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o the base pairs and may provide a binding site as the strands are not symmetrically located with respect to each other the grooves are unequally sized the major groove is 22 ångströms 2 2 nm wide while the minor groove is 12 å 1 2 nm in width 24 due to the larger width of the major groove the edges of the bases are more accessible in the major groove than in the minor groove as a result proteins such as transcription factors that can bind to specific sequences in double stranded dna usually make contact with the sides of the bases exposed in the major groove 25 this situation varies in unusual conformations of dna within the cell see below but the major and minor grooves are always named to reflect the differences in width that would be seen if the dna was twisted back into the ordinary b form base pairing further information base pair top a gc base pair with three hydrogen bonds bottom an at base pair with two hydrogen bonds non covalent hydrogen bonds between the pairs are shown as dashed lines in a dna double helix each type of nucleobase on one strand bonds with just one type of nucleobase on the other strand this is called complementary base pairing purines form hydrogen bonds to pyrimidines with adenine bonding only to thymine in two hydrogen bonds and cytosine bonding only to guanine in three hydrogen bonds this arrangement of two nucleotides binding together across the double helix from six carbon ring to six carbon ring is called a watson crick base pair dna with high gc content is more stable than dna with low gc content a hoogsteen base pair hydrogen bonding the 6 carbon ring to the 5 carbon ring is a rare variation of base pairing 26 as hydrogen bonds are not covalent they can be broken and rejoined relatively easily the two strands of dna in a double helix can thus be pulled apart like a zipper either by a mechanical force or high temperature 27 as a result of this base pair complementarity all the information in the double stranded sequence of a dna helix is duplicated on each strand which is vital in dna replication this reversible and specific interaction between complementary base pairs is critical for all the functions of dna in organisms 7 ssdna vs dsdna most dna molecules are actually two polymer strands bound together in a helical fashion by noncovalent bonds this double stranded dsdna structure is maintained largely by the intrastrand base stacking interactions which are strongest for g c stacks the two strands can come apart a process known as melting to form two single stranded dna ssdna molecules melting occurs at high temperatures low salt and high ph low ph also melts dna but since dna is unstable due to acid depurination low ph is rarely used the stability of the dsdna form depends not only on the gc content g c basepairs but also on sequence since stacking is sequence specific and also length longer molecules are more stable the stability can be measured in various ways a common way is the melting temperature also called t m value which is the temperature at which 50 of the double strand molecules are converted to single strand molecules melting temperature is dependent on ionic strength and the concentration of dna as a result it is both the percentage of gc base pairs and the overall length of a dna double helix that determines the strength of the association between the two strands of dna long dna helices with a high gc content have more strongly interacting strands while short helices with high at content have more weakly interacting strands 28 in biology parts of the dna double helix that need to separate easily such as the tataat pribnow box in some promoters tend to have a high at content making the strands easier to pull apart 29 in the laboratory the strength of this interaction can be measured by finding the melting temperature t m necessary to break half of the hydrogen bonds when all the base pairs in a dna double helix melt the strands separate and exist in solution as two entirely independent molecules these single stranded dna molecules have no single common shape but some conformations are more stable than others 30 amount schematic karyogram of a human it shows 22 homologous chromosomes both the female xx and male xy versions of the sex chromosome bottom right as well as the mitochondrial genome to scale at bottom left the blue scale to the left of each chromosome pair and the mitochondrial genome shows its length in terms of millions of dna base pairs further information karyotype in humans the total female diploid nuclear genome per cell extends for 6 37 gigabase pairs gbp is 208 23 cm long and weighs 6 51 picograms pg 31 male values are 6 27 gbp 205 00 cm 6 41 pg 31 each dna polymer can contain hundreds of millions of nucleotides such as in chromosome 1 chromosome 1 is the largest human chromosome with approximately 220 million base pairs and would be 85 mm long if straightened 32 in eukaryotes in addition to nuclear dna there is also mitochondrial dna mtdna which encodes certain proteins used by the mitochondria the mtdna is usually relatively small in comparison to the nuclear dna for example the human mitochondrial dna forms closed circular molecules each of which contains 16 569 33 34 dna base pairs 35 with each such molecule normally