Restriction fragment
Encyclopedia
A restriction fragment is a DNA
fragment resulting from the cutting of a DNA strand by a restriction enzyme
(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), and are four to eight nucleotide
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
or used in recombinant DNA
technology.
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 can form hydrogen bond
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
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.
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
fragment resulting from the cutting of a DNA strand by a restriction enzyme
Restriction enzyme
A Restriction Enzyme is an enzyme that cuts double-stranded DNA at specific recognition nucleotide sequences known as restriction sites. Such enzymes, found in bacteria and archaea, are thought to have evolved to provide a defense mechanism against invading viruses...
(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
Palindromic sequence
A palindromic sequence is a nucleic acid sequence that is the same whether read 5' to 3' on one strand or 5' to 3' on the complementary strand with which it forms a double helix....
, (the sequence of nucleotides is the same on both strands when read in the 5' to 3' direction), and are four to eight nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
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
Gel electrophoresis is a method used in clinical chemistry to separate proteins by charge and or size and in biochemistry and molecular biology to separate a mixed population of DNA and RNA fragments by length, to estimate the size of DNA and RNA fragments or to separate proteins by charge...
or used in recombinant DNA
Recombinant DNA
Recombinant DNA molecules are DNA sequences that result from the use of laboratory methods to bring together genetic material from multiple sources, creating sequences that would not otherwise be found in biological organisms...
technology.
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 can form hydrogen bond
Hydrogen bond
A hydrogen bond is the attractive interaction of a hydrogen atom with an electronegative atom, such as nitrogen, oxygen or fluorine, that comes from another molecule or chemical group. The hydrogen must be covalently bonded to another electronegative atom to create the bond...
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
Allele
An allele is one of two or more forms of a gene or a genetic locus . "Allel" is an abbreviation of allelomorph. Sometimes, different alleles can result in different observable phenotypic traits, such as different pigmentation...
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.