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Structure of simian virus 40-adeno-associated virus recombinant genomes.


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Copyright C 1985, American Society for Microbiology

Structure of Simian Virus 40-Adeno-Associated


Recombinant Genomes


Department ofVirology, Weizmann Institute of Science, Rehovot,


and Department of Microbiology, Cornell University Medical College, New York, New York 100212

Received 14 May1985/Accepted 16 July 1985

The structures of recombinant genomes formed by recombination between simian virus 40 (SV40) and

adeno-associated virus 2 (AAV) DNAs after either DNA cotransfection or coinfection by virions were

characterized. Twotypes ofstructures werefound.GroupAstructures,foundaftercotransfection and in one ofsevenrecombinantsarising fromcoinfection, representedasimple deletion of SV40 sequences replaced by

a slightly shorter AAV sequence. GroupB structures were found in six ofseven recombinantsarising after virioncoinfection. Allcontained eithertheleftorrightterminalsequences(approximately 250 to 450 bases) of theAAVgenomeadjacenttothe SV40origin ofDNA replication. Only 350to650bases(including the origin) remained of theSV40 sequence. The joined SV40-AAV sequenceswerepresentinthe recombinant genomeas a tandem repeat ofasize that can be packagedintoSV40capsids.

Togain abetterunderstandingof nonhomologous

recom-bination in animal cells, we are exploiting the capacity of

simian virus 40(SV40) to recombine withavariety of other DNAsof bothprocaryotic and eucaryotic origins (11-13, 41, 42). Inapreviousstudyof recombinationbetweendefective

adeno-associated virus (AAV) and SV40 (13),we compared recombination frequencies after both DNA cotransfection

andvirus coinfectionasmeasuredbythenumbersof

recom-binant-producingcells identified by infectious centerin situ plaque hybridization (40, 12). In most respects, the data

obtained by both methods of DNA delivery were quite comparable. Independent of the method of delivery, the

probabilitythatasuccessfully infectedcell would generatea

recombinantwasdependentontheinitialSV40 DNAdosage

aswell asthe AAV DNA concentration, and the maximum

proportion ofcells (relative tothetotalpopulation)

generat-ing recombinants after virion coinfection was similarto the maximum proportion of recombinant-producing cells after DNA cotransfection, despite the 5- to 10-fold higher effi-ciency of infection in the formercase.

Inone respect, however, the recombination process that

ensues after SV40and AAV virus coinfection differed from

that whichoccursafter SV40 and AAV DNAcotransfection.

The terminal sequences ofthe AAV genome werefound in

inordinately high proportions (>90%) of recombinants gen-erated after coinfection. In contrast, no such

over-representation was observed in recombinants generated

af-ter DNA cotransfection. It was also found that, for DNA

cotransfection systems, DNA sequences located at a free end possess no obvious advantage in recombination with

circular SV40 DNA (11, 13).

In the present work, we analyzed in detail SV40-AAV recombinant structures. The recombinants can be divided into two groups accordingto their SV40 and AAVcontent and accordingto theirgeneral structure. The recombinants in group A (those produced after cotransfection and one of

seven ofthose resulting from coinfection) retain more than

70% of the SV40 genome and carry single inserts derived from the inner parts of the AAVgenome. The SV40-AAV

recombinants in group B (sixof sevenof the recombinants

producedaftercoinfection) retain less than 20% of the SV40 genome (including the SV40 origin of replication) and con-tain an AAV segment that retains part of its terminal palindrome. The SV40 origin-containing segment isjoined

together with that of AAV in repeat units, usually in a

head-to-tail tandem array.

Overrepresentation ofAAVterminal sequences in

recom-binantsgenerated aftercoinfection and thespecificstructure

of the DNA of those recombinants containing the AAV

terminalrepeats maybe related to certain features

charac-teristic ofthe AAV genome whenit is deliveredtothe cell in



Cells and viruses. SV40 (strain 777) was propagated in BSC-1 cells maintained in Dulbecco modifiedEagle medium

with 10% calfserum(21). AAV (2H) (17)waspropagated in HeLa cells in suspension culture with adenovirus type 2

helperasdescribed before (27).

