the transposable element ( te ) was first described by mcclintock   as a controlling element that jumps from one position to another in the maize chromosome in the mid-1940s , long before the discovery by watson and crick of the double helix structure of dna as a genetic element .
it was a time when , after the rediscovery of mendel 's law of heredity in 1900 , the cytogenetic study of chromosomes was at the forefront of genetics and when genes were thought to be beads on a string located on the chromosome .
it was in the late 1970s and early 1980s when insertion sequence ( is ) elements and transposons ( tn ) were discovered and found to be similar to mcclintock 's controlling elements , and her ac / ds elements were confirmed at the dna sequence level as a te .
salient features of dna transposable elements ( dtes ) , including terminal inverted repeats ( tirs ) , target site duplication ( tsd ) , the transposase gene , and simple and replicative transposition mechanisms have been well established by extensive molecular biology and biochemistry studies .
then , retrotransposable elements ( rtes ) , including long terminal repeat ( ltr)-retrotransposons , non - ltr - retrotransposons , and other retro - elements , were being added to the repertoire since the 1980s to make the picture diverse and complicated .
many new families of tes are being added , especially from eukaryotes , even by computational screening in the post - genome era , which has necessitated a new classification based on their structures and mechanisms of transposition .
the presence of foldback intercoil ( fbi ) dna was first reported by kim in 1985   and shown by a space filling model to mediate intra - molecular homologous recombination of inversions and deletions .
it was further shown in 1987 that fbi dna can mediate inter - molecular dna rearrangements , such as site - specific insertions , at the foldback tip and dna transpositional integration at the intercoil end of the detached dte .
it will be examined in this review how fbi dna mediation of transposition can be extended to different classes and families of rtes .
readers are suggested to refer to many good reviews available on the classification , structures , genetic contents , and function of the gene products and on the mechanisms of transposition with excellent diagrammatic illustrations [ 5 , 9 , 10 , 11 , 12 ] .
this review will minimize duplicate descriptions and focus on the mechanistic features that are relevant to the application of fbi dna to the mechanisms of dna transposition .
to build the basis for comparison and understand transposition mechanisms , it is necessary to consider te structures based on the presence or absence of the following factors : 1 ) rna intermediates before transposition , 2 ) tirs or ltrs , 3 ) transposase or reverse transcriptase ( rt ) and other proteins related to autonomous or non - autonomous transposition , 4 ) tsd , and 5 ) other features , like dna replication modes , hairpin structure , and enhancers .
transposition of dtes involves direct movement of the dte intermediate either by a simple cut - and - paste mechanism , as in tn5 , tn7 , and tn10 , or by replicative transposition , in which case one copy stays in the original site and a daughter dte copy appears in a distant location [ 16 , 17 , 18 ] .
step - wise description of the transposition events includes the requirement and pairing of both dte ends [ 13 , 19 ] , binding of the transposase proteins to the terminal sequences , double - strand breaks ( dsbs ) of the dte terminals   and target ends , ligation of the 3'-oh donor end and the 5'-p target end , and gap repair of the single - strand gaps on the target that were generated by dsb . in the case of the mu bacteriophage
, the gap can be repaired while the entire transposon gets replicated in a cointegrate mechanism [ 21 , 22 ] .
transposition of rtes involves an rna intermediate that is reverse - transcribed by rt into a cdna .
this double - stranded linear dna functions as the direct precursor for integration by an integrase protein into a new location in the host chromosome in a ' copy and paste ' manner , as in the ' cut - and - paste ' transposition reaction in dtes [ 20 , 23 ] .
tirs are a hallmark of dtes , as ltrs have been that of rtes until they were joined by non - ltr retrotransposons , which have a 5'-untranslated region ( 5 ' utr ) and 3 ' utr , as typified by line-1 ( l1 ) , or which has neither of the terminal elements , as typified by the alu element .
it becomes clear that the presence of terminal repeats in the tes is no longer a common requirement for the transposition reaction .
