Ab initiosynthesis by DNA polymerases

Abstract

The polymerization of free nucleotides into new genetic elements by DNA polymerases in the absence of DNA, called ab initio DNA synthesis, is a little known phenomenon. DNA polymerases from prokaryotes can effectively synthesize long stretches of linear double‐stranded DNA in the complete absence of added primer and template DNAs. Ab initio DNA synthesis is extremely enhanced if a restriction endonuclease or nicking endonuclease is added to the reaction with DNA polymerase. The synthesized ab initio DNA have various tandem repeats. Sequences similar to those of ab initio DNA products are found in many natural genes. The significance of ab initio DNA synthesis is that genetic information can be created directly by protein. The ab initio DNA synthesis is considered a non‐specific synthesis in various DNA amplification techniques. In this review, we present the main studies devoted to this phenomenon and introduce possible mechanisms of this synthesis from our current knowledge.

Unusual isothermal multimerization and amplification by the strand-displacing DNA polymerases with reverse transcription activities

“…S10 ). This additional sequence was added probably due to DNA polymerases’ ab initio synthesis which usually required rather long incubation 30 .…”

Real-time kinetics and high-resolution melt curves in single-molecule digital LAMP to differentiate and study specific and non-specific amplification

“…Other potential mechanisms include LIMA (30) and UIMA (31), but are inconsistent with our sequencing results, which observe nearly equal reads of the forward and reverse strand as measured by counting the complementary sequences between each junction. Our proposed mechanism requires properties that have been observed with Bst enzymes: a strand-displacing polymerase lacking 3 -5 exonuclease activity--common to polymerases from thermophilic bacteria (32,33), template switching ability to allow synthesis across a discontinuous template (33), terminal transferase activity, or the ability to perform nontemplated synthesis (32,(34)(35). Briefly, the non-specific product likely arises from extension of a low probability homo-dimerization of the Backward Inner Primer (BIP), followed by elongation across a discontinuous junction ('template switching') to form a double-stranded product incorporating Forward Inner Primer (FIP).…”

DNA-based memory devices for recording cellular events

“…Correspondingly, biological processes and corresponding enzymatic machinery with aspects of these features (i.e. non-templated polymerases 141,142 , terminal deoxynucleotidyl transferases [G] (TdTs) 143,144 ) should be investigated and leveraged for next-generation recording applications. Other strategies not relying directly on the four natural base pairs can also be investigated; for example, unnatural bases could be used to expand the information density and capacity of recording 145 .…”