supertwists superhelical supertwist plectonemic underwinding underwound superhelicity plectoneme superhelix lk_ supercoil writhe supercoils supercoiled solenoidal supercoiling toroid intercalating topoisomerases unwound bossi 3093 1997pnas compacting plasmid helical denaturation 26455586 zechiedrich ncomms9440
briefly describe the cellular need for a type of enzyme that can relax supercoils
DNA supercoil - wikipedia DNA supercoil This article needs additional citations for verification . Please help improve this article by adding citations to reliable sources . Unsourced material may be challenged and removed . ( February 2010 ) ( Learn how and when to remove this template message ) Supercoiled structure of circular DNA molecules with low writhe . The helical nature of the DNA duplex is omitted for clarity . Supercoiled structure of linear DNA molecules with constrained ends . The helical nature of the DNA duplex is omitted for clarity . DNA supercoiling refers to the over - or under - winding of a DNA strand , and is an expression of the strain on that strand . Supercoiling is important in a number of biological processes , such as compacting DNA , and by regulating access to the genetic code , DNA supercoiling strongly affects DNA metabolism and possibly gene expression . Additionally , certain enzymes such as topoisomerases are able to change DNA topology to facilitate functions such as DNA replication or transcription . Mathematical expressions are used to describe supercoiling by comparing different coiled states to relaxed B - form DNA . Contents 1 Overview 2 Intercalation - induced supercoiling of DNA 3 Functions 3.1 Genome packaging 3.2 Gene expression 4 Mathematical description 5 Effects on sedimentation coefficient 6 See also 7 References 7.1 General references Overview ( edit ) In a `` relaxed '' double - helical segment of B - DNA , the two strands twist around the helical axis once every 10.4 -- 10.5 base pairs of sequence . Adding or subtracting twists , as some enzymes can do , imposes strain . If a DNA segment under twist strain were closed into a circle by joining its two ends and then allowed to move freely , the circular DNA would contort into a new shape , such as a simple figure - eight . Such a contortion is a supercoil . The noun form `` supercoil '' is often used in the context of DNA topology . Positively supercoiled ( overwound ) DNA is transiently generated during DNA replication and transcription , and , if not promptly relaxed , inhibits ( regulates ) these processes . The simple figure eight is the simplest supercoil , and is the shape a circular DNA assumes to accommodate one too many or one too few helical twists . The two lobes of the figure eight will appear rotated either clockwise or counterclockwise with respect to one another , depending on whether the helix is over - or underwound . For each additional helical twist being accommodated , the lobes will show one more rotation about their axis . As a general rule , the DNA of most organisms is negatively supercoiled . Lobal contortions of a circular DNA , such as the rotation of the figure - eight lobes above , are referred to as writhe . The above example illustrates that twist and writhe are interconvertible . Supercoiling can be represented mathematically by the sum of twist and writhe . The twist is the number of helical turns in the DNA and the writhe is the number of times the double helix crosses over on itself ( these are the supercoils ) . Extra helical twists are positive and lead to positive supercoiling , while subtractive twisting causes negative supercoiling . Many topoisomerase enzymes sense supercoiling and either generate or dissipate it as they change DNA topology . In part because chromosomes may be very large , segments in the middle may act as if their ends are anchored . As a result , they may be unable to distribute excess twist to the rest of the chromosome or to absorb twist to recover from underwinding -- the segments may become supercoiled , in other words . In response to supercoiling , they will assume an amount of writhe , just as if their ends