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Cloning & Enzymes

DNA assembly and construct verification with source and sequence locked

Keep restriction-ligation, Type IIS, and homology assembly distinct while tracing parts, junctions, expected constructs, and observed evidence as separate lineage.

Editable starter protocols

4 source-bound starters

What do these protocols do?

They preserve construct identity, part sequence, junction geometry, assumptions, and unknowns while separating transformation and verification through typed handoffs.

Supported assembly workflows

  • • Common construct, junction, handoff & evidence contract
  • • Restriction-ligation · explicit ratio and enzyme geometry
  • • Type IIS · BsaI-HFv2 ordered overhangs
  • • Homology · NEBuilder HiFi exact junctions

Scope boundary

They do not recommend universal ratios, enzyme conditions, overhang quality, or transformation recipes, interchange sequence, digest, and colony-PCR evidence, or declare a construct-level PASS.

PRT-CL-COMMON-001Common construct, junction, handoff & evidence contract

Cloning identity, ordered-part, junction, handoff and evidence contract

Cloning & Enzymes · CL-FAMILY-CONTRACT-1.0

Official guidance reviewed
EXACT_SOURCE_PROFILE_AND_REVISION_REQUIREDNO_DEFAULT_RATIO_OR_RECIPEORDERED_PART_AND_JUNCTION_GRAPHASSUMPTIONS_AND_UNKNOWNS_PRESERVEDTRANSFORMATION_IS_TYPED_HANDOFFVERIFICATION_IS_SEPARATE_CONSUMERNO_GLOBAL_BIOLOGICAL_PASSRESEARCH_USE_ONLY

Separate the assembly receipt from verification evidence

The verification ledger compares only evidence-supported axes. Digest or colony-PCR consistency never becomes sequence identity or a construct-level PASS.

1

1. LOCK CONSTRUCT IDENTITY

Record construct ID, topology, intended use and exact source-profile revision before any method-specific arithmetic or compatibility claim.

2

2. FREEZE ORDERED PARTS

Record every part ID, role, orientation, exact sequence identity, length, checksum and source receipt without filling missing sequence from a motif label.

3

3. DEFINE EVERY JUNCTION

Link upstream and downstream part IDs and preserve strategy, expected sequence, overhang or homology and frame disposition for every junction.

4

4. VALIDATE THE EXACT PROFILE

Check profile ID, revision, source stable ID, applicability and exclusions. Any source, chemistry or revision mismatch returns BLOCKED.

Condition: SOURCE REQUIRED — no generic assembly fallback.
5

5. RECORD ASSUMPTIONS AND UNKNOWNS

Keep user assumptions separate from unsupported evidence. Missing editable fields remain INCOMPLETE; unsupported claims remain UNKNOWN.

6

6. ISSUE TRANSFORMATION HANDOFF

Pass only assembly receipt, host requirement, selection identity and unknowns. Do not copy competent-cell amount, recovery time or colony threshold.

7

7. CREATE EXPECTED SNAPSHOT

Freeze construct checksum, expected junctions, critical regions and source references before observing verification evidence.

8

8. COMPARE EVIDENCE PER AXIS

Compare sequence, digest or colony-PCR evidence only on supported axes and preserve discrepancies; never emit a construct-level biological PASS.