Restriction Mapping
At the molecular level, the fine structure of a gene can be studied only through determination of nucleotide sequence of the concerned DNA segment. Sometimes this is done through isolation of DNA corresponding to a gene, which is a lengthy process (see Genetic Engineering and Biotechnology 3.  Isolation, Sequencing and Synthesis of Genes). Instead we can prepare a map of the DNA by cleavage of the DNA at specific sites with the help of restriction endonucleases (see Genetic Engineering and Biotechnology 1.  Recombinant DNA and PCR (Cloning and Amplification of DNA)). These sites of cleavage can be identified and mapped to give rise to a restriction map. On a restriction map, is found a linear sequence of sites, each for a specific enzyme and the distances between them are measured as number of base pairs of DNA. This technique can not be directly used in eukaryotes, due to some inherent difficulties as will be shown later in this section, but has been successfully utilized for preparing restriction maps in prokaryotes.

In a restriction map, the nucleotide sequence of DNA between sites close to one another (300 bp or less) can be determined. These regions can then be connected into a sequence of the entire gene, whose nucleotide sequence, then can be compared with amino-acid sequence of protein coded by it. This can be further extended to adjoining genes to saturate the genetic map, as is being attempted for human genome.