the description of the protein factors above will suffice for this review , except for the long interspersed nuclear element ( line ) open reading frames ( orfs ) .
the retrotransposition and integration of line have been viewed as a coupled process , called target - primed reverse - transcription [ 5 , 24 ] . however
, this model has recently been enhanced by the finding that l1 reverse - transcription does not require base pairing between the primer and template .
therefore , the cdna that was reverse - transcribed from the mrna expressed from the genomic copy of line is inserted into the host genome .
tsds are generated in almost all classes and families of tes , except for the helitron dte superfamily [ 6 , 9 , 10 ] .
the size of the tsd varies from 2 to 11 , but the sequences are not conserved .
the ubiquitous presence of tsds , which are generated by gap fillings ( gfs ) after te integration on the target , reflects the unity in transposition reactions , regardless of dte or rte , and the presence or absence of terminal repeats . yet , the meaning of the small oligomer size of the duplicated target is seldom discussed in terms of dna structure .
helitron , a eukaryotic dte , is considered , together with polintons , a third class of tes for many unique aspects .
they contain 16 - 20-bp hairpins 10 - 12 nucleotides inside of the 3'-end and transpose precisely between the 5'-a and t-3 ' with no tsd generation .
helitrons indiscriminately capture and mobilize gene sequences and may impact hybrid vigor or heterosis in maize .
since the hairpin sequence corresponds to the fbi dna motif , it will be interesting to consider whether it can not only serve as a terminator or rolling circle replication but also serve as a replication origin for its own replication and for frequent gene capture activities , which the helitron is capable of .
polinton is 15 - 20 kb long , with a 6-bp tsd and 100 - 1,000-bp tir at both ends .
polintons code up to 10 proteins , including a family of b dna polymerases ( polbs ) , a retroviral - like integrase , an a transposase , and an adenoviral - like cysteine protease .
polintons , however , with their structural characteristics and presence of tsd , should follow non - homologous end - joining ( nhej ) with the gf transposition mechanism , as ordinary dtes . what makes it unique is the presence of a self - encoded polb and a short 1 - 3-bp terminal tandem repeat that supports a protein - primed self - synthesis mechanism for polinton propagation .
this mechanism calls for an extrachromosomal single - stranded polinton intermediate that forms a racketlike structure and follows polb - mediated replication to become double - stranded before being integrated into the host genome .
it has been proposed that eukaryotic dtes follow three types of transposition mechanisms according to different replication modes : cut - and - paste for most dtes , rolling circle replication for helitrons , and synthetic replication for polintons .
in fact , there seems to be many different cases of transposon - related replication that need to be clarified in the future .
as mentioned earlier , continuation of dna replication of an inserted te molecule , like in mu co - integration , may also fill the gap to generate tsds .
it should be emphasized that dna transposition has been grouped in two : simple , conservative , or ' cut - and - paste ' mechanism and replicative transposition [ 16 , 17 , 29 ] . in tn5 , at the outer ends , ori - c - like 9-bp sequences are found , which may serve to direct host replication functions to the ends of the element during transposition .
a synthetic mechanism is proposed for polinton propagation to explain protein - primed replication of a racket - like structure of a single - stranded polinton .
if it gets to be understood that the heteroduplex structure that is derived from fbi dna may serve as the template of dna replication , many of the diverse cases of dna replication may be clarified ( see below ) .
fbi dna is formed by the folding back at one point of a non - helical parallel track of double - stranded dna at as sharp as 180 and the intertwining of the bent helixes within each other 's major groove to form an intercoil with a diameter of 2.2 nm ( fig .
fbi dna could be considered a double - stranded version of a hairpin or stem - and - loop structure of rna and single - stranded dna .
but , such sharp bending and formation of a four - stranded intercoil are not considered possible with a double helical b - dna with a diameter of 2.0 nm . in an extended definition , fbi dna may contain a loop and a much longer stem under biological conditions .
intercoil dna is designated to distinguish itself from supercoil dna , which is thicker than 2.2 nm .
intercoil dna is also termed to avoid the use of four - stranded dna , which has the connotation of four - stranded base pairing among homologous repeats .
