Monoplex/multiplex linear-after-the-exponential-PCR assays combined with PrimeSafe and Dilute-'N'-Go sequencing

Nat Protoc. 2007;2(10):2429-38. doi: 10.1038/nprot.2007.362.

Abstract

This protocol describes the design and execution of monoplex and multiplex linear-after-the-exponential (LATE)-PCR assays using a novel reagent, PrimeSafe, that suppresses all forms of mispriming. LATE-PCR is an advanced form of asymmetric amplification that uses a limiting primer and an excess primer for efficient exponential amplification of double-stranded DNA, followed by linear amplification of one strand. Each single-stranded amplicon can be quantitatively detected in real time or at end point. By separating primer annealing from product detection, LATE-PCR enables product analysis at low temperatures. Alternatively, each single strand can be sequenced by a convenient Dilute-'N'-Go procedure. Amplified samples are diluted with individual sequencing primers without the use of columns or spins. We have amplified and then sequenced 15 different single-stranded products generated in a single multiplexed LATE-PCR comprised of 15 pairs of unrelated primers. Dilute-'N'-Go dideoxy sequencing is more convenient, faster and less expensive than sequencing double-stranded amplicons generated via conventional symmetric PCR. The preparation of LATE-PCR products for Dilute-'N'-Go sequencing takes only 30 seconds.

MeSH terms

  • Benzothiazoles
  • DNA / analysis
  • DNA Primers
  • DNA, Single-Stranded / analysis
  • Diamines
  • Indicators and Reagents
  • Kinetics
  • Organic Chemicals
  • Polymerase Chain Reaction / methods*
  • Quinolines
  • Sequence Analysis, DNA
  • Temperature

Substances

  • Benzothiazoles
  • DNA Primers
  • DNA, Single-Stranded
  • Diamines
  • Indicators and Reagents
  • Organic Chemicals
  • Quinolines
  • SYBR Green I
  • DNA