A restriction fragment is a DNA fragment resulting from the cutting of a DNA strand by a

restriction enzyme A restriction enzyme, restriction endonuclease, REase, ENase or'' restrictase '' is an enzyme that cleaves DNA into fragments at or near specific recognition sites within molecules known as restriction sites. Restriction enzymes are one class o ...

(restriction endonucleases), a process called restriction. Each restriction enzyme is highly specific, recognising a particular short DNA sequence, or restriction site, and cutting both DNA strands at specific points within this site. Most restriction sites are palindromic, (the sequence of nucleotides is the same on both strands when read in the 5' to 3' direction of each strand), and are four to eight

nucleotide Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules wi ...

s long. Many cuts are made by one restriction enzyme because of the chance repetition of these sequences in a long DNA molecule, yielding a set of restriction fragments. A particular DNA molecule will always yield the same set of restriction fragments when exposed to the same restriction enzyme. Restriction fragments can be analyzed using techniques such as

gel electrophoresis Gel electrophoresis is a method for separation and analysis of biomacromolecules ( DNA, RNA, proteins, etc.) and their fragments, based on their size and charge. It is used in clinical chemistry to separate proteins by charge or size (IEF ...

or used in

recombinant DNA Recombinant DNA (rDNA) molecules are DNA molecules formed by laboratory methods of genetic recombination (such as molecular cloning) that bring together genetic material from multiple sources, creating sequences that would not otherwise be foun ...

technology.

Applications

In recombinant DNA technology, specific restriction endonucleases are used that will isolate a particular gene and cleave the sugar phosphate backbones at different points (retaining symmetry), so that the double-stranded restriction fragments have single-stranded ends. These short extensions, called ''

sticky ends DNA ends refer to the properties of the ends of linear DNA molecules, which in molecular biology are described as "sticky" or "blunt" based on the shape of the complementary strands at the terminus. In sticky ends, one strand is longer than the ...

'', can form

hydrogen bond In chemistry, a hydrogen bond (or H-bond) is a primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative "donor" atom or group (Dn), and another electronegative atom bearing a ...

ed base pairs with complementary sticky ends on any other DNA cut with the same enzyme (such as a bacterial plasmid). In agarose gel electrophoresis, the restriction fragments yield a band pattern characteristic of the original DNA molecule and restriction enzyme used, for example the relatively small DNA molecules of viruses and plasmids can be identified simply by their restriction fragment patterns. If the nucleotide differences of two different

allele An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is a variation of the same sequence of nucleotides at the same place on a long DNA molecule, as described in leading textbooks on genetics and evolution. ::"The chro ...

s occur within the restriction site of a particular restriction enzyme, digestion of segments of DNA from individuals with different alleles for that particular gene with that enzyme would produce different fragments and that will each yield different band patterns in gel electrophoresis.

References

Molecular biology Restriction enzymes {{genetics-stub