containing a full set of the mitochondrial genes each human mitochondrion contains on average approximately 5 such mtdna molecules 35 each human cell contains approximately 100 mitochondria giving a total number of mtdna molecules per human cell of approximately 500 35 however the amount of mitochondria per cell also varies by cell type and an egg cell can contain 100 000 mitochondria corresponding to up to 1 500 000 copies of the mitochondrial genome constituting up to 90 of the dna of the cell 36 sense and antisense further information sense molecular biology sense and antisense redirects here for the tv episode see sense and antisense millennium a dna sequence is called a sense sequence if it is the same as that of a messenger rna copy that is translated into protein 37 the sequence on the opposite strand is called the antisense sequence both sense and antisense sequences can exist on different parts of the same strand of dna i e both strands can contain both sense and antisense sequences in both prokaryotes and eukaryotes antisense rna sequences are produced but the functions of these rnas are not entirely clear 38 one proposal is that antisense rnas are involved in regulating gene expression through rna rna base pairing 39 a few dna sequences in prokaryotes and eukaryotes and more in plasmids and viruses blur the distinction between sense and antisense strands by having overlapping genes 40 in these cases some dna sequences do double duty encoding one protein when read along one strand and a second protein when read in the opposite direction along the other strand in bacteria this overlap may be involved in the regulation of gene transcription 41 while in viruses overlapping genes increase the amount of information that can be encoded within the small viral genome 42 supercoiling further information dna supercoil dna can be twisted like a rope in a process called dna supercoiling with dna in its relaxed state a strand usually circles the axis of the double helix once every 10 4 base pairs but if the dna is twisted the strands become more tightly or more loosely wound 43 if the dna is twisted in the direction of the helix this is positive supercoiling and the bases are held more tightly together if they are twisted in the opposite direction this is negative supercoiling and the bases come apart more easily in nature most dna has slight negative supercoiling that is introduced by enzymes called topoisomerases 44 these enzymes are also needed to relieve the twisting stresses introduced into dna strands during processes such as transcription and dna replication 45 alternative dna structures further information molecular structure of nucleic acids a structure for deoxyribose nucleic acid molecular models of dna and dna structure from left to right the structures of a b and z dna dna exists in many possible conformations that include a dna b dna and z dna forms although only b dna and z dna have been directly observed in functional organisms 14 the conformation that dna adopts depends on the hydration level dna sequence the amount and direction of supercoiling chemical modifications of the bases the type and concentration of metal ions and the presence of polyamines in solution 46 the first published reports of a dna x ray diffraction patterns and also b dna used analyses based on patterson functions that provided only a limited amount of structural information for oriented fibers of dna 47 48 an alternative analysis was proposed by wilkins et al in 1953 for the in vivo b dna x ray diffraction scattering patterns of highly hydrated dna fibers in terms of squares of bessel functions 49 in the same journal james watson and francis crick presented their molecular modeling analysis of the dna x ray diffraction patterns to suggest that the structure was a double helix 8 although the b dna form is most common under the conditions found in cells 50 it is not a well defined conformation but a family of related dna conformations 51 that occur at the high hydration levels present in cells their corresponding x ray diffraction and scattering patterns are characteristic of molecular paracrystals with a significant degree of disorder 52 53 compared to b dna the a dna form is a wider right handed spiral with a shallow wide minor groove and a narrower deeper major groove the a form occurs under non physiological conditions in partly dehydrated samples of dna while in the cell it may be produced in hybrid pairings of dna and rna strands and in enzyme dna complexes 54 55 segments of dna where the bases have been chemically modified by methylation may undergo a larger change in conformation and adopt the z form here the strands turn about the helical axis in a left handed spiral the opposite of the more common b form 56 these unusual structures can be recognized by specific z dna binding proteins and may be involved in the regulation of transcription 57 alternative dna chemistry further information hypothetical types of biochemistry for many years exobiologists have proposed the existence of a shadow biosphere a postulated microbial biosphere of earth that uses radically different biochemical and molecular processes than currently known life one of 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 ext...
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