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DNA obtained by ab initio synthesis forms hyperbranched net-like structure
1, 2 , * 2 , 3
1  Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia
2  Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia
3  Centre for Diagnostics of Functional Materials for Medicine, Pharmacology and Nanoelectronics of St. Petersburg State University, St. Petersburg, 198504 Russia
Academic Editor: Peter Nielsen


Ab initio DNA synthesis is unusual synthesis of dsDNA from tens bp to kbp long by thermophilic DNA polymerases from free dNTPs in the complete absence of added DNAs. As commonly believed, the reaction product is a linear double-stranded DNA in the B form. However, an extremely low efficiency of cloning and the failure to hydrolyze high-molecular-weight DNA, as well as the presence short repeats, palindromes, and AT-rich repeats in the sequence assumes more complex spatial structure of this DNA. The AFM coupled with nuclease analysis revealed that high-molecular-weight dsDNA products branched and formed net-like structures. The DNA contained single-stranded and triple-stranded segments. These net-like structures may be assumed to be three-dimensional (3D). The present work was the first detailed investigation of the ab initio synthesis products. The results may be useful to develop techniques requiring synthesis of large amounts of DNA with complex spatial structure.

Keywords: template/primer-independent DNA synthesis; DNA structures; atomic force microscopy