Preparation of virion stocks containing recombinant genomes. Virion stocks containing SV40-AAV recombinant

genomes (produced from a single transfected cell) were

isolated fromthe agaroverlays oftheinfectiouscenterassay

(42). Autoradiograms of filters hybridized to 32P-labeled

AAV DNAwerealignedwith the agaroverlays, andplugs of

agar corresponding to the autoradiographic signals were

picked, freeze-thawed, and used to infect fresh BSC-1 cell

monolayers in microwells; on the occurrence of full

cytopathic effect, the microwell supernatantswere assayed

for the presence ofAAV DNA sequences by dot-blot

hy-bridization. The yields ofpositive wells were passaged by infection offresh BSC-1 cells, and after the occurrence of

full cytopathic effect, the supernatants were collected and usedasinocula for progeny DNApreparation.

DNApreparations. SV40 DNAwaspreparedasdescribed

by Oren et al. (25). AAV virion DNA was purified by

sedimentation through alkaline sucrose gradients and

an-nealingof thecomplementary strands(2).Bacterialplasmids

were prepared from Escherichia coli HB101 or DH1 cells grown to saturation in LB medium (11) containing the


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e f





FIG. 1. Restriction mapping, before cloning, ofSV40-AAV

re-combinant DNA in isolates derived from single

recombinant-producing cells. DNAs of isolates 4 and 5 (see the text), either undigested ordigested with restriction enzymes which donot cut

within the AAV DNAinserts,werefractionatedon1%agarosegels,

transferred tonitrocellulose paper, andhybridizedwith 32P-labeled

AAV DNA. Lanes a tod, Isolate 4 DNA, undigested ordigested

withBcll, Ndel,andPvull,respectively;lanesetoi,isolate 5DNA,

undigestedordigestedwithSmnaI, Nael, Pvull,andNdel, respec-tively.Thesymbols I, II,and IIIdesignatethepositionsofwild-type

SV40DNAforms I, II,and III deducedfrom the ethidium bromide

stain of thegel before blothybridization. The number2,000

desig-nates a marker fragment 2,000 bp long. Autoradiograms were

exposedat -700C for 40 h.

appropriate antibiotic (100 ~ig of ampicillin or 12.5 p.g of

tetracycline perml) bythe quick boiling method of Holmes andQuigley(18),bythealkalilysismethod of Birnboim and

Doly (4), or by the cleared lysate procedure described by

Davis et al. (8). Plasmid DNA was purified by equilibrium

sedimentation in ethidiumbromide-containing cesium chlo-ride density gradients. Single-stranded M13 DNA was

pre-pared according toHu andMessing (19).

Plasmid DNAs and restrictionfragmentswere purified by

separationonagarosegels andbyadsorptiontoRPC-5 resin andelution withasolution withahighsaltconcentration(3).

DNA from agarose gels was eluted either by the glass

powder adsorption technique of Vogelstein and Gillespie

(40)orbydiffusion of the DNA(DNAfragmentsof less than

2,000 base pairs [bp]) from the agarose slices (which were

disrupted by passing through a syringe) into the extraction solution (0.01 M EDTA, 0.2 M NaCl, 0.01 M Tris

hydro-chloride [pH 7.5 to 8.0], 0.5 g of agarose per ml of extractionsolution). Gelparticleswereremovedbyfiltration

throughHA0.45-p.m(poresize)filters(Millipore Corp.),and the DNAs were concentrated by adsorption toRPC-5 resin


Recombinant viral DNA was isolated from cells by a

modificationof the Hirt(16)procedure. After sedimentation

of high-molecular-weight DNA from a total volume of 1.0

ml, 100 dlof0.25 M EDTA-0.15 M Trishydrochloride (pH

9.5)-3% sodium dodecyl sulfate was added to the

superna-tant which, after gentle mixing, was heated to 650C for 15 min. The preparation was digested with RNase, proteins

were removed by centrifugation for 10 min, and the super-natant was extracted by phenol-choloroform-isoamyl alco-hol (50:48:2). DNA was precipitated with ethanol, and the

driedpelletwasdissolvedin200plof TEbuffer(10 mMTris hydrochloride [pH 7.4], 1 mM EDTA).

