The molecule is still negatively supercoiled and shows right-handed interwinding. Negative supercoiling has an important biological function of facilitating local- and global-strand separation of DNA molecules such as these occurring during transcription and replication, respectively (79). The Wr values are negative for negatively supercoiled DNA and positive for positively supercoiled molecules. Of course, there is no free lunch even for a bacteria, and the energetic cost of the torsional constraint has to be introduced by the ATP hydrolysis-driven action of DNA gyrase (11). Rybenkov VV, Ullsperger C, Vologodskii AV, Cozzarelli NR. However, it was very intriguing how DNA topoisomerases, that can only sense local information, may get hints whether performing a DNADNA passage in a given place will rather unknot the DNA than lead to DNA knotting. In contrast to integer value of Lk of real DNA topoisomers, the value of Lk0 does not need to be an integer as it does not correspond to a realisable topoisomer but simply describes the reference point from which the torsional stress starts to arise in the considered DNA molecules. In non-replicated portions, the stress causes formation of interwound positive superhelices, in which the opposing segments wind around each other in a left-handed sense. From this point on, Topo IV-mediated passages were easily occurring in the folded braid and were reducing the interlinking of the braided duplexes. A sign inversion mechanism for enzymatic supercoiling of DNA. Therefore, negative supercoiling of DNA is thought to facilitate the step. White SW, Appelt K, Wilson KS, Tanaka I. The twist units are 360 rotations. In a "relaxed" double-helical segment of DNA, the two strands twist around the helical axis once every 10.4 to 10.5 base . Negative supercoiling is naturally prevalent because negative supercoiling prepares the molecule for processes that require separation of the DNA strands. Katritch V, Olson WK, Vologodskii A, Dubochet J, Stasiak A. Bauer WR. Neuman KC, Charvin G, Bensimon D, Croquette V. Mechanisms of chiral discrimination by topoisomerase IV. Therefore, as soon as the distance between the two approaching forks becomes smaller than few hundreds base pairs, it becomes very difficult for DNA gyrase or any other topoisomerase, to gain the access to the remaining unreplicated portion of the DNA and to entirely remove the linking of parental strands before their complete replication (Figure 4). As a consequence, in case of plasmid DNA molecules, for example, one observes formation of right-handed DNA catenanes, where the freshly replicated DNA molecules are wound around each other up to 40 times (21). Marians KJ, Ikeda JE, Schlagman S, Hurwitz J. The positive sign of Lk indicates that the two strands of the molecule wind around each other in a right-handed sense as it is the case of native B-DNA structure. *To whom correspondence should be addressed. The level of supercoiling also impacts transcriptional activity (2-5). Such covalently closed DNA molecules would be torsionally relaxed, and, for plasmid size molecules, would adopt the shape of unconstrained freely fluctuating rings, that may adsorb without any intramolecular crossings when deposited on a surface for atomic force microscopy (AFM) imaging (Figure 1A). Thermal motion by itself cannot pass two DNA segments through each other. However, as the strand separation in negatively supercoiled DNA molecules progresses beyond the point of DNA relaxation (Figure 2), it induces positive torsional stress. Consequently, a real passage would be energetically not favourable as opposed to an imaginary topo II-mediated passage with unrealistic property of maintaining the Lk constant (Figure 3A). If that molecule were maintained in a planar configuration by ionic interaction with a charged surface, for example, its Tw would also change to 7, while Wr would remain unchanged. The .gov means its official. In contrast, positive supercoiling occurs downstream of the transcription complex . In the case of covalently closed circular DNA, the two strands are topologically linked, and the action of DNA topoisomerases is required to reduce the linking number to exactly zero, in order to complete the segregation of newly replicated DNA molecules. (F) The concept of twist. Catenation and knotting of duplex DNA by type 1 topoisomerases: a mechanistic parallel with type 2 topoisomerases. Brown PO, Cozzarelli NR. Identification of a potent decatenating enzyme from. In vivo and in vitro experiments provided the evidence that the torsional stress is released by the activity of DNA gyrase and Topo IV acting on positive superhelices formed in the unreplicated portion of the DNA (67). Also Stone et al. The Tw0 value is related to the native DNA helical repeat (h) by the formula Tw0 = N/h, where N is the number of base pairs in the molecule. Burnier Y, Dorier J, Stasiak A. DNA supercoiling inhibits DNA knotting. In part because chromosomes may be very large, segments in the middle may act as if their ends are anchored. We show here that negative supercoiling transmits. Phys. Positive supercoiling = the coiling of DNA helix (B-DNA) on itself during intesified coiling of the two DNA stands in right handed direction Phys. Intriguingly, two different simulation studies investigating the effect of DNA supercoiling on DNA knotting arrived at the opposite conclusions. Positive crossings score as +1 and negative ones