were joined . Supercoiled DNA forms two structures ; a plectoneme or a toroid , or a combination of both . A negatively supercoiled DNA molecule will produce either a one - start left - handed helix , the toroid , or a two - start right - handed helix with terminal loops , the plectoneme . Plectonemes are typically more common in nature , and this is the shape most bacterial plasmids will take . For larger molecules it is common for hybrid structures to form -- a loop on a toroid can extend into a plectoneme . If all the loops on a toroid extend then it becomes a branch point in the plectonemic structure . DNA supercoiling is important for DNA packaging within all cells , and seems to also play a role in gene expression . Intercalation - induced supercoiling of DNA ( edit ) Based on the properties of intercalating molecules i.e. , fluorescing upon binding to DNA and unwinding of DNA base - pairs , recently a single - molecule technique has been introduced to directly visualize individual plectonemes along supercoiled DNA which would further allow to study the interactions of DNA processing proteins with supercoiled DNA . In that study , Sytox Orange ( an intercalating dye ) , has been used to induce supercoiling on surface tethered DNA molecules . Functions ( edit ) Genome packaging ( edit ) DNA supercoiling is important for DNA packaging within all cells . Because the length of DNA can be thousands of times that of a cell , packaging this genetic material into the cell or nucleus ( in eukaryotes ) is a difficult feat . Supercoiling of DNA reduces the space and allows for DNA to be packaged . In prokaryotes , plectonemic supercoils are predominant , because of the circular chromosome and relatively small amount of genetic material . In eukaryotes , DNA supercoiling exists on many levels of both plectonemic and solenoidal supercoils , with the solenoidal supercoiling proving most effective in compacting the DNA . Solenoidal supercoiling is achieved with histones to form a 10 nm fiber . This fiber is further coiled into a 30 nm fiber , and further coiled upon itself numerous times more . DNA packaging is greatly increased during nuclear division events such as mitosis or meiosis , where DNA must be compacted and segregated to daughter cells . Condensins and cohesins are structural maintenance of chromosome ( SMC ) proteins that aid in the condensation of sister chromatids and the linkage of the centromere in sister chromatids . These SMC proteins induce positive supercoils . Supercoiling is also required for DNA / RNA synthesis . Because DNA must be unwound for DNA / RNA polymerase action , supercoils will result . The region ahead of the polymerase complex will be unwound ; this stress is compensated with positive supercoils ahead of the complex . Behind the complex , DNA is rewound and there will be compensatory negative supercoils . Topoisomerases such as DNA gyrase ( Type II Topoisomerase ) play a role in relieving some of the stress during DNA / RNA synthesis . Gene expression ( edit ) Specialized proteins can unzip small segments of the DNA molecule when it is replicated or transcribed into RNA . But work published in 2015 illustrates how DNA opens on its own . Simply twisting DNA can expose internal bases to the outside , without the aid of any proteins . Also , transcription itself contorts DNA in living human cells , tightening some parts of the coil and loosening it in others . That stress triggers changes in shape , most notably opening up the helix to be read . Unfortunately , these interactions are very difficult to study because biological molecules morph shapes so easily . In 2008 it was noted that transcription twists DNA , leaving a trail of undercoiled ( or negatively supercoiled ) DNA in its wake . Moreover , they discovered that the DNA sequence itself effects how the molecule responds to supercoiling . For example , the researchers identified a specific sequence of DNA that regulates transcription speed ; as the amount of supercoil rises and falls , it slows or speeds the pace at which molecular machinery reads DNA . It is hypothesized that