Methods and compositions for prime editing nucleotide sequences

A prime editing system comprising:

• a) a prime editing guide RNA (PEgRNA) or one or more polynucleotides encoding the PEgRNA, wherein the PEgRNA comprises:
• i) a spacer sequence;
• ii) a gRNA core capable of complexing with a nucleic acid programmable DNA binding protein (napDNAbp) that is a nickase configured to cut a first strand of a double-stranded DNA sequence or a nuclease configured to cut both strands of the double-stranded DNA sequence;
• iii) an RNA extension arm comprising:
• (A) a DNA synthesis template comprising an edit template that encodes one or more edits compared a region downstream of the cut site in the first strand of the double-stranded DNA sequence, and (B) a primer binding site that is complementary to a region upstream of the cut site in the first strand of the double-stranded DNA sequence;
• and
• b) a prime editor, or one or more polynucleotides encoding the prime editor, the prime editor comprising:
• i) the nucleic acid programmable DNA binding protein (napDNAbp);
• and
• ii) a reverse transcriptase domain.