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four bases nearest to the junction on each arm it is evident that bases farther out can also affect the observed stacking conformations 2 in junctions with symmetrical sequences the branchpoint is mobile and can migrate in a random walk process the rate of branch migration varies dramatically with ion concentration with single step times increasing from 0 3 to 0 4 ms with no ions to 270 300 ms with 10 mm mg 2 the change in rate is correlated with the formation of the stacked versus the unstacked structures 2 holliday junctions with a nick or break in one of the strands at the junction point adopt a perpendicular orientation and always prefer the stacking conformer that places the nick on a crossover strand rather than a helical strand 2 rna holliday junctions assume an antiparallel stacked conformation at high magnesium concentrations a perpendicular stacked conformation at moderate concentrations and rotate into a parallel stacked conformation at low concentrations while even small calcium ion concentrations favor the antiparallel conformer 2 biological function edit the two pathways for homologous recombination in eukaryotes showing the formation and resolution of holliday junctions the holliday junction is a key intermediate in homologous recombination a biological process that increases genetic diversity by shifting genes between two chromosomes as well as site specific recombination events involving integrases they are additionally involved in repair of double strand breaks 2 in addition cruciform structures involving holliday junctions can arise to relieve helical strain in symmetrical sequences in dna supercoils 3 while four arm junctions also appear in functional rna molecules such as u1 spliceosomal rna and the hairpin ribozyme of the tobacco ringspot virus these usually contain unpaired nucleotides in between the paired double helical domains and thus do not strictly adopt the holliday structure 2 the holliday junctions in homologous recombination are between identical or nearly identical sequences leading to a symmetric arrangement of sequences around the central junction this allows a branch migration process to occur where the strands move through the junction point 2 cleavage or resolution of the holliday junction can occur in two ways cleavage of the original set of strands leads to two molecules that may show gene conversion but not chromosomal crossover while cleavage of the other set of two strands causes the resulting recombinant molecules to show crossover all products regardless of cleavage are heteroduplexes in the region of holliday junction migration 4 many proteins are able to recognize or distort the holliday junction structure one such class contains junction resolving enzymes that cleave the junctions sometimes in a sequence specific fashion such proteins distort the structure of the junction in various ways often pulling the junction into an unstacked conformation breaking the central base pairs and or changing the angles between the four arms other classes are branch migration proteins that increase the exchange rate by orders of magnitude and site specific recombinases 2 in prokaryotes holliday junction resolvases fall into two families integrases and nucleases that are each structurally similar although their sequences are not conserved 4 in eukaryotes two primary models for how homologous recombination repairs double strand breaks in dna are the double strand break repair dsbr pathway sometimes called the double holliday junction model and the synthesis dependent strand annealing sdsa pathway 5 in the case of double strand breakage the 3 end is degraded and the longer 5 end invades the contiguous sister chromatid forming a replication bubble as this bubble nears the broken dna the longer 5 antisense strand again invades the sense strand of this portion of dna transcribing a second copy when replication ends both tails are reconnected to form two holliday junctions which are then cleaved in a variety of patterns by proteins 6 an animation of this process can be seen here 7 double strand dna breaks in bacteria are repaired by the recbcd pathway of homologous recombination breaks that occur on only one of the two dna strands known as single strand gaps are thought to be repaired by the recf pathway both the recbcd and recf pathways include a series of reactions known as branch migration in which single dna strands are exchanged between two intercrossed molecules of duplex dna and resolution in which those two intercrossed molecules of dna are cut apart and restored to their normal double stranded state 8 homologous recombination occurs in several groups of viruses in dna viruses such as herpesvirus recombination occurs through a break and rejoin mechanism like in bacteria and eukaryotes 9 in bacteria branch migration is facilitated by the ruvabc complex or recg protein molecular motors that use the energy of atp hydrolysis to move the junction the junction must then be resolved into two separate duplexes restoring either the parental configuration or a crossed over configuration resolution can occur in either a horizontal or vertical fashion during homologous recombination giving patch products if in same orientation during double strand break repair or splice products if in different orientations during double strand break repair 10 11 ruva and ruvb are branch migration proteins while ruvc is a junction resolving enzyme 2 there is evidence for recombination in some rna viruses specifically positive sense ssrna viruses like retroviruses picornaviruses and coronaviruses there is controversy over whether homologous recombination occurs in negative sense ssrna viruses like influenza 12 resolution edit in budding yeast saccharomyces cerevisiae holliday junctions can be resolved by four different pathways that account for essentially all holliday junction resolution in vivo 13 the pathway that produces the majority of crossovers in s cerevisiae budding yeast and possibly in mammals involves proteins exo1 mlh1 mlh3 heterodimer called mutl gamma and sgs1 ortholog of bloom syndrome helicase 13 the mlh1 mlh3 heterodimer binds preferentially to holliday junctions 14 it is an endonuclease that makes single strand breaks in supercoiled double stranded dna 14 15 the mlh1 mlh3 heterodimer promotes the formation of crossover recombinants 16 while the other three pathways involving proteins mus81 mms4 slx1 and yen1 respectively can promote holliday junction resolution in vivo absence of all three nucleases has only a modest impact on formation of crossover products double mutants deleted for both mlh3 major pathway and mms4 minor pathway showed dramatically reduced crossing over compared to wild type 6 to 17 fold however spore viability was reasonably high 62 and chromosomal disjunction appeared mostly functional 16 although mus81 is a component of a minor crossover pathway in the meiosis of budding yeast plants and vertebrates 17 in the protozoan tetrahymena thermophila mus81 appears to be part of an essential if not the predominant crossover pathway 17 the mus81 pathway also appears to be the predominant crossover pathway in the fission yeast schizosaccharomyces pombe 17 the msh4 and msh5 proteins form a hetero oligomeric structure heterodimer in yeast and humans 18 19 20 in the yeast saccharomyces cerevisiae msh4 and msh5 act specifically to facilitate crossovers between homologous chromosomes during meiosis 18 the