these structural changes might trigger stress elsewhere along its length , which in turn might provide trigger points for replication or gene expression . This implies that it is a very dynamic process in which both DNA and proteins each influences how the other acts and reacts . Mathematical description ( edit ) Drawing showing the difference between a circular DNA chromosome ( a plasmid ) with a secondary helical twist only , and one containing an additional tertiary superhelical twist superimposed on the secondary helical winding . In nature , circular DNA is always isolated as a higher - order helix - upon - a-helix , known as a superhelix . In discussions of this subject , the Watson - Crick twist is referred to as a `` secondary '' winding , and the superhelices as a `` tertiary '' winding . The sketch at right indicates a `` relaxed '' , or `` open circular '' Watson - Crick double - helix , and , next to it , a right - handed superhelix . The `` relaxed '' structure on the left is not found unless the chromosome is nicked ; the superhelix is the form usually found in nature . For purposes of mathematical computations , a right - handed superhelix is defined as having a `` negative '' number of superhelical turns , and a left - handed superhelix is defined as having a `` positive '' number of superhelical turns . In the drawing ( shown at the right ) , both the secondary ( i.e. , `` Watson - Crick '' ) winding and the tertiary ( i.e. , `` superhelical '' ) winding are right - handed , hence the supertwists are negative ( - 3 in this example ) . The superhelicity is presumed to be a result of underwinding , meaning that there is a deficiency in the number of secondary Watson - Crick twists . Such a chromosome will be strained , just as a macroscopic metal spring is strained when it is either overwound or unwound . In DNA which is thusly strained , supertwists will appear . DNA supercoiling can be described numerically by changes in the linking number Lk . The linking number is the most descriptive property of supercoiled DNA . Lk , the number of turns in the relaxed ( B type ) DNA plasmid / molecule , is determined by dividing the total base pairs of the molecule by the relaxed bp / turn which , depending on reference is 10.4 ; 10.5 ; 10.6 . L k o = b p / 10.4 ( \ displaystyle Lk_ ( o ) = bp / 10.4 ) Lk is merely the number of crosses a single strand makes across the other . L , known as the `` linking number '' , is the number of Watson - Crick twists found in a circular chromosome in a ( usually imaginary ) planar projection . This number is physically `` locked in '' at the moment of covalent closure of the chromosome , and can not be altered without strand breakage . The topology of the DNA is described by the equation below in which the linking number is equivalent to the sum of TW , which is the number of twists or turns of the double helix , and Wr which is the number of coils or ' writhes ' . If there is a closed DNA molecule , the sum of Tw and Wr , or the linking number , does not change . However , there may be complementary changes in TW and Wr without changing their sum . L k = T w + W r ( \ displaystyle Lk = Tw + Wr ) Tw , called `` twist '' , refers to the number of Watson - Crick twists in the chromosome when it is not constrained to lie in a plane . We have already seen that native DNA is usually found to be superhelical . If one goes around the superhelically twisted chromosome , counting secondary Watson - Crick twists , that number will be different from the number counted when the chromosome is constrained to lie flat . In general , the number of secondary twists in the native , supertwisted chromosome is expected to be the `` normal '' Watson - Crick winding number , meaning a single 10 - base - pair helical twist for every 34 Å of DNA length . Wr , called `` writhe '' , is the number of superhelical twists . Since biological circular DNA is usually underwound , L will generally be less than Tw , which means that Wr will typically be negative . If DNA is underwound , it will be under strain , exactly as a metal spring is strained when