Reiterative template switching: the effect of single-strand homopolymeric DNA on non-template-directed nucleotide addition by DNA polymerase

Mechanism of DNA multimerization caused by strand-displacement DNA polymerases

It has been recently shown that for Bst DNA polymerase, the side isothermal amplification reaction named multimerization (MM) proceeds under certain conditions. MM hinders interpretation of amplification results and reduces the accuracy and reliability of DNA/RNA diagnostics. Here, the mechanism of MM caused by strand-displacement DNA polymerases is reported. The mechanism includes the following key stages: 1) envelopment of the enzyme globule by the synthesized DNA strand, facilitated by DNA breathing, 2) convergence of the 3'-ends of the DNA strands and pseudo-cyclic trigger DNA structure formation, 3) synthesis of the products with repeated motifs resulting in their expansion due to DNA slippage. Initiation of MM reaction occurs with extremely low probability, however, the resulting few trigger DNA structures are efficiently amplified and ultimately lead to the accumulation of nonspecific amplicons (multimers). Molecular models with certain steric and thermodynamic characteristics were used to confirm the proposed mechanism. The highest MM efficiency was observed for DNA templates and reaction conditions that facilitated DNA breathing, complete envelopment of the enzyme globule with DNA strands and convergence of their 3'-ends.

Inhibition of non-templated nucleotide addition by DNA polymerases in primer extension using twisted intercalating nucleic acid modified templates

A simple and elegant method for inhibition of non-templated nucleotide addition by DNA polymerases and for following DNA 3'-heterogeneity in enzymatic DNA synthesis by primer extension (PEX) is described. When template bearing ortho-twisted intercalating nucleic acid (ortho-TINA) at the 5'-end is used, non-templated nucleotide addition is reduced in both the A- and B-family DNA polymerases (KOD XL, KOD (exo-), Bst 2.0, Therminator, Deep Vent (exo-) and Taq). Formation of a single oligonucleotide product was observed with ortho-TINA modified template and KOD XL, KOD (exo-), Bst 2.0, Deep Vent (exo-) and Taq DNA polymerases. This approach can be applied to the synthesis of both unmodified and base-modified oligonucleotides.

Atomic force microscope observation of branching in single transcript molecules derived from human cardiac muscle

We have used an atomic force microscope to examine a clinically derived sample of single-molecule gene transcripts, in the form of double-stranded cDNA, (c: complementary) obtained from human cardiac muscle without the use of polymerase chain reaction (PCR) amplification. We observed a log-normal distribution of transcript sizes, with most molecules being in the range of 0.4-7.0 kilobase pairs (kb) or 130-2300 nm in contour length, in accordance with the expected distribution of mRNA (m: messenger) sizes in mammalian cells. We observed novel branching structures not previously known to exist in cDNA, and which could have profound negative effects on traditional analysis of cDNA samples through cloning, PCR and DNA sequencing.