msh4 msh5 complex binds and stabilizes double holliday junctions and promotes their resolution into crossover products an msh4 hypomorphic partially functional mutant of s cerevisiae showed a 30 genome wide reduction in crossover numbers and a large number of meioses with non exchange chromosomes 21 nevertheless this mutant gave rise to spore viability patterns suggesting that segregation of non exchange chromosomes occurred efficiently thus in s cerevisiae proper segregation apparently does not entirely depend on crossovers between homologous pairs recently it was shown that crispr associated cas12a nuclease from the acidominococcus bacteria can resolve holliday junction in vitro 22 use in dna nanotechnology edit this double crossover dx supramolecular complex contains two holliday junctions between the two double helical domains on the top and the bottom in this image this tile is capable of forming two dimensional arrays 23 main article dna nanotechnology dna nanotechnology is the design and manufacture of artificial nucleic acid structures as engineering materials for nanotechnology rather than as the carriers of genetic information in living cells the field uses branched dna structures as fundamental components to create more complex rationally designed structures holliday junctions are thus components of many such dna structures as isolated holliday junction complexes are too flexible to assemble into large ordered arrays structural motifs with multiple holliday junctions are used to create rigid tiles that can then assemble into larger arrays 24 25 diagrams of a tensegrity triangle complex containing three holliday junctions both in isolation a and as part of a crystal b c in addition to the two dimensional array shown this structure is capable of forming three dimensional crystals 26 the most common such motif is the double crossover dx complex which contains two holliday junctions in close proximity to each other resulting in a rigid structure that can self assemble into larger arrays the structure of the dx molecule forces the holliday junctions to adopt a conformation with the double helical domains directly side by side in contrast to their preferred angle of about 60 the complex can be designed to force the junctions into either a parallel or antiparallel orientation but in practice the antiparallel variety are more well behaved and the parallel version is rarely used 24 25 the dx structural motif is the fundamental building block of the dna origami method which is used to make larger two and three dimensional structures of arbitrary shape instead of using individual dx tiles a single long scaffold strand is folded into the desired shape by a number of short staple strands when assembled the scaffold strand is continuous through the double helical domains while the staple strands participate in the holliday junctions as crossover strands 27 some tile types that retain the holliday junction s native 60 angle have been demonstrated one such array uses tiles containing four holliday junctions in a parallelogram arrangement this structure had the benefit of allowing the junction angle to be directly visualized via atomic force microscopy tiles of three holliday junctions in a triangular fashion have been used to make periodic three dimensional arrays for use in x ray crystallography of biomolecules these structures are named for their similarity to structural units based on the principle of tensegrity which utilizes members both in tension and compression 24 25 history edit robin holliday proposed the junction structure that now bears his name as part of his model of homologous recombination in 1964 based on his research on the organisms ustilago maydis and saccharomyces cerevisiae the model provided a molecular mechanism that explained both gene conversion and chromosomal crossover holliday realized that the proposed pathway would create heteroduplex dna segments with base mismatches between different versions of a single gene he predicted that the cell would have a mechanism for mismatch repair which was later discovered 4 prior to holliday s model the accepted model involved a copy choice mechanism 28 where the new strand is synthesized directly from parts of the different parent strands 29 in the original holliday model for homologous recombination single strand breaks occur at the same point on one strand of each parental dna free ends of each broken strand then migrate across to the other dna helix there the invading strands are joined to the free ends they encounter resulting in the holliday junction as each crossover strand reanneals to its original partner strand it displaces the original complementary strand ahead of it this causes the holliday junction to migrate creating the heteroduplex segments depending on which strand was used as a template to repair the other the four cells resulting from meiosis might end up with three copies of one allele and only one of the other instead of the normal two of each a property known as gene conversion 4 holliday s original model assumed that heteroduplex dna would be present on both chromosomes but experimental data on yeast refuted this an updated model by matt meselson and charley radding in 1975 introduced the idea of branch migration 28 further observations in the 1980s led to the proposal of alternate mechanisms for recombination such as the double strand break model by jack szostak frank stahl and others and the single strand annealing model a third the synthesis dependent strand annealing model did not involve holliday junctions 4 the first experimental evidence for the structure of the holliday junction came from electron microscopy studies in the late 1970s where the four arm structure was clearly visible in images of plasmid and bacteriophage dna later in the 1980s enzymes responsible for initiating the formation of and binding to holliday junctions were identified although as of 2004 the identification of mammalian holliday junction resolvases remained elusive however see section resolution of holliday junctions above for more recent information in 1983 artificial holliday junction molecules were first constructed from synthetic oligonucleotides by nadrian seeman allowing for more direct study of their physical properties much of the early analysis of holliday junction structure was inferred from gel electrophoresis fret and hydroxyl radical and nuclease footprinting studies in the 1990s crystallography and nucleic acid nmr methods became available as well as computational molecular modelling tools 2 4 30 initially geneticists assumed that the junction would adopt a parallel rather than antiparallel conformation because that would place the homologous duplexes in closer alignment to each other 2 chemical analysis in the 1980s showed that the junction actually preferred the antiparallel conformation a finding that was considered controversial and robin holliday himself initially doubted the findings 2 4 the antiparallel structure later became widely accepted due to x ray crystallography data on in vitro molecules although as of 2004 the implications for the in vivo structure remained unclear especially the structure of the junctions is often altered by proteins bound to it 4 the conceptual foundation for dna nanotechnology was first laid out by nadrian seeman in the early 1980s 31 a number of natural branched dna structures were known at the time including the dna replication fork and the mobile holliday junction ...