Biology · Introductory biology · Worked example
Predict a digest and its gel pattern
A linear 6000 bp molecule has cuts at 1000 and 3500 bp. Find its fragments and predict the visible band positions.
State the molecule and the digest assumptions
We have linear DNA of length 6000 bp and two distinct internal cuts at 1000 and 3500 bp, measured from one end. Assume a complete digest. Since the DNA is linear, we must include both ends when finding the pieces.
Mark all boundaries in order
Place 0 at the left end, then the two cuts, then 6000 at the right end. There are three intervals between these four boundaries, so we expect three fragments.
Find each interval length
Subtract each boundary from the next one. The second and third intervals happen to have the same length; keep both fragments in the list.
Check that no DNA has been lost from the accounting
Add all three fragment lengths. Their sum is 6000 bp, matching the starting molecule. This catches the common mistake of forgetting the segment after the last cut.
Predict the band pattern
The two 2500 bp fragments migrate to the same size position. The 1000 bp fragment migrates farther. Expect two distinct band positions even though there are three fragments. Keep the duplicate 2500 bp entries when sending the digest to Gel.
| Fragment sizes | Distinct band positions |
|---|---|
| 1000, 2500, 2500 bp | 1000 and 2500 bp |
Compare the prediction with the tool
Open the restriction map and choose Send digest fragments to gel. Preview the copy and open it, then inspect the sample lane. You can add a ladder for comparison. Changes to either copied model do not automatically update the other.
Result
Three fragments produce two distinct band-size positions: 1000 and 2500 bp.
Your turn
Use circular DNA of length 6000 bp with the same cuts at 1000 and 3500 bp. Find the fragments and predict the number of distinct band-size positions.
Show the answer and explanation
The fragments are 2500 bp and 3500 bp, giving two distinct band-size positions.
One arc is 3500 − 1000 = 2500 bp. The other wraps past the coordinate origin and has length (6000 − 3500) + 1000 = 3500 bp. They sum to 6000 bp. Two cuts in a circle make two fragments; the linear end segments now belong to one continuous arc.
Keep exploring
Use the workspace to explore a changed input. Return to the concept if you want to revisit the reasoning.
Return to the concept →Sources and scope
Authored study material. Tool results depend on the stated inputs and model assumptions.