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High-throughput methods for measuring DNA thermodynamics.

ABSTRACT: Understanding the thermodynamics of DNA motifs is important for prediction and design of probes and primers, but melt curve analyses are low-throughput and produce inaccurate results for motifs such as bulges and mismatches. Here, we developed a new, accurate and high-throughput method for measuring DNA motif thermodynamics called TEEM (Toehold Exchange Energy Measurement). It is a refined framework of comparing two toehold exchange reactions, which are competitive strand displacement between oligonucleotides. In a single experiment, TEEM can measure over 1000 ?G° values with standard error of roughly 0.05 kcal/mol.

SUBMITTER: Bae JH

PROVIDER: S-EPMC7470960 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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High-throughput methods for measuring DNA thermodynamics.

Bae Jin H JH Fang John Z JZ Zhang David Yu DY

Nucleic acids research 20200901 15

Understanding the thermodynamics of DNA motifs is important for prediction and design of probes and primers, but melt curve analyses are low-throughput and produce inaccurate results for motifs such as bulges and mismatches. Here, we developed a new, accurate and high-throughput method for measuring DNA motif thermodynamics called TEEM (Toehold Exchange Energy Measurement). It is a refined framework of comparing two toehold exchange reactions, which are competitive strand displacement between ol ...[more]

PMID: 32544247

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