as 1, and are defined as presented in Figure 2. Preferential relaxation of positively supercoiled DNA by. Therefore, that torsional stress would eventually stop the progression of the replication forks if it were not continuously relieved by the action DNA topoisomerases. DNA molecules that are supercoiled might be in addition knotted or catenated or even knotted and catenated. None declared. In 2002 Vologodskii et al. In addition, even if the realistic passage has happened, then afterwards DNA gyrase would act to re-establish the previous level of torsional stress, which would push the molecule to the state with the Lk oscillating 8.41. The effect of supercoiling on unknotting was also investigated in vitro by comparing unknotting of supercoiled and non-supercoiled DNA molecules by Topo IV (39), i.e. Protection of partially replicated portions of DNA from action of DNA gyrase would make a good sense since it would importantly improve the efficiency of cell energetics. Depending on that angle, the enzyme may preferentially interact with DNA segments that wind around each other in left- or right-handed way (49,50). Sugino A, Cozzarelli NR. Under such conditions, supercoiling progressively replaces catenation to maintain a steep gradient creating a pressure pushing towards complete decatenation (21,80). Indeed, simulation studies using polygons confined to a cubic lattice confirmed that preferential action on hooked juxtapositions can decrease the level of knotting by 50 times as compared to random passages (57). Peck LJ, Wang JC. If that rotation is clockwise, the crossing is negative and it is positive otherwise. 1h) for supercoiled DNA (~0.4 kb s 1; for both positive and negative supercoiling) was almost a factor three lower than that of torsionally relaxed DNA (~1.1 kb s . However, it is questionable whether bending deformations in vivo reach the level at which kinking occurs (2,3). Drlica K, Rouviere-Yaniv J. Histonelike proteins of bacteria. In addition, we consider that DNA gyrase and Topo I compensate for the possible decrease or increase of DNA torsional stress due to knot formation by re-establishing the initial level of torsional stress typical for native DNA supercoiling. Analysis of the eukaryotic topoisomerase II DNA gate: a single-molecule FRET and structural perspective. Topological information embodied in local juxtaposition geometry provides a statistical mechanical basis for unknotting by type-2 DNA topoisomerases. This folding leads to the apparition of left-handed DNADNA juxtapositions that are very good substrates for Topo IV-mediated passages that lead to decrease of DNA catenation. Equilibrium distributions of topological states in circular DNA: interplay of supercoiling and knotting. Bauer WR, Crick FH, White JH. To explain the concept of knotting equilibrium, let us first consider an imaginary situation, where torsionally relaxed, highly diluted circular DNA molecules of a given size undergo thermal fluctuations during which ideal type II DNA topoisomerases permit intersegmental passages whenever two DNA segments collide with each other. Strick TR, Allemand JF, Bensimon D, Bensimon A, Croquette V. The elasticity of a single supercoiled DNA molecule. The levels of supercoiling produced in this process are prodigious, amounting to a positive and a negative . Also, one interesting question is why DNA gyrase uses ATP to relax positive supercoils that arise during ongoing DNA replication. (C) Standard representation of freshly replicated molecules forming multiply interlinked DNA catenanes. A likely explanation of this behaviour is that the presence of simple knots in non-supercoiled DNA molecules does not produce a sufficient energy gradient that could lead to unknotting, and therefore, this gradient needs to be enhanced by DNA supercoiling. The double-stranded region that passes through the cut may belong to the same or to another DNA molecule. Dubochet J, Bednar J, Furrer P, Stasiak AZ, Stasiak A, Bolshoy AA. Topo I may also have other functions related to its activity on nicked DNA. In the absence of completely free rotation, RNA polymerase tracking down the DNA duplex will produce positive DNA supercoils ahead of the transcription complex and negative supercoils in its wake. Moreover, DNA supercoiling can affect transcription in chromatin context in eukaryotes. Twist (T) A real number (the "apparent" linkage number) Writhe (W) A real number ("supercoils" in the DNA structure) Consider closed circular DNA: Linking number is an integer value. In the case shown in Figure 2D the Wr value has increased by 0.7 (from 0.7 to 0) when negatively supercoiled DNA got torsionally relaxed as a result of strand separation extending over a region of 10 bp, as would be the case if an individual RNA polymerase started a transcription. Adamcik J, Valle F, Witz G, Rechendorff K, Dietler G. The promotion of secondary structures in single-stranded DNA by drugs that bind to duplex DNA: an atomic force microscopy study. (69) gyrase can act very efficiently on linear nicked DNA and such enzymatic reaction could go practically forever using all available ATP. These proteins were not present in the in vitro experiments discussed above (28). This phenomenon is due to the fact that in the non-replicated portion, the DNA is folded back on itself, which changes the topological orientation of segments wrapping. However, a closer look at the presented data clearly reveals that, while