it needs to be emphasized that intercoil dna is formed by two intertwining duplexes of any sequence , but when homology is met at a certain region , homologous recombination may proceed via heteroduplex formation with the help of the proper enzymes involved .
fbi dna was first formulated based upon a rare but unique electron microscopy ( em ) configuration of plant mitochondrial dna ( mtdna ) molecules and space - filling models [ 7 , 8 ] . once the fbi dna structure was realized with the space filling model
, it was possible to perform homologous recombination with direct contact of the repeat sequences .
the intra - molecular homologous recombination of a deletion and inversion occurs via 1 ) synapsis of the repeats in the intercoil , 2 ) heteroduplex formation by 90 base flipping , and 3 ) nick - and - close resolution of the sugar phosphate backbone crossing over .
inter - molecular homologous recombination , known as site - specific insertion , on the other hand , is mediated by direct contact between the attp site at the tip of the fbi dna and the attb site on the target dna .
perpendicular approach of the foldback tip onto the target site effectively resolves the year - long topological puzzle encountered in four - stranded base pair winding of two circular dna molecules and explains that 6- or 7-bp attp and attb sites correspond to the diameter of the approaching fbi dna tip and the target width .
dna transposition is explainable by the perpendicular approach of the detached transposon ends in intercoil form to the host target , as described in detail below .
transposition of a dte molecule in fbi dna configuration is tested by a space filling model , as presented in fig . 1 and as a detailed diagram in fig
. 2 . the te molecule , detached from the host by a dsb in a blunt end cut , approaches , as shown in the diagram , at a perpendicular angle to the target site .
both 3'-oh ends of the te ligate with the 5'-p ends of the staggered - cut target , leaving the overhang target ends single - stranded , which would be repaired by gap filling . as shown in the diagram ( fig .
2 ) , when the te ends approach the target on the minor groove side , the target size would be 5 bp on the minor groove side and 7 bp on the major groove side .
this explains the meaning of the average size of the 5 - 7-bp target duplication , as it matches the diameter of the incoming intercoil dna , 2.2 nm . in reality , the target sizes vary between 2 to even over 10 bp in a te superfamily - specific manner .
this tsd size variation could be explained by several factors - namely , local squeeze and stretch of the dna double helix ; unequal cutting positions of the te ends , as exemplified in tn7 by the 3-nt overhang by staggered dsb ; the characteristics of the endonucleases involved ; and even temporary loosening of the intercoil end during a very elaborate and concerted coordination of the transpososome structure . in earlier days , when is and tn , and even the ltr retrotransposons , were the major players of transposition , it was the presence of terminal repeats that attracted attention for explaining the transpositional mechanism , as in homologous recombination .
therefore , it was somewhat puzzling to explain the cases of non - ltr retrotransposons with asymmetric termini sequences .
but , it is now tsd that attracts attention as a common factor for the transposition mechanism of all tes , except for helitrons .
it is the structural nature of the intercoil , which is formed by intertwining duplexes , regardless of the homology between the two termini . when both ends of a te synapse in the form of an intercoil , are cut by a dsb off the host duplex strand , and approach the target in perpendicular direction , their 3'-oh ends ligate to the staggered 5'-p ends of the broken target .
the resulting overhang single - strand dna gaps on both flanking ends of the target are repaired to generate the accompanying tsd .
the significance of the terminal repeats is then the homologous recombination that is required for further transactions of recombination , replication , and transcription .
the enhancer is a cis element of dna that affects , as a third factor , dna transactions , such as transcription , homologous recombination , and transposition [ 31 , 32 , 33 , 34 ] .
it has remained somewhat of an enigma , because the presence of an enhancer element and its binding proteins at a distance in a sequence and orientation non - specific manner enhances the efficiency of the reaction by 1,000 times .
rather unique configurations of rigid rod - like dna with a big protein complex at one end [ 35 , 36 
 fig . 4 - 2 ] may shed light on the enhancer concept and give us an idea of what actually happens under cellular conditions ( fig .