Restriction endonuclease digestion, electrophoresis, and blothybridization. Restriction endonucleases wereused

ac-cordingto the recommendations ofthe manufacturer (New England BioLabs, Inc.), and the productswereseparatedby electrophoresis (40 Vfor 20 h) in Tris-acetate bufferon 1%

agaroseslabgels. Thegelwasstainedwithethidiumbromide (0.5 ,ug/ml)andphotographed underUVlight.Theproducts

were transferred to nitrocellulose sheets (Schleicher &

Schuell, Inc.), and Southern (37) blot hybridization was

carried out according to Smith and Summers (35) in

Denhardt buffer(10).

DNA transfections.Cellsweretransfectedinsuspensionin the presence of DEAE-dextran (23) by the method of Mil-man and Herzberg (24), asdescribed previously (13).

Assay for recombination. The infectious center in situ


asdescribed previously (1, 13).

Molecular cloning. Cloning ofAAV DNA and segments thereof has been previously described (13). The closed circular DNA yields of individual recombinant-producing cells weredigested withthe appropriate restriction enzyme and ligated to cleaved and alkaline phosphatase-treated (6)

plasmidDNA(pBR322 orits derivates BdIH and pML2). E.

coliHB101 or DH1 cellswere transformed withtheligation products (11), and the SV40-AAV-containing colonies were isolated accordingto Hanahanand Meselson (15).

DNAsequencing. The nucleotide sequencesoftwo SV40-AAV recombinant regions (see below) weredetermined by thedideoxynucleotide chain terminator methodofSangeret

al. (30), as described by Smith et al. (36), with pBR322 Hindlll and EcoRI primers obtained from New England BioLabs. Single-stranded DNA sequencing by the M13 system was done according to Hu and Messing (19).

Acrylamide(6%) gels were used withTris-borate buffer.

Sourceofbacterialplasmids. pML2 plasmidwasobtained

from M.Botchan, and BdlH wasfrom D. Dorsett.


Isolation and preliminary characterization of SV40-AAV recombinants. SV40-AAV recombinants formed afterDNA

cotransfection (isolate 4) and virion coinfection (isolates 5

through 40)wereisolated from the agaroverlayasdescribed byWinocouretal.(42).ThesupercoiledDNAof SV40-AAV


DNAs. Wedeterminedthe loss orretention ofSV40 restric-tion sites in SV40-AAV recombinant genomes by digesting

theDNAwith restriction enzymeswhichcutwild-typeSV40 DNA but not AAV DNA (EcoRV, NaeI, NdeI, SphI, and


which have no recognition sites in AAV DNA and

one to three sites in SV40 DNA). The

digestion products

were separated by agarose gel electrophoresis and

trans-ferred to nitrocellulose paper(35), and thoseproducts

con-tainingAAV sequenceswereidentifiedbyhybridizationwith


AAVDNA.Furtheranalysiswasthendone with

restriction enzymes whichcut both SV40 and AAV DNAs (e.g.,

BamHI, BglI, BclI,

and EcoRI). Figure 1 illustrates suchan analysis.

