DNA Fingerprinting

NCERT grounding

Section 5.10 of the NCERT Class XII Biology textbook opens with a striking number: about 99.9 per cent of the base sequence among humans is identical. It is the remaining fraction — the differences in DNA sequence — that makes every individual unique in phenotypic appearance. Sequencing the entire genome of two people each time we wished to compare them would be a daunting and expensive task, so the textbook frames DNA fingerprinting as a very quick way to compare the DNA sequences of any two individuals.

NCERT then anchors the technique to a single principle. DNA fingerprinting involves identifying differences in some specific regions of the DNA sequence called repetitive DNA, because in these sequences a small stretch of DNA is repeated many times. These sequences show a high degree of polymorphism and form the basis of the entire method. The chapter explicitly credits Alec Jeffreys with initially developing the technique, using a satellite DNA as a probe that he named the Variable Number of Tandem Repeats (VNTR).

"DNA Fingerprinting is a technique to find out variations in individuals of a population at DNA level. It works on the principle of polymorphism in DNA sequences. It has immense applications in the field of forensic science, genetic biodiversity and evolutionary biology."
— NCERT Class XII Biology, Chapter 5 Summary

VNTR polymorphism and the technique

To understand why DNA fingerprinting works, begin with the molecule it interrogates. DNA polymorphism is variation at the genetic level, and it is the starting point of the whole subject. Polymorphism arises due to mutations. New mutations may appear in an individual either in somatic cells or in germ cells. A germ-cell mutation, if it does not seriously impair the individual's ability to have offspring, can spread to other members of the population through sexual reproduction. By definition, allelic sequence variation is described as a DNA polymorphism if more than one variant (allele) at a locus occurs in the population with a frequency greater than 0.01. In simpler terms, an inheritable mutation found in a population at high frequency is a DNA polymorphism.

Crucially, the probability of such variation being observed is far higher in non-coding DNA. Mutations in non-coding sequences usually have no immediate effect on an individual's reproductive ability, so they are not removed by selection — they keep accumulating generation after generation. This silent accumulation is exactly what makes non-coding repetitive DNA the richest source of inter-individual variability and the ideal target for fingerprinting.

Satellite DNA — separating the repeats

Repetitive DNA can be physically separated from the rest of the genome. When total genomic DNA is spun in a density gradient, the bulk DNA forms one major peak, while the repetitive sequences appear as additional small peaks known as satellite DNA. They form distinct peaks because their repeated, biased base composition gives them a buoyant density different from the average genomic DNA.

Why VNTRs are so informative

The VNTR belongs to the class of satellite DNA called minisatellite. Here a small DNA sequence is arranged tandemly — one repeat directly after another — in many copies. The decisive feature is that the copy number varies from chromosome to chromosome within a single individual, and the number of repeats shows a very high degree of polymorphism between individuals. Because the copy number differs, the total length of a VNTR locus varies enormously, ranging in size from about 0.1 to 20 kilobase pairs.

This length variation is what every band on a DNA fingerprint represents. After the genomic DNA is cut and probed, hybridisation with the VNTR probe produces many bands of differing sizes. Together these bands give a banding pattern that is characteristic of one individual's DNA. The pattern differs from individual to individual in a population — except in the case of monozygotic (identical) twins, who arise from the same zygote and therefore share the same copy numbers. Because the two alleles of a chromosome (one paternal, one maternal) carry different VNTR copy numbers, the pattern is also inherited in a traceable way: roughly half the bands of a child match the mother and half match the father.

The six-step technique

Alec Jeffreys' original procedure used Southern blot hybridisation with a radiolabelled VNTR as the probe. NCERT lists the technique as a fixed sequence of six steps. The ordering is examined directly, so it must be memorised exactly.

Reading the steps together clarifies the logic. Steps 1 and 2 free the DNA and chop it into sized fragments. Step 3 spreads those fragments out by length — the longer the VNTR (the more tandem repeats it carries), the slower it migrates and the higher it stops in the gel. Steps 4 and 5 are the heart of specificity: blotting fixes the fragment ladder onto a durable membrane, and the labelled VNTR probe then "lights up" only the fragments that contain the repeat sequence, ignoring the bulk of the genome. Step 6 makes the result visible. The position-by-length read-out means a longer fragment sits higher and a shorter fragment sits lower, so two people with different repeat numbers produce different band heights.

Scientists, sensitivity and applications

The technique was initially developed by Alec Jeffreys, who in the mid-1980s recognised that a satellite DNA probe with high polymorphism could individualise a sample. In India, the establishment and forensic use of DNA fingerprinting is closely associated with Lalji Singh, often regarded as the father of Indian DNA fingerprinting. The original method was limited by the amount of DNA needed for a clear blot. Sensitivity was later increased by the use of the polymerase chain reaction (PCR), so that DNA from even a single cell is now enough to perform a fingerprinting analysis.

The applications follow directly from two properties of VNTR polymorphism. First, because DNA from every tissue of an individual shows the same polymorphism, a sample of blood, hair, skin, bone or saliva from a crime scene can be matched to a person — the basis of forensic identification. Second, because the polymorphisms are inherited from parents to children, the technique is the basis of paternity testing in cases of dispute. Beyond identification, fingerprinting is used to determine population and genetic diversities and contributes to evolutionary biology. NCERT notes that currently many different probes are used to generate DNA fingerprints.

Worked examples

Common confusion & NEET traps

DNA fingerprinting questions are short, but they cluster around a few predictable confusions — mostly about which class of repeat is used, which scientist did what, and the exact step order.