D-loop
Encyclopedia
In molecular biology
, a displacement loop or D-loop is a DNA
structure where the two strands of a double-stranded DNA molecule are separated for a stretch and held apart by a third strand of DNA. The third strand has a base
sequence which is complementary
to one of the main strands and pairs
with it, thus displacing the other main strand in the region. Within that region the structure is thus a form of triple-stranded DNA
.
A diagram in the paper introducing the term illustrated the D-loop with a shape resembling a capital "D", where the displaced strand formed the loop of the "D".
(An unrelated use of the term D-loop, but not displacement loop, is for the loop of RNA
that forms the end of the D arm
of a transfer RNA
molecule.)
D-loops occur in a number of particular situations, including in DNA repair
, in telomere
s, and as a semi-stable structure in mitochondrial
circular DNA
molecules.
They found the third strand was a replicated segment of the heavy strand
(or H-strand) of the molecule, which it displaced, and was hydrogen bond
ed to the light strand (or L-strand). Since then, it has been shown that the third strand is the initial segment generated by a replication
of the heavy strand that has been arrested shortly after initiation and is often maintained for some period in that state.
The D-loop occurs in the main non-coding area of the mitochondrial DNA molecule, a segment called the control region
or D-loop region.
Replication of the mitochondrial DNA can occur in two different ways, both starting in the D-loop region.
One way continues replication of the heavy strand through a substantial part (e.g. two-thirds) of the circular molecule, and then replication of the light strand begins. The more recently reported mode starts at a different origin within the D-loop region and uses coupled-strand replication with simultaneous synthesis of both strands.
Certain bases within the D-loop region are conserved, but large parts are highly variable and the region has proven to be useful for the study of the evolutionary history of vertebrates.
The region contains promoters for the transcription
of RNA
from the two strands of mitochondrial DNA immediately adjacent to the D-loop structure that is associated with initiation of DNA replication.
The function of the D-loop is not yet clear, but recent research suggests that it participates in the organization of the mitochondrial nucleoid
.
s, which cap the end of chromosome
s, terminate in a lariat
-like structure termed a t-loop.
This is a loop of both strands of the chromosome which are joined to an earlier point in the double-stranded DNA by the 3' strand end
invading the strand pair to form a D-loop; a special protein stabilizes the joint. The t-loop which is completed by the D-loop splice protects the end of the chromosome from damage.
In humans, the protein RAD51
is central to the homologous search and formation of the D-loop. In the bacterium Escherichia coli
, a similar function is performed by the protein RecA
.
Molecular biology
Molecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...
, a displacement loop or D-loop is a DNA
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...
structure where the two strands of a double-stranded DNA molecule are separated for a stretch and held apart by a third strand of DNA. The third strand has a base
Nucleobase
Nucleobases are a group of nitrogen-based molecules that are required to form nucleotides, the basic building blocks of DNA and RNA. Nucleobases provide the molecular structure necessary for the hydrogen bonding of complementary DNA and RNA strands, and are key components in the formation of stable...
sequence which is complementary
Complementarity (molecular biology)
In molecular biology, complementarity is a property of double-stranded nucleic acids such as DNA, as well as DNA:RNA duplexes. Each strand is complementary to the other in that the base pairs between them are non-covalently connected via two or three hydrogen bonds...
to one of the main strands and pairs
Base pair
In molecular biology and genetics, the linking between two nitrogenous bases on opposite complementary DNA or certain types of RNA strands that are connected via hydrogen bonds is called a base pair...
with it, thus displacing the other main strand in the region. Within that region the structure is thus a form of triple-stranded DNA
Triple-stranded DNA
A triple-stranded DNA is a structure of DNA in which three oligonucleotides wind around each other and form a triple helix. In this structure, one strand binds to a B-form DNA double helix through Hoogsteen or reversed Hoogsteen hydrogen bonds....
.
A diagram in the paper introducing the term illustrated the D-loop with a shape resembling a capital "D", where the displaced strand formed the loop of the "D".
(An unrelated use of the term D-loop, but not displacement loop, is for the loop of RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
that forms the end of the D arm
D arm
The D arm is a feature in the tertiary structure of transfer RNA . It is composed of the two D stems and the D loop. The D loop contains the base dihydrouracil. The D loop's main function is that of recognition...
of a transfer RNA
Transfer RNA
Transfer RNA is an adaptor molecule composed of RNA, typically 73 to 93 nucleotides in length, that is used in biology to bridge the three-letter genetic code in messenger RNA with the twenty-letter code of amino acids in proteins. The role of tRNA as an adaptor is best understood by...
molecule.)
D-loops occur in a number of particular situations, including in DNA repair
DNA repair
DNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as UV light and radiation can cause DNA damage, resulting in as many as 1...
