The invention relates to a method for enrichment or isolation of a long nucleotide fragment comprising a known nucleotide sequence element, i.e. a sequence encoding a conserved active site or domain, the method being applicable i.a. to high throughput screening for DNA fragments containing a known sequence element. The methods include, inter alia, steps of providing a liquid sample of mixed DNA molecules comprising one or more specific target DNA molecules, formation of a multiple of liquid droplets, specific detection of droplets containing at least one of the target DNA molecules, physically selecting droplets containing at least one of the target DNA molecules, and general amplification of the DNA molecules in the coalesced selected droplets.
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