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the proposals was the existence of lifeforms that use arsenic instead of phosphorus in dna a report in 2010 of the possibility in the bacterium gfaj 1 was announced 58 59 though the research was disputed 59 60 and evidence suggests the bacterium actively prevents the incorporation of arsenic into the dna backbone and other biomolecules 61 quadruplex structures further information g quadruplex dna quadruplex formed by telomere repeats the looped conformation of the dna backbone is very different from the typical dna helix the green spheres in the center represent potassium ions 62 at the ends of the linear chromosomes are specialized regions of dna called telomeres the main function of these regions is to allow the cell to replicate chromosome ends using the enzyme telomerase as the enzymes that normally replicate dna cannot copy the extreme 3 ends of chromosomes 63 these specialized chromosome caps also help protect the dna ends and stop the dna repair systems in the cell from treating them as damage to be corrected 64 in human cells telomeres are usually lengths of single stranded dna containing several thousand repeats of a simple ttaggg sequence 65 these guanine rich sequences may stabilize chromosome ends by forming structures of stacked sets of four base units rather than the usual base pairs found in other dna molecules here four guanine bases known as a guanine tetrad form a flat plate these flat four base units then stack on top of each other to form a stable g quadruplex structure 66 these structures are stabilized by hydrogen bonding between the edges of the bases and chelation of a metal ion in the centre of each four base unit 67 other structures can also be formed with the central set of four bases coming from either a single strand folded around the bases or several different parallel strands each contributing one base to the central structure in addition to these stacked structures telomeres also form large loop structures called telomere loops or t loops here the single stranded dna curls around in a long circle stabilized by telomere binding proteins 68 at the very end of the t loop the single stranded telomere dna is held onto a region of double stranded dna by the telomere strand disrupting the double helical dna and base pairing to one of the two strands this triple stranded structure is called a displacement loop or d loop 66 branched dna further information branched dna and dna nanotechnology single branch multiple branches branched dna can form networks containing multiple branches in dna fraying occurs when non complementary regions exist at the end of an otherwise complementary double strand of dna however branched dna can occur if a third strand of dna is introduced and contains adjoining regions able to hybridize with the frayed regions of the pre existing double strand although the simplest example of branched dna involves only three strands of dna complexes involving additional strands and multiple branches are also possible 69 branched dna can be used in nanotechnology to construct geometric shapes see the section on uses in technology below artificial bases main article nucleic acid analogue several artificial nucleobases have been synthesized and successfully incorporated in the eight base dna analogue named hachimoji dna dubbed s b p and z these artificial bases are capable of bonding with each other in a predictable way s b and p z maintain the double helix structure of dna and be transcribed to rna their existence could be seen as an indication that there is nothing special about the four natural nucleobases that evolved on earth 70 71 on the other hand dna is tightly related to rna which does not only act as a transcript of dna but also performs as molecular machines many tasks in cells for this purpose it has to fold into a structure it has been shown that to allow to create all possible structures at least four bases are required for the corresponding rna 72 while a higher number is also possible but this would be against the natural principle of least effort acidity the phosphate groups of dna give it similar acidic properties to phosphoric acid and it can be considered as a strong acid it will be fully ionized at a normal cellular ph releasing protons which leave behind negative charges on the phosphate groups these negative charges protect dna from breakdown by hydrolysis by repelling nucleophiles which could hydrolyze it 73 macroscopic appearance impure dna extracted from an orange pure dna extracted from cells forms white stringy clumps 74 chemical modifications and altered dna packaging base modifications and dna packaging further information dna methylation and chromatin remodeling cytosine 5 methylcytosine thymine structure of cytosine with and without the 5 methyl group deamination converts 5 methylcytosine into thymine the expression of genes is influenced by how the dna is packaged in chromosomes in a structure called chromatin base modifications can be involved in packaging with regions that have low or no gene expression usually containing high levels of methylation of cytosine bases dna packaging and its influence on gene expression can also occur by covalent modifications of the histone protein core around which dna is wrapped in the chromatin structure or else by remodeling carried out by chromatin remodeling complexes see chromatin remodeling there is further crosstalk between dna methylation and histone modification so they can coordinately affect chromatin and gene expression 75 for one example cytosine methylation produces 5 methylcytosine which is important for x inactivation of chromosomes 76 the average level of methylation varies between organisms the worm caenorhabditis elegans lacks cytosine methylation while vertebrates have higher levels with up to 1 of their dna containing 5 methylcytosine 77 despite the importance of 5 methylcytosine it can deaminate to leave a thymine base so methylated cytosines are particularly prone to mutations 78 other base modifications include adenine methylation in bacteria the presence of 5 hydroxymethylcytosine in the brain 79 and the glycosylation of uracil to produce the j base in kinetoplastids 80 81 damage further information dna damage naturally occurring mutation and dna damage theory of aging a covalent adduct between a metabolically activated form of benzo a pyrene the major mutagen in tobacco smoke and dna 82 dna can be damaged by many sorts of mutagens which change the dna sequence mutagens include oxidizing agents alkylating agents and also high energy electromagnetic radiation such as ultraviolet light and x rays the type of dna damage produced depends on the type of mutagen for example uv light can damage dna by producing thymine dimers which are cross links between pyrimidine bases 83 on the other hand oxidants such as free radicals or hydrogen peroxide produce multiple forms of damage including base modifications particularly of guanosine and double strand breaks 84 a typical human cell contains about 150 000 bases that have suffered oxidative damage 85 of these oxidative lesions the most dangerous are double strand breaks as these are difficult to repair and can produce point mutations insertions deletions from the dna sequence and chromosomal translocations 86 these mutations can cause cancer because of inherent limits in the dna repair mechanisms if humans lived long enough they would all eventually develop cancer 87 88 dna damages that are naturally