Probing DNA polymerase-DNA interactions: examining the template strand in exonuclease complexes using 2-aminopurine fluorescence and acrylamide quenching

Biochemistry. 2007 Jun 5;46(22):6559-69. doi: 10.1021/bi700380a. Epub 2007 May 12.


The bacteriophage T4 DNA polymerase forms fluorescent complexes with DNA substrates labeled with 2-aminopurine (2AP) in the template strand; the fluorescence intensity depends on the position of 2AP. When preexonuclease complexes are formed, complexes at the crossroads between polymerase and exonuclease complexes, 2AP in the +1 position in the template strand is fully free of contacts with the adjacent bases as indicated by high fluorescence intensity and a long fluorescence lifetime of about 10.9 ns. Fluorescence intensity decreases for 2AP in the template strand when the primer end is transferred to the exonuclease active center to form exonuclease complexes, which indicates a change in DNA conformation; 2AP can now interact with adjacent bases, which quenches fluorescence emission. Some polymerase-induced base unstacking for 2AP in the template strand in exonuclease complexes is observed but is restricted primarily to the n and +1 positions, which indicates that the DNA polymerase holds the template strand in a way that forces base unstacking only in a small region near the primer terminus. A hold on the template strand will help to maintain the correct alignment of the template and primer strands during proofreading. Acrylamide quenches 2AP fluorescence in preexonuclease and in exonuclease complexes formed with DNA labeled with 2AP in the template strand, which indicates that the template strand remains accessible to solvent in both complexes. These studies provide new information about the conformation of the template strand in exonuclease complexes that is not available from structural studies.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 2-Aminopurine / chemistry*
  • Acrylamide / chemistry*
  • Bacteriophage T4 / enzymology*
  • Bacteriophage T4 / genetics
  • Base Pairing
  • Base Sequence
  • DNA / biosynthesis*
  • DNA / chemistry
  • DNA / genetics
  • DNA, Single-Stranded
  • DNA-Directed DNA Polymerase / genetics
  • DNA-Directed DNA Polymerase / metabolism*
  • Exodeoxyribonucleases / metabolism*
  • Fluorescence
  • Fluorescent Dyes / chemistry
  • Kinetics
  • Models, Chemical
  • Molecular Sequence Data
  • Protein Conformation
  • Spectrometry, Fluorescence
  • Templates, Genetic
  • Viral Proteins / genetics
  • Viral Proteins / metabolism


  • DNA, Single-Stranded
  • Fluorescent Dyes
  • Viral Proteins
  • Acrylamide
  • 2-Aminopurine
  • DNA
  • DNA-Directed DNA Polymerase
  • Exodeoxyribonucleases