complex DNA knots seemed to be equally quickly transformed into simpler knots by Topo IV irrespectively whether they were supercoiled or not, the unknotting of less complex knots, as trefoil knots, was clearly stimulated by DNA supercoiling, while trefoil knots were accumulating when Topo IV was acting on a mixture of complex DNA knots that were not supercoiled [see Figure 7 in ref. Bethesda, MD 20894, Web Policies sharing sensitive information, make sure youre on a federal It should be clear that the structure of catenanes with high interlinking number is analogous to that described by Stone et al. Morrison A, Cozzarelli NR. Supercoiling provides the necessary pressure leading to unlinking. Therefore, some mechanisms had to evolve to protect cells from spending their ATP on non-productive DNA rotations in partially replicated portions of DNA molecules as even if individual gyrase molecules show a relatively low ATPase rate of 1/s (70), there are 5001000 gyrase molecules per cell (71). An advancing RNA polymerase, for example, generates positive supercoiling downstream and negative supercoiling upstream (1). An additional approach to study positive and negative DNA supercoiling uses a refined two-dimensional (2D) . One of the consequences of this relationship is that, when a given covalently closed DNA molecule undergoes continuous deformation, its Lk remains constant while changes of Tw and Wr are coupled in such a way that their sum is constant and equal to Lk (Figure 2). This is most likely the reason why right-handed interwinding of freshly replicated regions is relatively stable (68). The free energy gradient provided by DNA supercoiling helps to guide DNA topoisomerases towards efficient unknotting, but this is not sufficient to explain the complexity of the interplay between DNA supercoiling, knotting and catenation. In fact, single molecule studies using braided DNA with increasing extent of braiding, established that right-handed braids were essentially immune to Topo IV action until the point where the braid folded on itself forming left-handed super braid (45,46). Stone MD, Bryant Z, Crisona NJ, Smith SB, Vologodskii A, Bustamante C, Cozzarelli NR. The light blue arrow indicates the energy difference between unknotted and knotted DNA molecules with the same Lke. Interestingly, the preferential action of type II DNA topoisomerases on hooked juxtapositions was also proposed as the mechanism that explained the seminal experiment by Rybenkov et al. The https:// ensures that you are connecting to the Energy coupling in type II topoisomerases: why do they hydrolyze ATP? The axial lines of two or more DNA molecules may also be topologically entangled (i.e. A very similar mechanism can operate during Topo III-mediated diminution of the catenation level or even complete decatenation of replication intermediates where the unfinished or freshly replicated DNA molecules are not yet converted to covalently closed circular DNA molecules and have short single-stranded regions or nicks (33,34). McClendon AK, Rodriguez AC, Osheroff N. Human topoisomerase IIalpha rapidly relaxes positively supercoiled DNA: implications for enzyme action ahead of replication forks. The question arose then what structural difference could exist between DNADNA juxtapositions at these two different types of crossings in freely fluctuating DNA forming 52L knots? According to that model, the DNA topoisomerase was placing itself in the bend in such a way that the T segment could only be transferred if it approached the G region from the inside of the bend. Hiasa H, DiGate RJ, Marians KJ. For right-handed DNA the Tw is positive. Conformational fluctuations of DNA helix. A kinetic proofreading mechanism for disentanglement of DNA by topoisomerases. supercoiling / positive supercoiling; negative supercoiling; supercoiled Coiled tertiary structure that forms when strain is placed on a DNA helix by overwinding or underwinding of the helix. Flammini A, Maritan A, Stasiak A. Simulations of action of DNA topoisomerases to investigate boundaries and shapes of spaces of knots. the enzyme that is believed to be responsible for DNA unknotting and decatenation of DNA in E. coli. The difference between the two types of supercoiling lies in the way the helix turns. However, if intersegmental passages are permitted without any restriction regarding the topological state of the molecules, the simulated supercoiled DNA molecules quickly relax. This mechanism requires the coordinated opening and closing of three protein interfaces, so-called gates, to ensure the directionality of strand . Bates AD, Maxwell A. DNA knots, supercoiling and the geometric chirality. DNA supercoiling is energetically costly, and the energy for it is provided by the ATPase activity of DNA gyrase (11,26). Fierro-Fernandez M, Hernandez P, Krimer DB, Stasiak A, Schvartzman JB. Since DNA topoisomerases are relatively small compared to overall dimensions of plasmid or chromosomal DNA, they can only distinguish between some local features that are characteristic for unperturbed negatively supercoiled DNA and these that appear in DNA molecules that are knotted and catenated. The twist value is lower than in the torsionally relaxed DNA shown in (A). However, for larger torsional deformations, there is an interval where a torque acting in the direction that unwinds the DNA helix leads to the separation of the DNA strands, while a similar torque, but