, in telomere
Telomere
A telomere is a region of repetitive DNA sequences at the end of a chromosome, which protects the end of the chromosome from deterioration or from fusion with neighboring chromosomes. Its name is derived from the Greek nouns telos "end" and merοs "part"...
s, and as a semi-stable structure in mitochondrial
Mitochondrion
In cell biology, a mitochondrion is a membrane-enclosed organelle found in most eukaryotic cells. These organelles range from 0.5 to 1.0 micrometers in diameter...
circular DNA
Circular DNA
Circular DNA is a form of DNA that is found in viruses, bacteria and archaea as well as in eukaryotic cells in the form of either mitochondrial DNA or plastid DNA....
molecules.
In mitochondria
Researchers at Caltech discovered in 1971 that the circular mitochondrial DNA from growing cells included a short segment of three strands which they called a displacement loop.They found the third strand was a replicated segment of the heavy strand
Heavy strand
Circular molecules of DNA, such as plasmids and typical mitochondrial genomes, consist of two strands of DNA called the heavy strand and the light strand . The two strands have different masses due to different proportions of heavier nucleic acids...
(or H-strand) of the molecule, which it displaced, and was 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 to the light strand (or L-strand). Since then, it has been shown that the third strand is the initial segment generated by a replication
Replication
Replication may refer to:Science* Replication is one of the main principles of the scientific method, a.k.a. reproducibility** Replication , the repetition of a test or complete experiment...
of the heavy strand that has been arrested shortly after initiation and is often maintained for some period in that state.
The D-loop occurs in the main non-coding area of the mitochondrial DNA molecule, a segment called the control region
MtDNA control region
The mtDNA control region is an area of the mitochondrial genome which is non-coding DNA. It is the most polymorphic region of the human mtDNA genome, with polymorphism concentrated in hypervariable regions. The average nucleotide diversity in these regions is 1.7%...
or D-loop region.
Replication of the mitochondrial DNA can occur in two different ways, both starting in the D-loop region.
One way continues replication of the heavy strand through a substantial part (e.g. two-thirds) of the circular molecule, and then replication of the light strand begins. The more recently reported mode starts at a different origin within the D-loop region and uses coupled-strand replication with simultaneous synthesis of both strands.
Certain bases within the D-loop region are conserved, but large parts are highly variable and the region has proven to be useful for the study of the evolutionary history of vertebrates.
The region contains promoters for the transcription
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
of RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
from the two strands of mitochondrial DNA immediately adjacent to the D-loop structure that is associated with initiation of DNA replication.
The function of the D-loop is not yet clear, but recent research suggests that it participates in the organization of the mitochondrial nucleoid
Nucleoid
The nucleoid is an irregularly-shaped region within the cell of a prokaryote that contains all or most of the genetic material. In contrast to the nucleus of a eukaryotic cell, it is not surrounded by a nuclear membrane. The genome of prokaryotic organisms generally is a circular, double-stranded...
.
In telomeres
In 1999 it was reported that telomereTelomere
A telomere is a region of repetitive DNA sequences at the end of a chromosome, which protects the end of the chromosome from deterioration or from fusion with neighboring chromosomes. Its name is derived from the Greek nouns telos "end" and merοs "part"...
s, which cap the end of chromosome
Chromosome
A chromosome is an organized structure of DNA and protein found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions.Chromosomes...
s, terminate in a lariat
Lariat
Lariat can refer to:*A rope in the form of a lasso*Lariat chain, a science demonstration*A professional wrestling move, a variation of a clothesline*A genetic structure in Splicing *Double Lariat, a popular song sung by Luka Megurine...
-like structure termed a t-loop.
This is a loop of both strands of the chromosome which are joined to an earlier point in the double-stranded DNA by the 3' strand end
Directionality (molecular biology)
Directionality, in molecular biology and biochemistry, is the end-to-end chemical orientation of a single strand of nucleic acid. The chemical convention of naming carbon atoms in the nucleotide sugar-ring numerically gives rise to a 5′-end and a 3′-end...
invading the strand pair to form a D-loop; a special protein stabilizes the joint. The t-loop which is completed by the D-loop splice protects the end of the chromosome from damage.
In DNA repair
When a double-stranded DNA molecule has suffered a break in both strands, one repair mechanism available in diploid eukaryotic cells is homologous recombination repair. This makes use of the intact chromosome homologous to the broken one as a template to bring the two double-stranded pieces into correct alignment for rejoining. Early in this process, one strand of one piece is matched to a strand of the intact chromosome and that strand is used to form a D-loop at that point, displacing the intact chromosome's other strand. Various ligation and synthesis steps follow to effect the rejoining.In humans, the protein RAD51
RAD51
RAD51 is a human gene. The protein encoded by this gene is a member of the RAD51 protein family which assist in repair of DNA double strand breaks. RAD51 family members are homologous to the bacterial RecA and yeast Rad51...
is central to the homologous search and formation of the D-loop. In the bacterium Escherichia coli
Escherichia coli
Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls...
, a similar function is performed by the protein RecA
RecA
RecA is a 38 kilodalton Escherichia coli protein essential for the repair and maintenance of DNA. RecA has a structural and functional homolog in every species in which it has been seriously sought and serves as an archetype for this class of homologous DNA repair proteins...
.