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The flexibility of locally melted DNA.

Forties RA, Bundschuh R, Poirier MG - Nucleic Acids Res. (2009)

Bottom Line: One proposed explanation suggests that local melting of a few base pairs introduces flexible hinges.We have expanded this model to incorporate sequence and temperature dependence of the local melting, and tested it for three sequences at temperatures from 23 degrees C to 42 degrees C.We find that small melted bubbles are significantly more flexible than double-stranded DNA and can alter DNA flexibility at physiological temperatures.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, The Ohio State University, 191 West Woodruff Avenue, Columbus, OH 43210-1117, USA.

ABSTRACT
Protein-bound duplex DNA is often bent or kinked. Yet, quantification of intrinsic DNA bending that might lead to such protein interactions remains enigmatic. DNA cyclization experiments have indicated that DNA may form sharp bends more easily than predicted by the established worm-like chain (WLC) model. One proposed explanation suggests that local melting of a few base pairs introduces flexible hinges. We have expanded this model to incorporate sequence and temperature dependence of the local melting, and tested it for three sequences at temperatures from 23 degrees C to 42 degrees C. We find that small melted bubbles are significantly more flexible than double-stranded DNA and can alter DNA flexibility at physiological temperatures. However, these bubbles are not flexible enough to explain the recently observed very sharp bends in DNA.

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Measured J factors as a function of temperature. In all plots, the predictions of the WLC are shown by the dashed line, and the predictions of the sequence-dependent Yan–Marko model for Fit 5 are shown by the solid line. Fits 1–4 are nearly indistinguishable from Fit 5, and are shown as Supplementary Data. (a) A 200-bp fragment of λ DNA, with our experimental data shown by the open triangles and data from (7) shown by the closed triangle. (b) The 116cl sequence (open diamonds) is a 116-bp sequence designed to minimize the formation of local bubbles, while (c) the 116o sequence (open circles) is designed to readily form local bubbles in several locations.
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Figure 4: Measured J factors as a function of temperature. In all plots, the predictions of the WLC are shown by the dashed line, and the predictions of the sequence-dependent Yan–Marko model for Fit 5 are shown by the solid line. Fits 1–4 are nearly indistinguishable from Fit 5, and are shown as Supplementary Data. (a) A 200-bp fragment of λ DNA, with our experimental data shown by the open triangles and data from (7) shown by the closed triangle. (b) The 116cl sequence (open diamonds) is a 116-bp sequence designed to minimize the formation of local bubbles, while (c) the 116o sequence (open circles) is designed to readily form local bubbles in several locations.

Mentions: The results of cyclization experiments plotted alongside our sequence-dependent Yan–Marko model predictions for the three DNA molecules are shown in Figure 4. Also shown is the result of Vologodskaia and Vologodskii (7) for the 200 bp λ sequence, which quantitatively agrees with our measurements at 23°C. We adjusted the dsDNA persistence lengths of the 200 bp λ, 116cl and 116o molecules to 51, 44 and 48 nm, respectively, to fit the measured J factors at 23°C. These persistence length values are within the range reported in the literature (6–9,11,13). At 23°C, the excitations of melted base pairs are so rare that they do not contribute significantly to the J factor (Figure 4). These variations in J factors are likely to be due to other effects such as sequence-dependent permanent bend, twist and anisotropic bending and twisting fluctuations (19,20,30,31,33). We also note that TA stacks (a T followed by an A in the DNA sequence) periodic with the helical repeat have been suggested to promote cyclization (14,15), and that the 116o sequence contains eight TA stacks not found in the 116cl sequence. We therefore placed these TA stacks such that no pair is separated by an integer number of helical repeats to minimize any contribution to cyclization from this effect. It is possible that if this effect is due to permanent bendedness of TA stacks, such out of phase bends could be partially responsible for the 116o sequence having a smaller J factor than the 116cl sequence at 23°C.Figure 4.


