Analysis and suppression of DNA polymerase pauses associated with a trinucleotide consensus

We have studied a novel class of DNA sequences that cause DNA polymerases to pause. These sequences have the central consensus Py-G-C and are not necessarily adjacent Its hairpins in the DNA template. Since most consensus sequences do not cause pauses under standard conditions, additional template features must arise that make it difficult to incorporate nucleotides at these positions. We believe that these pauses result from constraints that make the conformation change involved in nucleotide selection more difficult. These pauses can obscure parts ok DNA sequencing ladders and prevent DNA amplification by the polymerase chain reaction. The addition of betaine, and some related compounds, relieves these pauses.