Gel Matrix Choice: When Agarose Misses a Scar Page Shows
Agarose versus PAGE resolution is a matrix job, not a brand of gel tank. Agarose and PAGE are two gel matrices with two resolution jobs. Agarose is the routine matrix for nucleic-acid fragments from roughly a hundred base pairs to many kilobases. PAGE uses a tighter, tunable pore and is the matrix that can separate small fragments or two bands that differ by only a few bases. Prefer PAGE when the decision is “did this scar or oligo ladder actually separate.” Prefer agarose when the decision is “is this insert in the expected kilobase window.” Reject the idea that one gel brand answers both jobs. Diagnostic versus cloning digests still owns the enzyme job. Clone verification by digest still owns the checklist. This page only chooses the matrix those bands will enter.
Small Scar Differences Often Need PAGE; Large Fragments Usually Do Not
A protocol-basics note on agarose places ordinary agarose in the hundred-base to tens-of-kilobase window and sends very small fragments, or fragments that differ by only a few bases, to polyacrylamide. A native-PAGE protocol is more specific for small DNA: ordinary agarose poorly resolves fragments under about 500 bp, while polyacrylamide in the 3.5–20% range is used from tens to about a thousand base pairs. Those ranges are working windows, not official Zetta specifications and not a promised single-base guarantee on every gel. After the expected-band job is named, ZettaGene can show the predicted fragment sizes on the map. Official simulation is restriction, Gibson, and homologous alignment. The map does not pour the gel.
What Each Matrix Is Allowed to Resolve
| Job | Agarose is usually enough | PAGE is the better matrix | Neither matrix is the claim |
|---|---|---|---|
| Insert versus empty vector | Kilobase-scale difference on a routine horizontal gel | Not required | Not proof the clone is sequence-correct |
| Diagnostic digest of large fragments | Expected bands hundreds of bases to many kb apart | When two predicted bands sit too close for agarose | Not a cloning-quality ligatable end |
| Small scar, oligo, or closely sized pair | Often a smear or one fat band | Tighter pores can separate the difference you care about | Not an official single-base certificate |
| Protein | Not the default nucleic-acid tool | SDS-PAGE is a protein job, a different claim | Do not use a DNA agarose photo as a protein result |
Prefer agarose for colony screens, routine PCR products, and most plasmid digests whose predicted bands are far apart. Prefer PAGE when the expected difference is a short scar, a small oligo, or two fragments that agarose has already failed to split. Acrylamide is a neurotoxin in the unpolymerized form; that handling cost is part of the matrix choice, not a reason to pretend agarose resolved a 10-base gap. This page does not publish a universal cutoff in base pairs that every lab must use. It publishes the job test: if the decision needs a difference agarose cannot show, change matrix or change assay.
Where the Matrix Choice Fails
The usual fail is declaring two clones identical because a 1% agarose gel showed “the same band” when the maps differed by a short scar. The second fail is pouring a high-percentage PAGE for a 6 kb fragment that will barely enter. The third fail is treating a predicted-band screenshot as if the gel had already been run. Simulation sizes tell you which matrix is plausible. They do not replace the lane. If the next job is still enzyme choice, return to the diagnostic-versus-cloning page. If the next job is the verification walk, return to the digest checklist.
Predict the Bands, Then Pick the Matrix
Write the expected sizes and the difference you must resolve before you melt agarose or mix acrylamide. A digest checklist can still pass the wrong matrix if nobody asked whether the expected difference is a scar or a kilobase insert. ZettaGene can display those predicted fragments on the named map. It is a planning surface, not a gel tank and not a PAGE product. If the difference you care about is still smaller than the matrix can show, do not call the clone verified. Call the gel the wrong job.
Frequently Asked Questions
Can agarose resolve a ten-base scar?
Usually not on a routine agarose gel. A difference of a few bases is the job that sends people to PAGE or to a different assay. This page does not promise a single-base agarose result.
Is PAGE required for every cloning digest?
No. Kilobase-scale insert checks and well-separated diagnostic bands usually stay on agarose. Use PAGE when the difference is small or already unresolved on agarose.
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