What is Restriction Enzyme Finder?

Restriction enzyme site finder — Searches an input DNA sequence for recognition sites of major type II restriction enzymes (e.g., EcoRI = GAATTC, BamHI = GGATCC, HindIII = AAGCTT) and reports position (bp) and cut count. Searches both forward and reverse complement strands.

When should I use Restriction Enzyme Finder?

(1) Cloning strategy — pick enzymes compatible with both vector MCS and insert (2) Verify restriction digest — compare expected fragment sizes with gel bands (3) Check for unwanted internal cut sites in inserts during subcloning (4) Confirm introduced cut sites after site-directed mutagenesis

Can you show me an example of Restriction Enzyme Finder?

Example) Search pUC19 (2686 bp) for EcoRI + HindIII → EcoRI (GAATTC): 1 cut at position 396 (MCS) → HindIII (AAGCTT): 1 cut at position 447 (MCS) → Double digest yields 51 bp small fragment + 2635 bp backbone → → suitable for cloning (insert between EcoRI/HindIII in MCS)

Restriction Enzyme Finder

특정 효소 인식 부위 검색

DNA SEQUENCE

도구 가이드

정의

제한효소 인식 부위 검색기 — 입력 DNA 서열에서 주요 type II restriction enzyme의 인식 부위(예: EcoRI = GAATTC, BamHI = GGATCC, HindIII = AAGCTT)를 검색해 위치(bp)와 cut count를 표시합니다. Forward strand + reverse complement 양방향 탐색.

목적

(1) Cloning strategy — Vector MCS와 insert의 호환 enzyme 선택 (2) Restriction digest 확인 — 예상 fragment 길이와 실제 gel band 비교 (3) Subcloning 시 원하지 않는 internal cut site 확인 (insert 내부) (4) Site-directed mutagenesis 후 새로운 cut site 도입 여부 검증

사용법

① DNA 서열 입력 (대소문자 무관, 공백 자동 제거) ② 검색할 enzyme 선택 (single 또는 multiple — EcoRI, BamHI, HindIII, NotI, XhoI, SalI, KpnI 등) ③ 자동 출력: • 각 enzyme의 cut count • Cut position(bp 인덱스, 1-based) • Forward/Reverse strand 매칭 정보 • Fragment 길이 (linear vector 가정 시) IUPAC ambiguity (예: HincII = GTYRAC) 지원.

예시

예) pUC19 (2686 bp) full sequence에서 EcoRI + HindIII 검색 → EcoRI (GAATTC): 1 cut at position 396 (MCS) → HindIII (AAGCTT): 1 cut at position 447 (MCS) → Double digest 시 51 bp small fragment + 2635 bp backbone → → cloning에 사용 가능 (insert 위치 EcoRI~HindIII MCS 사이)