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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 j-factor measured for λ phage DNA fragments with EcoRI sticky ends at 5°C (top) and HindIII sticky ends at 42°C (bottom). The lines correspond to the theoretical fit of the data. The best fit shown by the solid lines, correspond to DNA persistence length of 53.2 nm and γ of 10.43 for 5°C and 42.5 nm and γ of 10.56 for 42°C; the value of C was equal to 3.10−19 erg·cm for both temperatures. The dotted lines correspond to the theoretical equation with a reduced/increased by 1 nm from the best fits.
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Figure 3: The j-factor measured for λ phage DNA fragments with EcoRI sticky ends at 5°C (top) and HindIII sticky ends at 42°C (bottom). The lines correspond to the theoretical fit of the data. The best fit shown by the solid lines, correspond to DNA persistence length of 53.2 nm and γ of 10.43 for 5°C and 42.5 nm and γ of 10.56 for 42°C; the value of C was equal to 3.10−19 erg·cm for both temperatures. The dotted lines correspond to the theoretical equation with a reduced/increased by 1 nm from the best fits.

Mentions: In accordance with the above tests we performed j-factor measurements for the DNA fragments of λ phage at 5 and 42°C, for EcoRI and HindIII sticky ends, respectively. The fragment was chosen because it does not contain any known intrinsically curved elements of the double helix (17). The procedure of the j-factor measurement is based on the measurement of relative amounts of circles and dimers formed during the ligation and has been described in detail earlier (6,17). The experimental data and their theoretical fit that allows determination of a are shown in Figure 3. These data show strong temperature dependence of DNA persistence length.Figure 3.


Temperature dependence of DNA persistence length.

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

The j-factor measured for λ phage DNA fragments with EcoRI sticky ends at 5°C (top) and HindIII sticky ends at 42°C (bottom). The lines correspond to the theoretical fit of the data. The best fit shown by the solid lines, correspond to DNA persistence length of 53.2 nm and γ of 10.43 for 5°C and 42.5 nm and γ of 10.56 for 42°C; the value of C was equal to 3.10−19 erg·cm for both temperatures. The dotted lines correspond to the theoretical equation with a reduced/increased by 1 nm from the best fits.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 3: The j-factor measured for λ phage DNA fragments with EcoRI sticky ends at 5°C (top) and HindIII sticky ends at 42°C (bottom). The lines correspond to the theoretical fit of the data. The best fit shown by the solid lines, correspond to DNA persistence length of 53.2 nm and γ of 10.43 for 5°C and 42.5 nm and γ of 10.56 for 42°C; the value of C was equal to 3.10−19 erg·cm for both temperatures. The dotted lines correspond to the theoretical equation with a reduced/increased by 1 nm from the best fits.
Mentions: In accordance with the above tests we performed j-factor measurements for the DNA fragments of λ phage at 5 and 42°C, for EcoRI and HindIII sticky ends, respectively. The fragment was chosen because it does not contain any known intrinsically curved elements of the double helix (17). The procedure of the j-factor measurement is based on the measurement of relative amounts of circles and dimers formed during the ligation and has been described in detail earlier (6,17). The experimental data and their theoretical fit that allows determination of a are shown in Figure 3. These data show strong temperature dependence of DNA persistence length.Figure 3.

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