Figure 2 schematically summarizes the retention ofSV40 sequencesineightdifferent isolateswhichwereanalyzedby


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Isolate 40

Isokate 38

Ri Iorn Isolate22



x N Born

---AE k



---~~~~~----BcIl RV RI P Boam

ii A IIi I

pcii p x tx 0** Rv RI P

I l?ttT. I 8,



4000 50005243/0) 000 2000 2600

Isolate 16


Isolate 9


Isolate 4

SV40 wilidtype

FIG. 2. Retention ofSV40 sequences in SV40-AAV recombinants. We determined the loss or retention of SV40 restriction sites in

SV40-AAV recombinant genomes by digesting the DNA with restriction enzymes, fractionating the digested DNA by agarose gel electrophoresis,andperformingblothybridizationto 32P-labeledAAVprobe.Thesolid boxes denoteSV40sequencesthatwereretained and

aredrawn relativetothemapof thewild-typeSV40genome. Isolate 4wasderived fromaDNAcotransfectionexperiment; all of the other

isolates(5to40)werederived from virion coinfection.Isolates 4 and 22 retainedmorethan70% of theSV40sequences; in theothers, less

than 20% of theSV40genome (includingthe originofreplication) wasconserved. The AAV segments contained about 800 nucleotides in

isolate 4 and 500 orlessinall of the others(see Fig.6and 7 and the text).Symbols: Bgll; 'T Hinfl; N,Nael; T ,Ncol; f Ndel;

T,Pvull;P,Pstl; T Sphl; t Taql; Bam,BamHl; RI, EcoRI; Rv,EcoRv.

theabove method. All of the recombinantsweresmaller than

wild-type SV40(genomes of4,000to5,000bp). Theisolates could be clearly divided into two groups: (i) group A,

containing isolates 4 (derived from a DNA cotransfection

experiment)and 22(derivedfromavirion coinfection exper-iment), which retained morethan70% of the SV4O genome;

and(ii) group B,containing isolates 5, 9, 15, 16, 38, and 40

(all derived from virion coinfection experiments), which retained less than 20% of the SV40genome. Inallcases, the

SV40 origin ofreplication was retained.

Weidentified the AAV inserts in the isolatesby hybridiz-ingblotsto32p_labeled,defined AAV DNAprobes. GroupA

isolates 4and 22 contained inserts from the inner segments

of the AAV genome; isolate 4 hybridized to the Pstl A

fragmentof AAV (nucleotides 1959 to 4258), and isolate 22

hybridized tothe Pstl B fragment of AAV (nucleotides 496

to 1958). All of the group B isolates contained terminal

sequences of the AAV genome. Since these latter isolates

hybridized to both the Pstl C (nucleotides 1 to 495; not shown)and PstI D(nucleotides 4259 to 4675; Fig. 3 and4) segmentsof AAVDNA, they probably contain atleastpart

of the terminal inverted repeat of the AAVgenome.

Group B recombinants contained less than 20% of the

SV40genomeandno morethan15% of the AAVgenomeyet

were 4,000 to 5,000 bp in length (Fig. 2). This apparent

discrepancy can be explained if it is assumed that, in any

given recombinant, the sequences that are retained appear

morethan once. To investigatethis possibility, we digested

the DNAs with restriction enzymes that cut once either in

the SV40 sequence or in the AAV sequence that was

retained in the recombinants, namely Hindlll, which cuts SV40in theorigin region(nucleotide 5171), andBall, which

