Improvements achieved by the KLM-PCR protocol and an overview of the MeKL-chip method. (A) Quantitative PCR assessment of fold increase in amplification using KLM-PCR with oligo_1 (dark grey) and Rbp3 primers (light grey) as a direct comparison to the standard LM-PCR protocol (no kinase, 5% PEG-8000) using different amounts of PEG-8000 (%), with (+) and without (−) kinase treatment. The relative improvement of each reaction was calculated as a fold-change in comparison to the standard LM-PCR protocol. Amplification at Rbp3 was used as a between-conditions loading control. Error bars based on standard error of the mean (n = 5). (B) Overview of the MeKL-chip method with the procedures for the input and enriched DNA as marked. The optional quality control steps are indicated by dashed arrows. KLM-PCR: kinase-modified ligation-mediated PCR; LM-PCR: ligation-mediated PCR; MeKL: MBD2b/MBD3L1 enrichment of DNA followed by KLM-PCR.