forcefully unwound , and that the appearance of supertwists will allow the chromosome to relieve its strain by taking on negative supertwists , which correct the secondary underwinding in accordance with the topology equation above . The topology equation shows that there is a one - to - one relationship between changes in Tw and Wr . For example , if a secondary `` Watson - Crick '' twist is removed , then a right - handed supertwist must have been removed simultaneously ( or , if the chromosome is relaxed , with no supertwists , then a left - handed supertwist must be added ) . The change in the linking number , ΔLk , is the actual number of turns in the plasmid / molecule , Lk , minus the number of turns in the relaxed plasmid / molecule Lk . Δ L k = L k − L k o ( \ displaystyle \ Delta ( Lk = Lk - Lk_ ( o ) ) ) If the DNA is negatively supercoiled ΔLk < 0 . The negative supercoiling implies that the DNA is underwound . A standard expression independent of the molecule size is the `` specific linking difference '' or `` superhelical density '' denoted σ , that represents the number of turns added or removed relative to the total number of turns in the relaxed molecule / plasmid , indicating the level of supercoiling . σ = Δ L k / L k o ( \ displaystyle \ sigma = \ Delta ( Lk / Lk_ ( o ) ) ) The Gibbs free energy associated with the coiling is given by the equation below Δ G / N = 10 R T σ 2 ( \ displaystyle ( \ Delta G / N = 10RT \ sigma ^ ( 2 ) ) ) The difference in Gibbs free energy between the supercoiled circular DNA and uncoiled circular DNA with N > 2000 bp is approximated by : Δ G / N = 700 K c a l / b p ∗ ( Δ L k / N ) ( \ displaystyle ( \ Delta G / N = 700Kcal / bp * ( \ Delta Lk / N ) ) ) or , 16 cal / bp . Since the linking number L of supercoiled DNA is the number of times the two strands are intertwined ( and both strands remain covalently intact ) , L can not change . The reference state ( or parameter ) L of a circular DNA duplex is its relaxed state . In this state , its writhe W = 0 . Since L = T + W , in a relaxed state T = L. Thus , if we have a 400 bp relaxed circular DNA duplex , L ~ 40 ( assuming ~ 10 bp per turn in B - DNA ) . Then T ~ 40 . Positively supercoiling : T = 0 , W = 0 , then L = 0 T = + 3 , W = 0 , then L = + 3 T = + 2 , W = + 1 , then L = + 3 Negatively supercoiling : T = 0 , W = 0 , then L = 0 T = - 3 , W = 0 , then L = - 3 T = - 2 , W = - 1 , then L = - 3 Negative supercoils favor local unwinding of the DNA , allowing processes such as transcription , DNA replication , and recombination . Negative supercoiling is also thought to favour the transition between B - DNA and Z - DNA , and moderate the interactions of DNA binding proteins involved in gene regulation . Effects on sedimentation coefficient ( edit ) Figure showing the various conformational changes which are observed in circular DNA at different pH . At a pH of about 12 ( alkaline ) , there is a dip in the sedimentation coefficient , followed by a relentless increase up to a pH of about 13 , at which pH the structure converts into the mysterious `` Form IV '' . The topological properties of circular DNA are complex . In standard texts , these properties are invariably explained in terms of a helical model for DNA , but in 2008 it was noted that each topoisomer , negative or positive , adopts a unique and surprisingly wide distribution of three - dimensional conformations . When the sedimentation coefficient , s , of circular DNA is ascertained over a large range of pH , the following curves are seen . Three curves are shown here , representing three species of DNA . From top - to - bottom they are : `` Form IV '' ( green ) , `` Form I '' ( blue ) and `` Form II '' ( red ) . `` Form I '' ( blue curve ) is the traditional nomenclature used for the native form of duplex circular DNA , as recovered from viruses and intracellular plasmids . Form I is covalently closed , and any plectonemic winding which may be present is therefore locked in . If one or more nicks are introduced to Form I , free rotation of one strand with respect to the other becomes possible , and