DNA meter: Energy tunable, quantitative hybridization assay

William Braunlin, Jens Völker, G. Eric Plum, Kenneth J. Breslauer

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


We describe a novel hybridization assay that employs a unique class of energy tunable, bulge loop-containing competitor strands (C*) that hybridize to a probe strand (P). Such initial «pre-binding» of a probe strand modulates its effective «availability» for hybridizing to a target site (T). More generally, the assay described here is based on competitive binding equilibria for a common probe strand (P) between such tunable competitor strands (C*) and a target strand (T).We demonstrate that loop variable, energy tunable families of C*P complexes exhibit enhanced discrimination between targets and mismatched targets, thereby reducing false positives/negatives. We refer to a C*P complex between a C* competitor single strand and the probe strand as a "tuning fork," since the C* strand exhibits branch points (forks) at the duplex-bulge interfaces within the complex. By varying the loop to create families of such "tuning forks," one can construct C*P "energy ladders" capable of resolving small differences within the target that may be of biological/functional consequence. The methodology further allows quantification of target strand concentrations, a determination heretofore not readily available by conventional hybridization assays. The dual ability of this tunable assay to discriminate and quantitate targets provides the basis for developing a technology we refer to as a "DNA Meter." Here we present data that establish proof-of-principle for an in solution version of such a DNA Meter. We envision future applications of this tunable assay that incorporate surface bound/spatially resolved DNA arrays to yield enhanced discrimination and sensitivity.

Original languageEnglish (US)
Pages (from-to)408-417
Number of pages10
Issue number6
StatePublished - Jun 2013

All Science Journal Classification (ASJC) codes

  • Biophysics
  • Biochemistry
  • Biomaterials
  • Organic Chemistry


  • DNA arrays
  • DNA meter
  • novel hybridization assay


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