cuts AAV at nucleotide 4554 (all other sites of these two

enzymeswere notpreservedin theserecombinants). Figure

4 summarizes this experiment. Since HindIll, which cuts

only SV40 sequences, and Ball, which cuts only AAV


. .... I I

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b c d e

f g h j




d e



~~~~~~~~~4 soon_

FIG. 3. Restriction mapping (before cloning) of isolates 38 and 40. DNAs of isolates 38 and 40 were digested with restriction enzymesandfractionatedonagarosegels, and the blotwas hybrid-ized with 32P-labeledPstl Dfragment ofAAV (nucleotides4259 to 4675). Lanes: a to d, isolate 38; e to h, isolate 40, undigested or digested with EcoRI, PvuII, and NdeI, respectively; j, wild-type SV40 DNA, digested with PvuII. The symbols I, II, and III designate the positionsof wild-typeSV40DNAformsI, II,and111. (A)Ethidium bromidestainingofthe gel. Thedigestionpatternsof virus DNA (the only DNA visible) indicates that all reactions went tocompletion. (B) Autoradiogram of the blot after hybridization. Only recombinantDNAreacted; note that therecombinantDNAs were notdigestedby the enzymes.

sequences, generated small fragments of the same size in isolates 5, 16, and 40, it appears likely that a tandemly repeated structurecontaining SV40 and AAV sequences was present in these isolates. Isolate 38 also appears to have a repetitive structure, but of a more complex nature. It is noteworthy that the reiterated structure was found only when the recombinant contained inserts derived from the

terminalrepeat unit ofthe AAV genome.

Molecular cloning and structureoftwoSV40-AAV

recom-binants belonging to groupA. Wecloned the twoisolatesof

group A(isolates 4 and 22) by inserting their DNA into the EcoRI site ofthe pBR-related plasmid Bd1H. Screening for the AAV-containing plasmids was performed according to Hanahan and Meselson (15). The proportions of colonies

which reacted against


AAV DNA were 30 and 0.01% in isolates 4 and 22, respectively, of those which

reacted against


SV40 DNA, indicatingthat the

ratios ofSV40-AAVrecombinants toSV40 DNA molecules were 1:3 and 1:10,000. Cloned SV40-AAV recombinant DNAs were mapped by restriction endonuclease digestion

analysis (Fig. 5).

AAV sequencesin the recombinant genomes were identi-fied by hybridization of


recombinant DNAs to

PstI digests of plasmids containing different Pstl fragments

ofthe AAV genome (13). Recombinant 4 DNA hybridized onlyto segmentAofAAVDNA(nucleotides1959 to4258), and recombinant 22 DNAhybridized onlyto segment B of AAV DNA(nucleotides 496to 1958). Figure6shows maps thatwere constructed on the basis of the data from these procedures.

The essential features of the group A recombinant struc-tures are asfollows.(i)Thetworecombinants carried inserts

derived from the inner partsof the AAV genome (rather than the terminal sequence). (ii) The AAV sequences (500 to 800 bp) were present as single inserts located within the early SV40 region. (iii) The deletion of SV40 sequences was

greater than the size ofthe AAV insert, resulting in short-eningoftherecombinant genome relativetowild-type SV40 (4,800 bp for recombinant 4 and 4,200 bp for recombinant 22).(iv) In thetworecombinants,the remainderof the SV40 DNA(other than the deletion which accomodated the AAV DNA insert and, in recombinant 4, the 600-bp SV40 dupli-cation of theorigin region)wasretained in unaltered form, as

judgedby restriction mapping.

Molecular cloning and structure analysis of two recombi-nants containing AAV terminal repeat sequences (group B

recombinants). The special structureoftherecombinants in

this group necessitated adifferent cloningstrategy. We were unabletoclone the entire recombinant genome inaplasmid,

sinceall of therestrictionenzymesthatweretried either did not digest the recombinant DNAor digested the DNAinto

small fragments (Fig. 1 to4). Therefore, we focusedonthe cloning ofrepeat units which contain the SV40-AAV junc-tions. Hindlll-Hindlll fragments of recombinants 16 (771

bp) and 40(886 bp) (Fig. 7) were inserted into theHindIll site ofpBR322. The two 32P-labeled constructs containing

the recombinant DNAs hybridized to both terminal

seg-ments C (nucleotides 1 to425) and D (nucleotides 4255 to

4675) ofPstI-digested AAV DNA (13), indicating that the inserts carry the AAV terminal repeat; 32P-labeled

