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The first direct comparison of surface immobilization and free-solution oligonucleotide hybridization using back-scattering interferometry (BSI) showed that surface immobilization perturbs hybridization by as much as 50 %. BSI can distinguish between a perfect complement and a two-base-pair mismatch with an internal mismatch significantly destabilizing the duplex.
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Pesciotta et al. (2010) studied this question.
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