with results of DNA-stretching experiments. The moderately broad distributions of bend angles induced by both proteins are inconsistent with either a static kink model, or a purely flexible hinge model for DNA distortion by protein binding. Therefore, the mechanism by which HMGB proteins enhance the flexibility of DNA must differ from that of the Escherichia coli HU protein, which in previous studies showed a flat angle distribution consistent with a flexible hinge model.

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Local DNA bend angle versus segment step size. A linear fit is shown for the intermediate range of step sizes (from 24 to 66 nm).
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Figure 3: Local DNA bend angle versus segment step size. A linear fit is shown for the intermediate range of step sizes (from 24 to 66 nm).

Mentions: We used a second method to estimate the persistence length of the bare dsDNA, which involved measuring the local DNA angle distribution. This method was first proposed by Landau and Lifshitz in 1958 (34). More recently, Rivetti et al. (19) and Abels et al. (35) deduced persistence length using a similar approach. By tracing the dsDNA contours, we calculated the local bend angle, θ, of two consecutive segments at different step size l. Using the probability distribution function for the WLC model in two dimensions it can be shown that:3Equation (3) can be transformed to Equation (4) by taking the natural logarithm on both sides:4From a linear fit of this equation to the data, the slope 1/2p, is extracted. The equation should only be valid up to l ∼ p, and angle measurement errors are significant at small l, thus a good linear fit is expected only for intermediate values (19,36). Step sizes of 24 nm < l < 66 nm were found to be optimal for determining p (Figure 3). The persistence length obtained by this method was p = 49.5 ± 3.5 nm, which agrees, within error, with the value found by the end-to-end distance method, and with 45–50 nm expected from solution studies (37). This illustrates the near equivalence of locally measured and globally measured polymer properties. In fact, the locally measured value should be more reliable than the end-to-end distance method because the choice of a limited step size range avoids excluded volume effects that can occur for longer polymers (19,36).Figure 3.


Mechanism of DNA flexibility enhancement by HMGB proteins.

Zhang J, McCauley MJ, Maher LJ, Williams MC, Israeloff NE - Nucleic Acids Res. (2009)

Local DNA bend angle versus segment step size. A linear fit is shown for the intermediate range of step sizes (from 24 to 66 nm).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651801&req=5

Figure 3: Local DNA bend angle versus segment step size. A linear fit is shown for the intermediate range of step sizes (from 24 to 66 nm).
Mentions: We used a second method to estimate the persistence length of the bare dsDNA, which involved measuring the local DNA angle distribution. This method was first proposed by Landau and Lifshitz in 1958 (34). More recently, Rivetti et al. (19) and Abels et al. (35) deduced persistence length using a similar approach. By tracing the dsDNA contours, we calculated the local bend angle, θ, of two consecutive segments at different step size l. Using the probability distribution function for the WLC model in two dimensions it can be shown that:3Equation (3) can be transformed to Equation (4) by taking the natural logarithm on both sides:4From a linear fit of this equation to the data, the slope 1/2p, is extracted. The equation should only be valid up to l ∼ p, and angle measurement errors are significant at small l, thus a good linear fit is expected only for intermediate values (19,36). Step sizes of 24 nm < l < 66 nm were found to be optimal for determining p (Figure 3). The persistence length obtained by this method was p = 49.5 ± 3.5 nm, which agrees, within error, with the value found by the end-to-end distance method, and with 45–50 nm expected from solution studies (37). This illustrates the near equivalence of locally measured and globally measured polymer properties. In fact, the locally measured value should be more reliable than the end-to-end distance method because the choice of a limited step size range avoids excluded volume effects that can occur for longer polymers (19,36).Figure 3.

Bottom Line: These results are consistent with analysis of the observed global persistence length changes derived from end-to-end distance measurements, and with results of DNA-stretching experiments.The moderately broad distributions of bend angles induced by both proteins are inconsistent with either a static kink model, or a purely flexible hinge model for DNA distortion by protein binding.Therefore, the mechanism by which HMGB proteins enhance the flexibility of DNA must differ from that of the Escherichia coli HU protein, which in previous studies showed a flat angle distribution consistent with a flexible hinge model.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, Northeastern University, Boston, MA 02115, USA.

ABSTRACT
The mechanism by which sequence non-specific DNA-binding proteins enhance DNA flexibility is studied by examining complexes of double-stranded DNA with the high mobility group type B proteins HMGB2 (Box A) and HMGB1 (Box A+B) using atomic force microscopy. DNA end-to-end distances and local DNA bend angle distributions are analyzed for protein complexes deposited on a mica surface. For HMGB2 (Box A) binding we find a mean induced DNA bend angle of 78 degrees, with a standard error of 1.3 degrees and a SD of 23 degrees, while HMGB1 (Box A+B) binding gives a mean bend angle of 67 degrees, with a standard error of 1.3 degrees and a SD of 21 degrees. These results are consistent with analysis of the observed global persistence length changes derived from end-to-end distance measurements, and with results of DNA-stretching experiments. The moderately broad distributions of bend angles induced by both proteins are inconsistent with either a static kink model, or a purely flexible hinge model for DNA distortion by protein binding. Therefore, the mechanism by which HMGB proteins enhance the flexibility of DNA must differ from that of the Escherichia coli HU protein, which in previous studies showed a flat angle distribution consistent with a flexible hinge model.

Show MeSH
Related in: MedlinePlus