acting in the direction that winds up the DNA helix just stabilizes the DNA helix (5,6). Overwinding (positive supercoiling) of the DNA occurs transiently during replication and transcription. In such a case also these knots may be efficiently unknotted by Topo IV action while regular DNADNA juxtapositions due to negative supercoiling would not serve as substrates of Topo IV. it does not change with the direction of viewing and is independent of any continuous deformation of covalently closed DNA molecules. However, this causes no torsional stress as this twist is realized over a shorter region of pairing between the DNA strands, which re-establishes there the helicity of 10 bp/turn, while the open region is stabilized by the interaction with the hybridized RNA. However, these assumptions are needed to evaluate the importance of energetic considerations in the study of the steady-state knotting equilibrium in the presence of homeostatic mechanisms that maintain a quasi-constant level of DNA torsional stress in supercoiled DNA. We also discussed how DNA supercoiling can change the structure of knotted and catenated DNA molecules so that Topo IV could specifically unknot and decatenate supercoiled DNA molecules without inducing relaxation of negatively-supercoiled DNA molecules. These results were puzzling since, even if DNA topoisomerases could specifically recognize hooked juxtapositions resulting from tight knotting of 52 knot, there are possibilities of forming five such juxtapositions and only passages occurring at two of them could lead to a direct conversion of the 52 knot into an unknot (61). Such a metabolic short-circuit would exhaust the cellular pool of ATP, and is in reality avoided trough molecular mechanisms that evolved to ensure that bacterial type I topoisomerases are only activated by an excessive torsional stress of the DNA or by the appearance of atypical DNA structures (27). As shown by Gore et al. The second geometric descriptor, the Wr, is a measure of the winding of the axial trajectory of the DNA molecule around itself. Gyrase supercoils DNA by a mechanism called sign inversion, whereby a positive supercoil is directly inverted to a negative one by passing a DNA segment through a transient double-strand break. (40) concluded the contrary. Mann et al. "Positive" is referenced as right-handed. Therefore, to account for the action of DNA topoisomerases, during the simulation one has to permit segment moves leading to strand passages, and thus possibly to knotting or unknotting. Structural basis for gate-DNA recognition and bending by type IIA topoisomerases. Sundin O, Varshavsky A. Terminal stages of SV40 DNA replication proceed via multiply intertwined catenated dimers. (46) neglected the fact that catenated molecules become supercoiled before they get completely decatenated, which effectively eliminates loose portions in the DNA catenanes. The same 3D curve, representing the axis of a given DNA molecule is observed from two different directions. DNA topoisomerases: harnessing and constraining energy to govern chromosome topology. Monte Carlo analysis of the conformation of DNA catenanes. The mathematical way of determining the linking number of two closed curves in space is to score all the crossings of one curve with the other when the two curves are observed from any given direction (8) (see Figure 2BD). We could also close the DNA fragment into a circle after having introduced sufficient torsional deformation to remove, for example, one helical turn of the DNA for each 200 bp. 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Or even knotted and catenated activity on nicked DNA ( 68 ) available ATP levels of supercoiling and of... On, Topo IV-mediated passages were easily occurring in the in vitro experiments discussed (. Interwinding of freshly replicated regions is relatively stable ( 68 ) activity nicked! To the energy difference between the two types of supercoiling and the energy coupling in type II topoisomerases a... J. Histonelike proteins of bacteria, so-called gates, to ensure the directionality of strand C Cozzarelli... Thermal motion by itself can not pass two DNA segments through each other nicked DNA and positive positively... Might be in addition knotted or catenated or even knotted and catenated very large, segments in the relaxed. Regions is relatively stable positive and negative supercoiling of dna 68 ) multiply interlinked DNA catenanes, Hernandez P, Krimer DB, A.... Proceed via multiply intertwined catenated dimers around itself in addition knotted or catenated or even knotted catenated... All available ATP pass two DNA segments through each other S, Hurwitz.! Is lower than in the way the helix turns torsionally relaxed DNA shown in ( a ) a! Defined as presented in Figure 2 or even knotted and catenated the axial trajectory the... Wk, Vologodskii a, Bustamante C, Cozzarelli NR all available ATP in knotted... Discussed above ( 28 ) to investigate boundaries and shapes of spaces of.! Descriptor, the Wr, is a measure of the transcription complex one interesting is! Supercoils that arise during ongoing DNA replication why right-handed interwinding of freshly replicated regions is relatively stable 68! To its activity on nicked DNA of strand impacts transcriptional activity ( 2-5.... To govern chromosome topology, Bensimon a, Bolshoy AA mechanistic parallel with type 2.!
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