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Temperature dependence of DNA persistence length.

Geggier S, Kotlyar A, Vologodskii A - Nucleic Acids Res. (2010)

Bottom Line: The major contribution into the distribution variance comes from the fluctuations of DNA writhe in the nicked circular molecules which are specified by the value of a.The computation-based analysis of the measured variances was used to obtain the values of a for temperatures up to 60°C.We found a good agreement between the results obtained by these two methods.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, New York University, New York, NY 10003, USA.

ABSTRACT
We have determined the temperature dependence of DNA persistence length, a, using two different methods. The first approach was based on measuring the j-factors of short DNA fragments at various temperatures. Fitting the measured j-factors by the theoretical equation allowed us to obtain the values of a for temperatures between 5°C and 42°C. The second approach was based on measuring the equilibrium distribution of the linking number between the strands of circular DNA at different temperatures. The major contribution into the distribution variance comes from the fluctuations of DNA writhe in the nicked circular molecules which are specified by the value of a. The computation-based analysis of the measured variances was used to obtain the values of a for temperatures up to 60°C. We found a good agreement between the results obtained by these two methods. Our data show that DNA persistence length strongly depends on temperature and accounting for this dependence is important in quantitative comparison between experimental results obtained at different temperatures.

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The temperature dependence of supercoiling free energy, . The shown data represent temperature dependence of K that specifies  according to Equation (6). The lines correspond to the data obtained in the current study (blue solid line), references (42) (green line), (43) (red line) and (44) (dotted blue line).
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Figure 8: The temperature dependence of supercoiling free energy, . The shown data represent temperature dependence of K that specifies according to Equation (6). The lines correspond to the data obtained in the current study (blue solid line), references (42) (green line), (43) (red line) and (44) (dotted blue line).

Mentions: One application of the obtained results is related to the free energy of DNA supercoiling, . It was shown in the pioneering studies by Depew and Wang (23) and Pulleyblank et al. (24) that this energy can be presented as(6)where K is a coefficient that does not depend on DNA length, N, if it exceeds 3000 bp. The value of K depends on temperature, however. This temperature dependence is important for our general understanding of DNA supercoiling and, in particular, for studying the base pair opening assisted by negative supercoiling. All earlier experimental studies of the temperature dependence showed that K is reducing with temperature increase (Figure 8). In the microcalorimetric study, Seidl and Hinz found a large positive value of ΔH for DNA supercoiling at 37°C (42). When they combined their result with the data from references (23,24) for , they concluded that ΔS is also positive, thus the is reducing with temperature (42). We can see from Figure 8 that their result is in very good agreement with our data for temperature around 37°C. Bauer and Benham estimated temperature dependence of indirectly, from the analysis of early melting of supercoiled DNA (43). Although their data correspond to different ionic conditions, they are in reasonable agreement with our results for the temperature range between 30°C and 65°C (Figure 8), where the supercoiling-induced melting was observed. Duguet used the same approach as we did in the current study, although his data are less accurate since they are based on staining DNA in the gel rather than on radioactive labeling (44). Thus all available experimental data on the temperature dependence of the supercoiling free energy are in a reasonable agreement.Figure 8.


Temperature dependence of DNA persistence length.

Geggier S, Kotlyar A, Vologodskii A - Nucleic Acids Res. (2010)

The temperature dependence of supercoiling free energy, . The shown data represent temperature dependence of K that specifies  according to Equation (6). The lines correspond to the data obtained in the current study (blue solid line), references (42) (green line), (43) (red line) and (44) (dotted blue line).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3045604&req=5

Figure 8: The temperature dependence of supercoiling free energy, . The shown data represent temperature dependence of K that specifies according to Equation (6). The lines correspond to the data obtained in the current study (blue solid line), references (42) (green line), (43) (red line) and (44) (dotted blue line).
Mentions: One application of the obtained results is related to the free energy of DNA supercoiling, . It was shown in the pioneering studies by Depew and Wang (23) and Pulleyblank et al. (24) that this energy can be presented as(6)where K is a coefficient that does not depend on DNA length, N, if it exceeds 3000 bp. The value of K depends on temperature, however. This temperature dependence is important for our general understanding of DNA supercoiling and, in particular, for studying the base pair opening assisted by negative supercoiling. All earlier experimental studies of the temperature dependence showed that K is reducing with temperature increase (Figure 8). In the microcalorimetric study, Seidl and Hinz found a large positive value of ΔH for DNA supercoiling at 37°C (42). When they combined their result with the data from references (23,24) for , they concluded that ΔS is also positive, thus the is reducing with temperature (42). We can see from Figure 8 that their result is in very good agreement with our data for temperature around 37°C. Bauer and Benham estimated temperature dependence of indirectly, from the analysis of early melting of supercoiled DNA (43). Although their data correspond to different ionic conditions, they are in reasonable agreement with our results for the temperature range between 30°C and 65°C (Figure 8), where the supercoiling-induced melting was observed. Duguet used the same approach as we did in the current study, although his data are less accurate since they are based on staining DNA in the gel rather than on radioactive labeling (44). Thus all available experimental data on the temperature dependence of the supercoiling free energy are in a reasonable agreement.Figure 8.

Bottom Line: The major contribution into the distribution variance comes from the fluctuations of DNA writhe in the nicked circular molecules which are specified by the value of a.The computation-based analysis of the measured variances was used to obtain the values of a for temperatures up to 60°C.We found a good agreement between the results obtained by these two methods.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, New York University, New York, NY 10003, USA.

ABSTRACT
We have determined the temperature dependence of DNA persistence length, a, using two different methods. The first approach was based on measuring the j-factors of short DNA fragments at various temperatures. Fitting the measured j-factors by the theoretical equation allowed us to obtain the values of a for temperatures between 5°C and 42°C. The second approach was based on measuring the equilibrium distribution of the linking number between the strands of circular DNA at different temperatures. The major contribution into the distribution variance comes from the fluctuations of DNA writhe in the nicked circular molecules which are specified by the value of a. The computation-based analysis of the measured variances was used to obtain the values of a for temperatures up to 60°C. We found a good agreement between the results obtained by these two methods. Our data show that DNA persistence length strongly depends on temperature and accounting for this dependence is important in quantitative comparison between experimental results obtained at different temperatures.

Show MeSH
Related in: MedlinePlus