Journal
BIOPOLYMERS
Volume 99, Issue 6, Pages 408-417Publisher
WILEY-BLACKWELL
DOI: 10.1002/bip.22213
Keywords
novel hybridization assay; DNA meter; DNA arrays
Categories
Funding
- NIH [GM23509, GM34469, CA47995, AI074089]
- NSF [CBET-1033788]
- Div Of Chem, Bioeng, Env, & Transp Sys
- Directorate For Engineering [1033788] Funding Source: National Science Foundation
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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. (c) 2012 Wiley Periodicals, Inc. Biopolymers 99: 408417, 2013.
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