The flexibility of locally melted DNA.

Forties RA, Bundschuh R, Poirier MG - Nucleic Acids Res. (2009)

Measured J factors as a function of temperature. In all plots, the predictions of the WLC are shown by the dashed line, and the predictions of the sequence-dependent Yan–Marko model for Fit 5 are shown by the solid line. Fits 1–4 are nearly indistinguishable from Fit 5, and are shown as Supplementary Data. (a) A 200-bp fragment of λ DNA, with our experimental data shown by the open triangles and data from (7) shown by the closed triangle. (b) The 116cl sequence (open diamonds) is a 116-bp sequence designed to minimize the formation of local bubbles, while (c) the 116o sequence (open circles) is designed to readily form local bubbles in several locations.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Figure 4: Measured J factors as a function of temperature. In all plots, the predictions of the WLC are shown by the dashed line, and the predictions of the sequence-dependent Yan–Marko model for Fit 5 are shown by the solid line. Fits 1–4 are nearly indistinguishable from Fit 5, and are shown as Supplementary Data. (a) A 200-bp fragment of λ DNA, with our experimental data shown by the open triangles and data from (7) shown by the closed triangle. (b) The 116cl sequence (open diamonds) is a 116-bp sequence designed to minimize the formation of local bubbles, while (c) the 116o sequence (open circles) is designed to readily form local bubbles in several locations.
Mentions: The results of cyclization experiments plotted alongside our sequence-dependent Yan–Marko model predictions for the three DNA molecules are shown in Figure 4. Also shown is the result of Vologodskaia and Vologodskii (7) for the 200 bp λ sequence, which quantitatively agrees with our measurements at 23°C. We adjusted the dsDNA persistence lengths of the 200 bp λ, 116cl and 116o molecules to 51, 44 and 48 nm, respectively, to fit the measured J factors at 23°C. These persistence length values are within the range reported in the literature (6–9,11,13). At 23°C, the excitations of melted base pairs are so rare that they do not contribute significantly to the J factor (Figure 4). These variations in J factors are likely to be due to other effects such as sequence-dependent permanent bend, twist and anisotropic bending and twisting fluctuations (19,20,30,31,33). We also note that TA stacks (a T followed by an A in the DNA sequence) periodic with the helical repeat have been suggested to promote cyclization (14,15), and that the 116o sequence contains eight TA stacks not found in the 116cl sequence. We therefore placed these TA stacks such that no pair is separated by an integer number of helical repeats to minimize any contribution to cyclization from this effect. It is possible that if this effect is due to permanent bendedness of TA stacks, such out of phase bends could be partially responsible for the 116o sequence having a smaller J factor than the 116cl sequence at 23°C.Figure 4.

Bottom Line: One proposed explanation suggests that local melting of a few base pairs introduces flexible hinges.We have expanded this model to incorporate sequence and temperature dependence of the local melting, and tested it for three sequences at temperatures from 23 degrees C to 42 degrees C.We find that small melted bubbles are significantly more flexible than double-stranded DNA and can alter DNA flexibility at physiological temperatures.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, The Ohio State University, 191 West Woodruff Avenue, Columbus, OH 43210-1117, USA.

ABSTRACT
Protein-bound duplex DNA is often bent or kinked. Yet, quantification of intrinsic DNA bending that might lead to such protein interactions remains enigmatic. DNA cyclization experiments have indicated that DNA may form sharp bends more easily than predicted by the established worm-like chain (WLC) model. One proposed explanation suggests that local melting of a few base pairs introduces flexible hinges. We have expanded this model to incorporate sequence and temperature dependence of the local melting, and tested it for three sequences at temperatures from 23 degrees C to 42 degrees C. We find that small melted bubbles are significantly more flexible than double-stranded DNA and can alter DNA flexibility at physiological temperatures. However, these bubbles are not flexible enough to explain the recently observed very sharp bends in DNA.

Show MeSH
Related in: MedlinePlus