recombi-nant 16also hybridized to segment A (nucleotides 1959 to


b c









FIG. 4. Restriction analysis (before cloning) ofSV40-AAV re-combinantDNAsofgroup B. DNAofisolates 5(atoc),16(dtof), 38(g toi),and 40( to1),eitherundigestedordigestedwithHindlll (cutsonly in the SV40 segment of the recombinant) orBalI (cuts onlyin AAV sequences), respectively.The DNAwasfractionated on1%agarosegel, transferredtonitrocellulose,andhybridizedwith

32P-labeled PstI D segment of AAV (nucleotides 4259 to 4675). HindIll andBalIcreated thesamesize fragmentsin isolates5, 16, and 40, indicating a tandem repeat structure. Isolate 38 DNA contains several sitesforHindllI orBalI,butapparentlythe units are notarrangedin tandem.


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[image:4.612.] [image:4.612.320.555.382.622.2]

4254). Schematic maps of the cloned repeat units are pre-sented in Fig. 7.

Sequenceanalysisof theSV40-AAVjunctions of recombinants 16 and 40. The repeat units of isolates 16 and 40 were inserted into the


site of pBR322. Dideoxynucleotide sequencing (30) Qf the double-stranded template inpBR322

was done according to Smith et al. (36), with pBR322


and EcoRI primers obtained from New England BioLabs. For addition sequencing in M13, the inserts were recloned in the Mp9 vector(HindIII-PstIfragment of recom-binant 16 and the HindIII-BalIfragment of recombinant 40; Fig. 7). The full nucleotide sequences of the repeated units were determined (771 and 886 bp for recombinants 16 and 40, respectively). The sequences of the junctions are shown in Fig. 8A, and several features of note can be summarized as follows. (i) In the two recombinants examined in each repetitive unit, the AAV sequences were inserted as one block, and in each case one of the junctions was within the inverted repeat (AAV nucleotide position 4591 in recombi-nant 16 and nucleotide 4604 [38] in recombirecombi-nant 40 [Fig. 8A; junctions 16-1 and40-1]). (ii) A portion of the AAV inverted repeat sequences was inserted into the SV40 genome near the SV40 origin of replication. (iii) The recombinant junc-tions in recombinant 16 were not identical with those in recombinant 40 with respect to either the SV40 or AAV sequence at the crossover points. (iv) In all four junctions, one or two bases were common to the parental DNAs. (v) A

small palindromic structure could be drawn for the AAV sequences at the secondjunction in each recombinant (Fig. 8B; junctions 16-2 and 40-2). (vi) The crossover point at junction 40-1 was within a pentanucleotide (CTTTG) in the AAV sequence that overlapped the same pentanucleotide in the SV40 sequence just to the right of crossover. Junction 16-1 was flanked by three complementary bases to the left in the AAV sequence and five complementary bases to the right in theSV40sequence (Fig. 8A). Otherregions of direct or complementation homology between SV40 and AAV DNAs (5 to 10 nucleotides) were located within 35 nucleo-tides on either side of the crossover points in all four junctions (not shown in Fig. 8A). The significance of these


is discussed below.


TheSV40-AAV recombinants classified as group A type, which arose from cells either cotransfected withSV40 and AAV DNAs (recombinant 4) or coinfected with SV40 and

AAV virions (recombinant 22), resemble the SV40-4X174 simple insertion-deletion type described previously (41) in that they contained single AAV inserts (derived from any part of the authentic AAV genome), the deletion ofSV40

DNA was larger than the insert, and at least 70% of the

wild-type SV40 DNA was retained in the recombinant. SV40-AAV recombinant 4 contained one additional SV40

replication origin linked to the AAV insert. In contrast, a different picture emerged after analyzing the structure of the

recombinants of group B. The six recombinants from this group were composed of repeating units which contained SV40 and AAV segments. Other than the origin of replica-tion, very little of theSV40genome was retained, and both

the segment that was retained and the inserted AAV

se-quences were duplicated several times. All of the recombi-nants of group B contained terminal sequences of the AAV genome and were isolated from virion coinfection

experi-ments. Previously, we have shown that, after SV40 and AAV coinfection, more than 90% of the recombinants

