Biology · Introductory biology · Worked example

Predict restriction fragments and gel bands

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

The DNA is linear, $6, 000 bp$ long, with two cuts at $1, 000$ and $3, 500 bp$ , measured from one end. Assume a complete digest, with both sites cut in every molecule. A linear molecule has two ends, and both count as boundaries.

Mark all boundaries in order

Place $0$ at the left end, then the two cuts, then $6, 000$ at the right end. Four boundaries leave three intervals, so expect three fragments.

0, 1000, 3500, 6000 bp

Linear DNA: keep both ends when finding fragment lengths

Find each interval length

Subtract each boundary from the next one, in base pairs. The second and third intervals happen to have the same length, and both stay in the list.

\begin{array}{l} 1000 - 0 = 1000 \\ 3500 - 1000 = 2500 \\ 6000 - 3500 = 2500 \end{array}

Check that no DNA has been lost

Why add them? Cutting removes no DNA, so the fragments must add up to $6, 000 bp$ . A short sum would mean the piece after the last cut was forgotten.

1000 + 2500 + 2500 = 6000

Predict the band pattern

The two $2, 500 bp$ fragments travel the same distance and make one band. The $1, 000 bp$ fragment travels farther. Three fragments give two bands. Keep both $2, 500 bp$ entries when the digest goes to the gel, because the band holds twice the DNA.

Fragments versus observed size positions
Fragment sizes	Distinct band positions
$1000$ , $2500$ , $2500 bp$	$1000$ and $2500 bp$

Compare the prediction with the tool

Restriction digest & gel draws the predicted gel under the map. Choose a ladder to compare sizes, or choose Open this digest in Read a gel to record the bands you see. A change in one copy does not update the other.

Result

The fragments are $1, 000$ , $2, 500$ and $2, 500 bp$ , adding to $6, 000$ . They make two bands, at $2, 500 bp$ and at $1, 000 bp$ , with the $1, 000 bp$ band farther from the well.

Your turn

1. One like the example

A linear $8, 000 bp$ molecule is cut at $1, 500$ , $4, 000$ and $6, 500 bp$ . Find the fragments and the number of bands.

Show the answer and explanation

Four fragments, $1, 500$ , $2, 500$ , $2, 500$ and $1, 500 bp$ , which make two bands.

The boundaries are $0$ , $1, 500$ , $4, 000$ , $6, 500$ and $8, 000$ . Subtracting neighbors gives $1, 500$ , $2, 500$ , $2, 500$ and $1, 500$ , which add to $8, 000$ . Equal lengths share a band, so there are bands at $2, 500$ and at $1, 500 bp$ .

\begin{array}{l} 4000 - 1500 = 2500 \\ 6500 - 4000 = 2500 \\ 8000 - 6500 = 1500 \\ 1500 + 2500 + 2500 + 1500 = 8000 \end{array}

\begin{array}{l} 4000 - 1500 = 2500 \\ 6500 - 4000 = 2500 \\ 8000 - 6500 = 1500 \\ 1500 + 2500 + 2500 + 1500 \\ = 8000 \end{array}

2. A variation

The same two cuts, at $1, 000$ and $3, 500 bp$ , are made in a circular molecule of $6, 000 bp$ . Find the fragments and the number of bands.

Show the answer and explanation

Two fragments, $2, 500$ and $3, 500 bp$ , which make two bands.

One fragment runs from $1, 000$ to $3, 500$ , which is $2, 500 bp$ . The other wraps from $3, 500$ past the end of the numbering to $1, 000$ , which is $6, 000 - 3, 500 + 1, 000$ $= 3, 500 bp$ . A circle has no ends, so two cuts make two fragments.

\begin{array}{l} 3500 - 1000 = 2500 \\ 6000 - 3500 + 1000 = 3500 \\ 2500 + 3500 = 6000 \end{array}

3. Somewhere new

The linear $6, 000 bp$ digest is run with too little enzyme, so some molecules are cut at only one site or at none. Which extra bands appear besides $1, 000$ and $2, 500 bp$ ?

Show the answer and explanation

Bands at $3, 500 bp$ , $5, 000 bp$ and $6, 000 bp$ .

A molecule cut only at $1, 000$ gives $1, 000$ and $5, 000 bp$ . One cut only at $3, 500$ gives $3, 500$ and $2, 500 bp$ . An uncut molecule stays at $6, 000 bp$ . Each extra band is a sum of neighboring fragments, $1, 000 + 2, 500 = 3, 500$ and $2, 500 + 2, 500 = 5, 000$ .

\begin{array}{l} 1000 + 2500 = 3500 \\ 2500 + 2500 = 5000 \end{array}

Keep exploring

The digest opens in Restriction digest & gel with cuts at $1000$ and $3500 bp$ . Change the topology to circular and watch three fragments become two.

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Sources and scope

Authored study material. Tool results depend on the stated inputs and model assumptions.

After reading

Study it, then try it

Practice the key terms as flashcards, then open the example in its tool, change a value and keep a useful result on your board.

Study the 8 key terms Explore the restriction map Open worked example on a board Restriction-enzyme reference

Your existing work stays on this device. Examples open as editable copies.

State the molecule and the digest assumptions

Mark all boundaries in order

Find each interval length

Check that no DNA has been lost

Predict the band pattern

Compare the prediction with the tool

Result

Your turn

1. One like the example

Four fragments, 1,5001,500, 2,5002,500, 2,5002,500 and 1,500 bp1,500 bp, which make two bands.

2. A variation

Two fragments, 2,5002,500 and 3,500 bp3,500 bp, which make two bands.

3. Somewhere new

Bands at 3,500 bp3,500 bp, 5,000 bp5,000 bp and 6,000 bp6,000 bp.

Keep exploring

Study it, then try it

Four fragments, $1, 500$ , $2, 500$ , $2, 500$ and $1, 500 bp$ , which make two bands.

Two fragments, $2, 500$ and $3, 500 bp$ , which make two bands.

Bands at $3, 500 bp$ , $5, 000 bp$ and $6, 000 bp$ .