molecular cloning
A glossary of cloning terms
Read a cloning plan and mark vector, insert, MCS, ends, ligase, phosphatase, transformation, and clone against the map before you mix a tube.
8 October 2026 · 8 min read
Topic cluster
Molecular cloning
Plasmid maps, assembly methods, colony screening and the evidence that an insert is present, oriented and intact.
All topicsBuffers and laboratory water26Cell culture26Chromatography26Cold chain and sample storage26Cytometry and microscopy26DNA sequencing26Gels and blotting26Gene expression26Genome editing26Immunoassays26Laboratory labware26Laboratory safety26Liquid handling26Microbiology26Molecular cloning26Nucleic acid purification26PCR and amplification26Protein biochemistry26Proteomics26Research sourcing and study design26
biosafetyspecificationsequencingglossarytroubleshootingcloningcontrolsexpressionsangertransformationcoloniesligationglycerol stockplasmid mapscreeningselectioncodonscolony pcr
26 articles
molecular cloning
Antibiotic selection is not proof of an insert
What selection, marker, satellite and clone mean on an antibiotic plate, and why a colony can grow with no insert, the wrong insert or only a parent vector.
8 October 2026 · 7 min read
molecular cloning
Avoiding mutations during PCR cloning
Why a PCR insert can be the right length and still carry mutations, and how enzyme class, fewer cycles, extra colonies and a full sequence limit the damage.
8 October 2026 · 8 min read
molecular cloning
Choosing restriction sites that actually cut
Why a restriction site on a plasmid map may not cut the DNA in your tube, and how methylation, star activity and buffer choice decide the digest.
8 October 2026 · 9 min read
molecular cloning
Colony PCR versus diagnostic digest
When to triage colonies by PCR and when a miniprep digest is worth it, including false positives from agar DNA, orientation, and why neither is a sequence.
8 October 2026 · 8 min read
molecular cloning
Comparing cloning methods for a short insert
Pick restriction ligation, Gibson assembly, Golden Gate, or annealed oligos for a short insert using length, scars, and an orientation check.
8 October 2026 · 8 min read
molecular cloning
Competent cells and transformation controls
How to choose chemical competence or electroporation, and which plates report efficiency, no-DNA background and a ligation that had no insert.
8 October 2026 · 8 min read
molecular cloning
Dephosphorylation methylation and cloning strain choice
Choose one fix that matches the evidence: vector phosphatase, a dam/dcm strain when the card says so, or a strain for ccdB or unstable inserts.
8 October 2026 · 7 min read
molecular cloning
Documenting a construct so the next person can use it
Define the words on a minimal construct sheet so the next person can find the map, the frame, the strain, and what was never confirmed.
8 October 2026 · 7 min read
molecular cloning
Gateway and recombination cloning overview
Follow att-site recombination from an entry clone to a destination clone, and treat ccdB as a strain choice rather than a recipe.
8 October 2026 · 9 min read
molecular cloning
Glycerol stocks and plasmid backups
A glycerol freezer stock and a plasmid DNA tube fail in different ways. Use both when a thaw, a contaminated culture, or a mutant colony is the risk.
8 October 2026 · 8 min read
molecular cloning
Golden Gate and type IIS concepts
How type IIS enzymes such as BsaI or BbsI cut outside their site so designed overhangs assemble and the site is lost, compared with ligation and Gibson.
8 October 2026 · 8 min read