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Gel electrophoresis appears in the biotechnology chapter as a few lines, and those lines carry several facts examiners like to test: which electrode DNA moves to, why small pieces go farther, what makes bands visible, and what elution means. This post explains each fact, then shows how a researcher reads fragment sizes from a gel, with two worked examples.
Where is this in the syllabus?
The NEET (UG) 2026 syllabus lists "Principles and process of Biotechnology: Genetic engineering (Recombinant DNA technology)". The CBSE 2026-27 biology curriculum includes Chapter 9, Biotechnology: Principles and Processes. The text is in NCERT Class 12 Biotechnology: Principles and Processes (reprint 2026-27), under "Separation and isolation of DNA fragments". Check the syllabus for your exam year.
Why does DNA move through the gel?
NCERT's explanation has three parts:
Charge. DNA fragments are negatively charged, so in an electric field they move towards the anode, the positive electrode.
Matrix. The fragments are forced through a gel. The most common matrix is agarose, a natural polymer extracted from seaweed.
Sieving. The gel acts as a sieve, so fragments separate by size: the smaller the fragment, the farther it moves.
A protocol by Lee and colleagues (2012) in the Journal of Visualized Experiments adds the reason size is what matters. The negative charge sits on the phosphate backbone, and DNA has a uniform mass to charge ratio, so charge does not tell fragments apart. Size does, through the pores of the gel.
How are the bands seen and recovered?
You cannot see DNA in visible light without a stain. NCERT describes staining with ethidium bromide and exposing the gel to UV light, which shows bright orange bands. The bands are then cut out of the gel and the DNA extracted, a step called elution. The purified fragments are used to build recombinant DNA with cloning vectors.
Lee and colleagues add practical points worth knowing. Loading dye adds density so the sample sinks into the well, and its coloured dyes show how far the run has gone. Ethidium bromide is a suspected mutagen and carcinogen, so gloves are worn, and alternatives such as SYBR stains exist. Higher agarose concentrations give smaller pores; most gels are 0.5% to 2% agarose.
How do you read a fragment's size from a ladder?
Each gel usually has a lane of DNA fragments of known size, called a ladder or standard. The protocol notes that the distance a fragment travels is inversely proportional to the log of its molecular weight, and that sizes are found by plotting log size against distance for the ladder bands.
Worked example (sample numbers). A ladder gives bands at 3000 bp (14 mm from the well), 2000 bp (19 mm), 1000 bp (27 mm) and 500 bp (35 mm). An unknown band sits at 23 mm.
It lies between the 2000 bp band (19 mm) and the 1000 bp band (27 mm), exactly halfway.
Interpolate on the log scale: log 2000 ≈ 3.301 and log 1000 = 3.000. Halfway is 3.1505.
10^3.1505 ≈ 1414 bp, about 1.4 kb.
Interpolating on an ordinary scale would give 1500 bp. The log scale is the reason the halfway point is nearer 1414, the geometric mean of 1000 and 2000.
Worked example: mapping cut sites
A linear DNA molecule of 10 kb is cut with two enzymes (sample numbers).
Enzyme X alone gives bands of 3 kb and 7 kb, so it cuts once, 3 kb from one end.
Enzyme Y alone gives 4 kb and 6 kb, so it also cuts once.
Cutting with both gives 3, 3 and 4 kb.
If Y cut 4 kb from the same end as X, the double digest would give 3, 1 and 6 kb. It gave 3, 3 and 4, so Y must cut 4 kb from the other end, at 6 kb from X's end: the pieces run 0 to 3, 3 to 6 and 6 to 10 kb. The sizes in each lane must add to 10 kb, which is a quick check.
Which mistakes cost marks?
Saying DNA moves to the cathode. It is negative, so it moves to the anode.
Calling the band nearest the wells the smallest. It is the largest.
Saying bands are visible on their own. They need a stain and UV light.
Confusing elution with loading. Elution is recovering DNA from a cut-out band.
Assuming one band means one molecule size in every form. Lee and colleagues note that supercoiled plasmid DNA runs fastest, then linear DNA of the same size, with the open circular form slowest.
For restriction enzymes, vectors and PCR, see our post on biotechnology principles, and for a use of these gels in forensics, DNA fingerprinting.
A practice routine
Three-line summary: from memory, write charge, matrix and sieving, then check against NCERT.
Draw a gel: mark the wells, the anode and four bands, and label the largest and smallest.
Ladder drill: with your own sample ladder, estimate two unknown sizes on a log scale.
Mapping drill: make up a single and double digest and work out where the sites are.
If the movement of charged fragments through a gel is hard to picture, the Fermi Simulation Lab has interactive simulations for ideas that are easier to see than to read.
Today, sketch a gel with an uncut sample and two digests, and explain to someone why the smallest band ran farthest.
