The present disclosure relates to methods 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 herein comprise the steps of forming an emulsion of multiple liquid droplets from a DNA fragment containing liquid sample, specific detection of droplets containing at least one target DNA molecule, physically selecting droplets containing at least one target DNA molecule, and performing a general amplification of the DNA molecules containing at least one target DNA molecules.