The structural peculiarities of condensed DNA micro- and nanoparticles formed in PCR

Abstract

Studies of DNA condensation have opened new perspectives in biotechnology and medicine. DNA condensation induced by polyamines or trivalent metal ions in vitro at room temperature has been investigated in detail. Our recent studies have demonstrated Mg²⁺-mediated formation of DNA condensates during the PCR. In this study, we report the unique morphology and fine structure of PCR-generated condensed DNA particles using electron and atomic force microscopy. The principal morphologies of studied DNA condensates are 3D particles of micrometer dimensions, oval microdisks of nanometer thickness, filaments, and compact nano-sized particles. SEM examinations have revealed a new structural type of spherical and elliptical 3D microparticles formed by numerous definitely oriented microdisks and their segments. AFM revealed a granular structure of the microdisk surface and the smallest nano-sized disks and thinnest nanofibrils – that appear to be the primary products of DNA condensation during the PCR. We suggest that the formation of DNA nanofibrils and nanodisks in PCR occurs due to Mg²⁺ – mediated intermolecular (lateral) and intramolecular condensation of ssDNA. Aggregation of elementary nanodisks in the course of thermal PCR cycles, occurring both by magnesium cations and via complementary interactions, give a rise to large nano-sized aggregates and more complex microparticles.

Keywords:

• inter- and intramolecular DNA condensation
• micro- and nanoparticles
• polymerase chain reaction
• electron microscopy
• atomic force microscopy

Acknowledgments

We are grateful to E.A. Vasilenko for technical assistance in obtaining condensed DNA samples and E.V. Pechnikova for electron microscopy images of micro- and nanoparticles.

Funding

This work was supported by Russian Foundation for Basic Research (project No. 10-08-00184 a).