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Nucleic Acids Research, Vol 24, Issue 14 2774-2781, Copyright © 1996 by Oxford University Press

ARTICLES

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

DS Mytelka and MJ Chamberlin
Graduate Group in Genetics, University of California, Berkeley 94720, USA.

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 to hairpins in the DNA template. Since most consensus sequences do not cause pauses under standard conditions, additional template features must exist 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 of DNA sequencing ladders and prevent DNA amplification by the polymerase chain reaction. The addition of betaine, and some related compounds, relieves these pauses.
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