3 ) . folding back of a dna duplex at a distant point would bring an enhancer site into juxtaposition with the base of a te , which has also branched out as fbi dna ( figs . 4 and 5 ) .
proteins binding to the enhancer site and to both ends of the te and any other additional factors together would form a tight dna - protein complex , called a transpososome .
this transpososome would provide a tight and stable surgical platform for a series of highly concerted precision cut - and- paste reactions : namely , dsb of the te termini , sealing of the host duplexes by nhej , staggered cuts on the target site , nhej of the te 3'-oh ends and target 5'-p ends , and finally , gap - filling of the 5 - 7-nucleotide single - strand portions to flank the transposed te . in replicative transposition ( fig .
first , the gap - filling reaction during tsd may continue on to the te molecule by displacement or polarized replication , even though the direction of replication may be reversible .
second , as shown in the diagram , tirs in the fbi dna configuration may transform into heteroduplexes and serve as primers for bidirectional replication of the internal te , thus keeping one copy at the original site and depositing the other copy to the target site in juxtaposition .
inversion of the replicated te may result from homologous recombination , as predicted [ 7 , 16 ] .
tsd serves as a common landmark of unity on transposition mechanisms for both dtes and rtes .
the only exception so far is the helitron superfamily , which lacks tsd and employs a rolling circle replication model . as long as a tsd
is generated during te integration into the host chromosome , it indicates that the immediate intermediate of integration is in a double - stranded dna form , regardless of rna or single - stranded dna being the initial intermediate . from the em pictures of fbi and rigid rod configurations of native dna ( fig .
it becomes apparent that vertical insertion of the dsb ends of the te in an intercoil alignment is probably the best - fitting mechanism of dna transposition .
small sizes of the target , around 6 - 7 bp , encountered in tsd as well as in attp and attb in site - specific insertion all point to the fact that they correspond to the diameter of fbi dna 2.2 nm .
the transpososome , made of fbi dna configurations of the te and the enhancer element , may effectively abolish lingering mechanistic puzzles about keeping four broken strands of the te and the host from flying apart and answer how a te molecule jumps onto a new target site at a distance .
replicative transposition is explained likewise , even utilizing the terminal homology as a possible origin of replication .
it would be , however , difficult , if not impossible , to reproduce such a transpososome complex in vitro by fbi dna configuration , which is critically needed for em observations and crystallography analysis .
there are four main modes of transactions by which the fbi dna motif may be utilized in dna functions in the cell : alpha deletion , omega inversion , needle point site - specific insertion , and nhej - gf integration of te .
with such an abundant presence in strategically important positions in the genome and very dynamic functional roles , it is hoped that fbi dna receives the proper recognition and interpretation for a better understanding of the life process .
 foldback intercoil ( fbi ) dna is formed by the folding back at one point of a non - helical parallel track of double - stranded dna at as sharp as 180 and the intertwining of two double helixes within each other 's major groove to form an intercoil with a diameter of 2.2 nm . fbi dna has been suggested to mediate intra - molecular homologous recombination of a deletion and inversion . inter - molecular homologous recombination , known as site - specific insertion , on the other hand , is mediated by the direct perpendicular approach of the fbi dna tip , as the attp site , onto the target dna , as the attb site . 
 transposition of dna transposons involves the pairing of terminal inverted repeats and 5 - 7-bp tandem target duplication . 
 fbi dna configuration effectively explains simple as well as replicative transposition , along with the involvement of an enhancer element . 
 the majority of diverse retrotransposable elements that employ a target site duplication mechanism is also suggested to follow the fbi dna - mediated perpendicular insertion of the paired intercoil ends by non - homologous end - joining , together with gap filling . a genome - wide perspective of transposable elements in light of fbi dna is discussed . 
Introduction
Structures of TEs and Mechanisms of Transposition
FBI DNA
DNA Transposition Explained by FBI DNA
FBI DNA and Enhancer Concept for DNA Transposition
Conclusions and Perspectives