Prime editing (PE) is a next-generation gene editing technology that utilizes a Cas9 protein fused to a prime editing guide ribonucleic acid (pegRNA) to achieve high CRISPR/Cas9 editing efficiency and precision. However, the length requirement of pegRNAs at 120–250 nucleotides (nt) and their high level of secondary structure formation present analytical challenges for the purity analysis of chemically synthesized pegRNAs during development and quality control (QC).