occurring due to normal cellular processes that produce reactive oxygen species the hydrolytic activities of cellular water etc also occur frequently although most of these damages are repaired in any cell some dna damage may remain despite the action of repair processes these remaining dna damages accumulate with age in mammalian postmitotic tissues this accumulation appears to be an important underlying cause of aging 89 90 91 many mutagens fit into the space between two adjacent base pairs this is called intercalation most intercalators are aromatic and planar molecules examples include ethidium bromide acridines daunomycin and doxorubicin for an intercalator to fit between base pairs the bases must separate distorting the dna strands by unwinding of the double helix this inhibits both transcription and dna replication causing toxicity and mutations 92 as a result dna intercalators may be carcinogens and in the case of thalidomide a teratogen 93 others such as benzo a pyrene diol epoxide and aflatoxin form dna adducts that induce errors in replication 94 nevertheless due to their ability to inhibit dna transcription and replication other similar toxins are also used in chemotherapy to inhibit rapidly growing cancer cells 95 biological functions location of eukaryote nuclear dna within the chromosomes dna usually occurs as linear chromosomes in eukaryotes and circular chromosomes in prokaryotes the set of chromosomes in a cell makes up its genome the human genome has approximately 3 billion base pairs of dna arranged into 46 chromosomes 96 the information carried by dna is held in the sequence of pieces of dna called genes transmission of genetic information in genes is achieved via complementary base pairing for example in transcription when a cell uses the information in a gene the dna sequence is copied into a complementary rna sequence through the attraction between the dna and the correct rna nucleotides usually this rna copy is then used to make a matching protein sequence in a process called translation which depends on the same interaction between rna nucleotides in an alternative fashion a cell may copy its genetic information in a process called dna replication the details of these functions are covered in other articles here the focus is on the interactions between dna and other molecules that mediate the function of the genome genomes genomic dna is tightly and orderly packed in the process called dna condensation to fit the small available volumes of the cell in eukaryotes dna is located in the cell nucleus with small amounts in mitochondria and chloroplasts in prokaryotes the dna is held within an irregularly shaped body in the cytoplasm called the nucleoid 97 the functional genetic information in a genome is located in genes regulatory sequences origins of replication centromeres telomeres and segments required for the three dimensional structure of chromatin in many complex eukaryotes only a small fraction of the total sequence is devoted to the various functional elements for example in humans less than 10 of the genome has a defined functional role and the rest 90 is probably junk dna see also non coding dna transcription and translation further information genetic code transcription genetics and protein biosynthesis a gene is a sequence of dna that contains genetic information and can influence the phenotype of an organism within a gene the sequence of bases along a dna strand defines a messenger rna sequence which then defines one or more protein sequences the relationship between the nucleotide sequences of genes and the amino acid sequences of proteins is determined by the rules of translation known collectively as the genetic code the genetic code consists of three letter words called codons formed from a sequence of three nucleotides e g act cag ttt in transcription the codons of a gene are copied into messenger rna by rna polymerase this rna copy is then decoded by a ribosome that reads the rna sequence by base pairing the messenger rna to transfer rna which carries amino acids since there are 4 bases in 3 letter combinations there are 64 possible codons 4 3 combinations these encode the twenty standard amino acids giving most amino acids more than one possible codon there are also three stop or nonsense codons signifying the end of the coding region these are the tag taa and tga codons uag uaa and uga on the mrna replication further information dna replication dna replication the double helix is unwound by a helicase and topo iso merase next one dna polymerase produces the leading strand copy another dna polymerase binds to the lagging strand this enzyme makes discontinuous segments called okazaki fragments before dna ligase joins them together cell division is essential for an organism to grow but when a cell divides it must replicate the dna in its genome so that the two daughter cells have the same genetic information as their parent the double stranded structure of dna provides a simple mechanism for dna replication here the two strands are separated and then each strand s complementary dna sequence is recreated by an enzyme called dna polymerase this enzyme makes the complementary strand by finding the correct base through complementary base pairing and bonding it onto the original strand as dna polymerases can only extend a dna strand in a 5 to 3 direction different mechanisms are used to copy the antiparallel strands of the double helix 98 in this way the base on the old strand dictates which base appears on the new strand and the cell ends up with a perfect copy of its dna extracellular nucleic acids naked extracellular dna edna most of it released by cell death is nearly ubiquitous in the environment its concentration in soil may be as high as 2 μg l and its concentration in natural aquatic environments may be as high at 88 μg l 99 various possible functions have been proposed for edna it may be involved in horizontal gene transfer 100 it may provide nutrients 101 and it may act as a buffer to recruit or titrate ions or antibiotics 102 extracellular dna acts as a functional extracellular matrix component in the biofilms of several bacterial species it may act as a recognition factor to regulate the attachment and dispersal of specific cell types in the biofilm 103 it may contribute to biofilm formation 104 and it may contribute to the biofilm s physical strength and resistance to biological stress 105 cell free fetal dna is found in the blood of the mother and can be sequenced to determine a great deal of information about the developing fetus 106 under the name of environmental dna edna has seen increased use in the natural sciences as a survey tool for ecology monitoring the movements and presence of species in water air or on land and assessing an area s biodiversity 107 108 interactions with proteins all the functions of dna depend on interactions with proteins these protein interactions can be non specific or the protein can bind specifically to a single dna sequence enzymes can also bind to dna and of these the polymerases that copy the dna base sequence in transcription and dna replication are particularly important dna binding proteins further information dna binding protein interaction of dna in orange with histones in blue these proteins basic amino acids bind to the acidic phosphate groups on dna structural proteins that bind dna are well understood examples of non specific dna protein interactions within...
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