Reaction-sensitive DNA amplification method simplifies screening for novel reactions

Researchers in the US have adapted a DNA amplification technique to develop a simpler way to rapidly screen chemical reactions. The process should improve reaction screening methods known as ’chemical speed-dating’ - where hundreds of different substrates are mixed together but only a few interact strongly. 

These reaction screens are a great way to quickly probe chemical space to discover new reactions, and this new technique builds on the polymerase chain reaction (PCR) to eliminate some awkward processing steps, boost efficiency and accuracy. 

The speed-dating process works by attaching hundreds of different substrates to short, single strands of DNA. When warmed to 60?C, the strands are too short to pair up naturally - but where two substrates have reacted, their DNA tails pair up, forming a short piece of DNA that resembles a hairpin. 

Traditionally, one of the substrates typically needs to be mounted on a bead to isolate and identify the compounds that have reacted, which can be a time-consuming practice. Now, David Liu’s team at Harvard University, US, have simplified the method by modifying the polymerase chain reaction (used to copy single strands of DNA millions of times) to selectively replicate only the DNA strands where a reaction has occurred. 


Source: © JACS

Principles underlying reactivity-dependent PCR

’By carefully designing primers to only ignite exponential PCR amplification upon formation of the 8 base pairs, we can cause only the DNA strands that have undergone a reaction to be amplified,’ explains Liu. ’This method, which we call reaction-dependent PCR, can be done entirely in solution - and is a much more direct way to selectively amplify molecules that have undergone bond formation or bond cleavage.’ 

By skipping a processing step, Liu’s team hope that the method will hasten and simplify existing processes for reaction discovery, for example to reveal useful new biomarkers or enzymes. The team is also confident that the technique can be made responsive to other types of interaction, and not just covalent bond formation and cleavage. 

Lewis Brindley