Form II ( red curve ) is seen . Form IV ( green curve ) is the product of alkali denaturation of Form I. Its structure is unknown , except that it is persistently duplex , and extremely dense . Between pH 7 and pH 11.5 , the sedimentation coefficient s , for Form I , is constant . Then it dips , and at a pH just below 12 , reaches a minimum . With further increases in pH , s then returns to its former value . It does n't stop there , however , but continues to increase relentlessly . By pH 13 , the value of s has risen to nearly 50 , two to three times its value at pH 7 , indicating an extremely compact structure . If the pH is then lowered , the s value is not restored . Instead , one sees the upper , green curve . The DNA , now in the state known as Form IV , remains extremely dense , even if the pH is restored to the original physiologic range . As stated previously , the structure of Form IV is almost entirely unknown , and there is no currently accepted explanation for its extraordinary density . About all that is known about the tertiary structure is that it is duplex , but has no hydrogen bonding between bases . These behaviors of Forms I and IV are considered to be due to the peculiar properties of duplex DNA which has been covalently closed into a double - stranded circle . If the covalent integrity is disrupted by even a single nick in one of the strands , all such topological behavior ceases , and one sees the lower Form II curve ( Δ ) . For Form II , alterations in pH have very little effect on s . Its physical properties are , in general , identical to those of linear DNA . At pH 13 , the strands of Form II simply separate , just as the strands of linear DNA do . The separated single strands have slightly different s values , but display no significant changes in s with further increases in pH . A complete explanation for these data is beyond the scope of this article . In brief , the alterations in s come about because of changes in the superhelicity of circular DNA . These changes in superhelicity are schematically illustrated by four little drawings which have been strategically superimposed upon the figure above . Briefly , the alterations of s seen in the pH titration curve above are widely thought to be due to changes in the superhelical winding of DNA under conditions of increasing pH . Up to pH 11.5 , the purported `` underwinding '' produces a right - handed ( `` negative '' ) supertwist . But as the pH increases , and the secondary helical structure begins to denature and unwind , the chromosome ( if we may speak anthropomorphically ) no longer `` wants '' to have the full Watson - Crick winding , but rather `` wants '' , increasingly , to be `` underwound '' . Since there is less and less strain to be relieved by superhelical winding , the superhelices therefore progressively disappear as the pH increases . At a pH just below 12 , all incentive for superhelicity has expired , and the chromosome will appear as a relaxed , open circle . At higher pH still , the chromosome , which is now denaturing in earnest , tends to unwind entirely , which it can not do so ( because L is covalently locked in ) . Under these conditions , what was once treated as `` underwinding '' has actually now become `` overwinding '' . Once again there is strain , and once again it is ( in part at least ) relieved by superhelicity , but this time in the opposite direction ( i.e. , left - handed or `` positive '' ) . Each left - handed tertiary supertwist removes a single , now undesirable right - handed Watson - Crick secondary twist . The titration ends at pH 13 , where Form IV appears . See also ( edit ) Mechanical properties of DNA Ribbon theory References ( edit ) Jump up ^ Bar , A. ; Mukamel , D. ; Kabakçoǧlu , A. ( 2011 ) . `` Denaturation of circular DNA : Supercoil mechanism '' . Physical Review E. 84 ( 4 ) . arXiv : 1108.5444 . Bibcode : 2011PhRvE ... 84d1935B . doi : 10.1103 / physreve. 84.041935 . Jump up ^ Champoux J ( 2001 ) . `` DNA topoisomerases : structure , function , and mechanism '' . Annu Rev Biochem. 70 : 369 -- 413 . doi : 10.1146 / annurev. biochem. 