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helix has an exposed 5 phosphate on one strand and an exposed 3 hydroxyl group oh on the other dna is a long polymer made from repeating units called nucleotides 6 7 dna does not usually exist as a single strand but instead as a pair of strands that are held tightly together 8 9 these two long strands coil around each other in the shape of a double helix the nucleotide contains both a segment of the backbone of the molecule which holds the chain together and a nucleobase which interacts with the other dna strand in the helix a nucleobase linked to a sugar is called a nucleoside and a base linked to a sugar and to one or more phosphate groups is called a nucleotide a biopolymer comprising multiple linked nucleotides as in dna is called a polynucleotide 10 the structure of dna is dynamic along its length being capable of coiling into tight loops and other shapes 11 in all species it is composed of two helical chains bound to each other by hydrogen bonds the two chains are coiled around the same axis but not directly opposite one to the other and have the same pitch of 34 ångströms 3 4 nm ignoring the identities of the bases the line group is d 1 q where q stands for the turn per base pair which is around a tenth of a full turn in the usual form b dna the twist is right handed like a normal screw that advances when turned clockwise the pair of chains have a radius of 10 å 1 0 nm 8 according to another study when measured in a different solution the dna chain measured 22 26 å 2 2 2 6 nm wide and one nucleotide unit measured 3 3 å 0 33 nm long 12 the buoyant density of most dna is 1 7g cm 3 13 the backbone of the dna strand is made from alternating phosphate and sugar groups 14 the sugar in dna is 2 deoxyribose which is a pentose five carbon sugar the sugars are joined by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings these are known as the 3 end three prime end and 5 end five prime end carbons the prime symbol being used to distinguish these carbon atoms from those of the base to which the deoxyribose forms a glycosidic bond 9 therefore any dna strand normally has one end at which there is a phosphate group attached to the 5 carbon of a ribose the 5 phosphoryl and another end at which there is a free hydroxyl group attached to the 3 carbon of a ribose the 3 hydroxyl the orientation of the 3 and 5 carbons along the sugar phosphate backbone confers directionality sometimes called polarity to each dna strand in a nucleic acid double helix the direction of the nucleotides in one strand is opposite to their direction in the other strand the strands are antiparallel the asymmetric ends of dna strands are said to have a directionality of five prime end 5 and three prime end 3 with the 5 end having a terminal phosphate group and the 3 end a terminal hydroxyl group one major difference between dna and rna is the sugar with the 2 deoxyribose in dna being replaced by the related pentose sugar ribose in rna 9 a section of dna the bases lie horizontally between the two spiraling strands 15 animated version the dna double helix is stabilized primarily by two forces hydrogen bonds between nucleotides and base stacking interactions among aromatic nucleobases 16 the four bases found in dna are adenine a cytosine c guanine g and thymine t these four bases are attached to the sugar phosphate to form the complete nucleotide as shown for adenosine monophosphate adenine pairs with thymine and guanine pairs with cytosine forming a t and g c base pairs 17 18 nucleobase classification the nucleobases are classified into two types the purines a and g which are fused five and six membered heterocyclic compounds and the pyrimidines the six membered rings c and t 9 a fifth pyrimidine nucleobase uracil u usually takes the place of thymine in rna and differs from thymine by lacking a methyl group on its ring in addition to rna and dna many artificial nucleic acid analogues have been created to study the properties of nucleic acids or for use in biotechnology 19 non canonical bases modified bases occur in dna the first of these recognized was 5 methylcytosine which was found in the genome of mycobacterium tuberculosis in 1925 20 the reason for the presence of these noncanonical bases in bacterial viruses bacteriophages is to avoid the restriction enzymes present in bacteria this enzyme system acts at least in part as a molecular immune system protecting bacteria from infection by viruses 21 modifications of the bases cytosine and adenine the more common and modified dna bases play vital roles in the epigenetic control of gene expression in plants and animals 22 a number of noncanonical bases are known to occur in dna 23 most of these are modifications of the canonical bases plus uracil modified adenine n6 carbamoyl methyladenine n6 methyadenine modified guanine 7 deazaguanine 7 methylguanine modified cytosine n4 methylcytosine 5 carboxylcytosine 5 formylcytosine 5 glycosylhydroxymethylcytosine 5 hydroxycytosine 5 methylcytosine modified thymidine α glutamythymidine α putrescinylthymine uracil and modifications base j uracil 5 dihydroxypentauracil 5 hydroxymethyldeoxyuracil others deoxyarchaeosine 2 6 diaminopurine 2 aminoadenine grooves dna major and minor grooves the latter is a binding site for the hoechst stain dye 33258 twin helical strands form the dna backbone another double helix may be found tracing the spaces or grooves between the strands these voids are adjacent to 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 c...
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