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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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Comparison between theoretical and experimental values of the linking number variance, . Experimental data (filled circle) for 37°C were taken from reference (25). The data from the current study (open triangle) and from reference (33) (open circle) were adjusted to 37°C according to the temperature dependence of  presented in Figure 5. The line represents the best theoretical fit of the data. The shown curve corresponds to C of 3.1 × 10−19 erg ·cm, a of 45 nm and DNA effective diameter of 5 nm (33), in very good agreement with other available data.
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Figure 6: Comparison between theoretical and experimental values of the linking number variance, . Experimental data (filled circle) for 37°C were taken from reference (25). The data from the current study (open triangle) and from reference (33) (open circle) were adjusted to 37°C according to the temperature dependence of presented in Figure 5. The line represents the best theoretical fit of the data. The shown curve corresponds to C of 3.1 × 10−19 erg ·cm, a of 45 nm and DNA effective diameter of 5 nm (33), in very good agreement with other available data.

Mentions: A few theoretical studies analyzed the equilibrium distribution of DNA topoisomers (18,19,26–31). All these studies assumed that the torsional and bending fluctuations in nicked DNA, which is subject to ligation, are independent, so(4)where and are the variances of twist, Tw and writhe, Wr, in nicked circular form of DNA. The value of is completely specified by the DNA torsional rigidity, C and temperature, T:(5)where N is the DNA length in bp, and l is the length of 1 bp (0.34 nm). The value of can be obtained by computer simulation. A proper model for this kind of simulation is the discrete worm-like chain with a particular diameter d of the chain segments (19). Thus, the value of depends on two parameters of the DNA model, a and d, and, of course, on DNA length L. The computer simulation results are well described by the interpolation equations for (see ‘Material and Methods’ section). It should be noted that this theoretical description of is in very good agreement with the available experimental data (Figure 6). We used this description to analyze the values of presented in Figure 5.Figure 6.


Temperature dependence of DNA persistence length.

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

Comparison between theoretical and experimental values of the linking number variance, . Experimental data (filled circle) for 37°C were taken from reference (25). The data from the current study (open triangle) and from reference (33) (open circle) were adjusted to 37°C according to the temperature dependence of  presented in Figure 5. The line represents the best theoretical fit of the data. The shown curve corresponds to C of 3.1 × 10−19 erg ·cm, a of 45 nm and DNA effective diameter of 5 nm (33), in very good agreement with other available data.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 6: Comparison between theoretical and experimental values of the linking number variance, . Experimental data (filled circle) for 37°C were taken from reference (25). The data from the current study (open triangle) and from reference (33) (open circle) were adjusted to 37°C according to the temperature dependence of presented in Figure 5. The line represents the best theoretical fit of the data. The shown curve corresponds to C of 3.1 × 10−19 erg ·cm, a of 45 nm and DNA effective diameter of 5 nm (33), in very good agreement with other available data.
Mentions: A few theoretical studies analyzed the equilibrium distribution of DNA topoisomers (18,19,26–31). All these studies assumed that the torsional and bending fluctuations in nicked DNA, which is subject to ligation, are independent, so(4)where and are the variances of twist, Tw and writhe, Wr, in nicked circular form of DNA. The value of is completely specified by the DNA torsional rigidity, C and temperature, T:(5)where N is the DNA length in bp, and l is the length of 1 bp (0.34 nm). The value of can be obtained by computer simulation. A proper model for this kind of simulation is the discrete worm-like chain with a particular diameter d of the chain segments (19). Thus, the value of depends on two parameters of the DNA model, a and d, and, of course, on DNA length L. The computer simulation results are well described by the interpolation equations for (see ‘Material and Methods’ section). It should be noted that this theoretical description of is in very good agreement with the available experimental data (Figure 6). We used this description to analyze the values of presented in Figure 5.Figure 6.

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