Methodology article

Production of highly knotted DNA by means of cosmid circularization inside phage capsids

Sonia Trigueros^1,2 and Joaquim Roca¹

¹Institut de Biologia Molecular de Barcelona, CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain

²Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK

author email corresponding author email

BMC Biotechnology 2007, 7:94doi:10.1186/1472-6750-7-94

Published:	21 December 2007

Abstract

Background

The formation of DNA knots is common during biological transactions. Yet, functional implications of knotted DNA are not fully understood. Moreover, potential applications of DNA molecules condensed by means of knotting remain to be explored. A convenient method to produce abundant highly knotted DNA would be highly valuable for these studies.

Results

We had previously shown that circularization of the 11.2 kb linear DNA of phage P4 inside its viral capsid generates complex knots by the effect of confinement. We demonstrate here that this mechanism is not restricted to the viral genome. We constructed DNA cosmids as small as 5 kb and introduced them inside P4 capsids. Such cosmids were then recovered as a complex mixture of highly knotted DNA circles. Over 250 μg of knotted cosmid were typically obtained from 1 liter of bacterial culture.

Conclusion

With this biological system, DNA molecules of varying length and sequence can be shaped into very complex and heterogeneous knotted forms. These molecules can be produced in preparative amounts suitable for systematic studies and applications.