A new direct single-molecule observation method for DNA synthesis reaction using fluorescent replication protein A

Sensors (Basel). 2014 Mar 12;14(3):5174-82. doi: 10.3390/s140305174.

Abstract

Using a single-stranded region tracing system, single-molecule DNA synthesis reactions were directly observed in microflow channels. The direct single-molecule observations of DNA synthesis were labeled with a fusion protein consisting of the ssDNA-binding domain of a 70-kDa subunit of replication protein A and enhanced yellow fluorescent protein (RPA-YFP). Our method was suitable for measurement of DNA synthesis reaction rates with control of the ssλDNA form as stretched ssλDNA (+flow) and random coiled ssλDNA (-flow) via buffer flow. Sequentially captured photographs demonstrated that the synthesized region of an ssλDNA molecule monotonously increased with the reaction time. The DNA synthesis reaction rate of random coiled ssλDNA (-flow) was nearly the same as that measured in a previous ensemble molecule experiment (52 vs. 50 bases/s). This suggested that the random coiled form of DNA (-flow) reflected the DNA form in the bulk experiment in the case of DNA synthesis reactions. In addition, the DNA synthesis reaction rate of stretched ssλDNA (+flow) was approximately 75% higher than that of random coiled ssλDNA (-flow) (91 vs. 52 bases/s). The DNA synthesis reaction rate of the Klenow fragment (3'-5'exo-) was promoted by DNA stretching with buffer flow.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / metabolism
  • DNA Polymerase I / metabolism
  • DNA, Single-Stranded / biosynthesis*
  • Fluorescence
  • Luminescent Proteins / metabolism*
  • Microfluidics / methods*
  • Replication Protein A / metabolism*
  • Time Factors

Substances

  • Bacterial Proteins
  • DNA, Single-Stranded
  • Luminescent Proteins
  • Replication Protein A
  • yellow fluorescent protein, Bacteria
  • DNA Polymerase I