70.1. 369 . PMID 11395412 . ^ Jump up to : Singer , Emily ( 5 January 2016 ) . `` How Strange Twists in DNA Orchestrate Life '' . Quanta Magazine . Retrieved 2016 - 01 - 07 . ^ Jump up to : Irobalieva , Rossitza N. ; Zechiedrich , Lynn ; et al. ( 12 October 2015 ) . `` Structural diversity of supercoiled DNA '' . Nature Communications . 6 ( 8440 ) . Bibcode : 2015NatCo ... 6E8440I . doi : 10.1038 / ncomms9440 . PMC 4608029 . PMID 26455586 . Retrieved 2016 - 01 - 07 . Jump up ^ Ganji , Mahipal ; Kim , Sung Hyun ; van der Torre , Jaco ; Abbondanzieri , Elio ; Dekker , Cees ( 2016 - 07 - 13 ) . `` Intercalation - Based Single - Molecule Fluorescence Assay To Study DNA Supercoil Dynamics '' . Nano Letters. 16 ( 7 ) : 4699 -- 4707 . Bibcode : 2016NanoL ... 16.4699 G . doi : 10.1021 / acs. nanolett. 6b02213 . ISSN 1530 - 6984 . Jump up ^ Albert AC , Spirito F , Figueroa - Bossi N , Bossi L , Rahmouni AR ( 1996 ) . `` Hyper - negative template DNA supercoiling during transcription of the tetracycline - resistance gene in topA mutants is largely constrained in vivo '' . Nucleic Acids Res. 24 ( 15 ) : 3093 -- 3099 . doi : 10.1093 / nar / 24.15. 3093 . PMC 146055 . PMID 8760899 . Jump up ^ Shimada , Jiro ; Yamakawa , Hiromi ( 1984 ) , `` Ring - closure probabilities for twisted wormlike chains . Application to DNA '' , Macromolecules , ACS Publications , 17 ( 4 ) : 689 -- 698 , Bibcode : 1984MaMol ... 17 ... 689S , doi : 10.1021 / ma00134a028 Jump up ^ Essevaz - Roulet , Baptiste and Bockelmann , Ulrich and Heslot , Francois ( 1997 ) , `` Mechanical separation of the complementary strands of DNA '' , Proceedings of the National Academy of Sciences , National Acad Sciences , 94 ( 22 ) : 11935 -- 11940 , Bibcode : 1997PNAS ... 9411935E , doi : 10.1073 / pnas. 94.22. 11935 , PMC 23661 , PMID 9342340 CS1 maint : Multiple names : authors list ( link ) Jump up ^ Lavery , Richard and Lebrun , Anne and Allemand , Jean - François and Bensimon , David and Croquette , Vincent ( 2002 ) , `` Structure and mechanics of single biomolecules : experiment and simulation '' , Journal of Physics : Condensed Matter , IOP Publishing , 14 ( 14 ) : R383 -- R414 , Bibcode : 2002JPCM ... 14R. 383L , doi : 10.1088 / 0953 - 8984 / 14 / 14 / 202 CS1 maint : Multiple names : authors list ( link ) Jump up ^ Moroz , J David ; Nelson , Philip ( 1997 ) , `` Torsional directed walks , entropic elasticity , and DNA twist stiffness '' , Proceedings of the National Academy of Sciences , National Acad Sciences , 94 ( 26 ) : 14418 -- 14422 , arXiv : cond - mat / 9708158 , Bibcode : 1997PNAS ... 9414418M , doi : 10.1073 / pnas. 94.26. 14418 Jump up ^ Vologodskii AV , Lukashin AV , Anshelevich VV , et al. ( 1979 ) . `` Fluctuations in superhelical DNA '' . Nucleic Acids Res. 6 ( 3 ) : 967 -- 982 . doi : 10.1093 / nar / 6.3. 967 . PMC 327745 . PMID 155809 . Jump up ^ H.S. Chawla ( 2002 ) . Introduction to Plant Biotechnology . Science Publishers . ISBN 1 - 57808 - 228 - 5 . General references ( edit ) Bloomfield , Victor A. ; Crothers , Donald M. ; Tinoco , Jr. , Ignacio ( 2000 ) . Nucleic acids : structures , properties , and functions . Sausalito , California : University Science Books . pp. 446 -- 453 . ISBN 0935702490 . Retrieved from `` https://en.wikipedia.org/w/index.php?title=DNA_supercoil&oldid=846521989 '' Categories : DNA Helices Molecular biology Hidden categories : CS1 maint : Multiple names : authors list Articles needing additional references from February 2010 All articles needing additional references Talk Contents About Wikipedia Català Čeština Dansk Deutsch Español Français Galego Italiano ქართული Lietuvių 日本 語 Português Русский Slovenščina Српски / srpski Srpskohrvatski / српскохрватски Türkçe Українська 中文 11 more Edit links This page was last edited on 19 June 2018 , at 08 : 28 ( UTC ) . Text is available under the Creative Commons Attribution - ShareAlike License ; additional terms may apply . By using this site , you agree to the Terms of Use and Privacy Policy . Wikipedia ® is a registered trademark of the Wikimedia Foundation , Inc. , a non-profit organization . About Wikipedia