con-X ^ > d e



IA lw




--- 76



FIG. 5. Restriction mapping of SV40-AAV recombinant DNA derived from isolate 4 and cloned inEcoRI site ofplasmid Bd1H. Lanes: a,undigested DNA; b toj, DNAdigested withSmaI,EcoRI,

KpnI, Nael, BamHI plus Sall, BglI, SphI, HindIII, and TaqI,

respectively. Note that BgIl, HindIIl, and SphI, which cut in the SV40origin region and do not cut AAV in segment A(seethetext), create a fragment of 1,400 bp which contains the AAV sequences (suggestingaduplication oftheSV40replicationoriginregion). The numbers to the right indicate sizemarkers.

tained AAV terminal sequences (13). This was observed even when AAV infection preceded SV40 infection by as

long as 10 days. In contrast, no overrepresentation of terminal sequences was observed inrecombinants generated

after DNAcotransfection. Similarly, after DNA cotransfec-tion withcircular SV40 DNA andcircular



form I DNA (11, 12), with circular SV40 DNA and


replicative form I DNA linearized at the single PstI



with pBR322 plasmids containing AAV segments, it has been shown that all'parts of the AAV or 4X174 genomes were equallyrepresented inthe population of recombinants (13). Hence, in general, with regard to cotransfection, DNA sequences located at a free end possess no obvious

advan-tage in recombination with circularSV40 DNA.

Delivery ofviral genomes into the cell as virions doesnot

necessarily dictate recombinant structures of the group B type. Recombinants isolated frommousecells after coinfec-tion ofpolyomavirus and SV40 virus belong togroup A, as

do recombinants derived from DNA cotransfection

experi-ments (Z. Grossman, unpublished


Also, recombinant

22, cited above, which was derived from AAV-SV40 covirion infection, belongs to group A. Importantly, only recombinants that were derived from virion coinfection of SV40 and AAV and which contained the AAV terminal

sequences exhibited the' group B-type structure. Over-representation of the AAV terminal sequences and' the repetitive structure may be related to certain features of the AAVgenome when it is delivered to the cell in virions. The AAV genome in the virion is a linear, single-stranded DNA molecule that contains an inverted terminalrepetitionof 145

bases, the first 125 of which are palindromic and capable of forming a hairpin structure (1). One possibility is that inser-tion of the AAV palindromic inverted terminal repeat near

the SV40 origin of replication triggers a special mode of

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SV40/AAV Rec. 22






J _.v ,,,-4 Ldl-__ _

I*- dl 9

SV40/AVV Rec.4









-WT SV40

EcoR I B Bc P T X

II I~~~~~~~~~

3000 4000

early 0

1000 1782



late - 0

FIG. 6. Schematic structures of two SV40-AAV recombinant (Rec.) genomes belonging to group A. The maps of recombinant DNAs 4 and 22 aredrawnrelativetothatof thewild-type(WT) SV40genomeandarebased on data from restriction cleavage blot hybridization (see the text). The shadedboxesdenoteAAVinserts, the solid box denotes the duplicated area containing the SV40 replicationorigin,the open boxes denote SV40DNAsequences, and dl refers to the deletion of SV40DNA sequences. This deletion is greater than the AAV insert; as a consequence, the recombinant genomesareshorterthantheSV40WTgenomebyanamountcorresponding to the dashed lines (the size order isWT>4 >22).TheWTSV40 map also showsthe sites of the restriction enzymes used to analyze the structures ofrecombinant genomes. Symbols: B, BamHI; Bc,Bcl; j,BglI;


HindIII; p,HinflII; H, HpaII; N,NaeI;; 9, Neo;X, Nde; 9,SphI;P,PstI;T, PvuII; +, TaqI.

replication, leading to the structure observed for group B structuri

recombinants. Normally, SV40 replication occurs via that des Cairns-type theta structures (32). The tandem repeats of recomb group Brecombinants may arise by arolling-circle mode of coritaini

replicationsuch as has been suggested to occur late during 4X174r

SV40 DNA replication (26) and which has been shown to frequen(

occurwhenlinear forms oforigin-containing SV40DNA are which a

transfected into monkey cells (9). Moreover, the reiterated SV40DI


14 -617bp-4 1 l -617b

201 4828

Bal 4334 1-270bp-'4

201 4828

4604Bal 4334 l*-270bp-l

re ofSV40-AAV groupB recombinants is similarto



for a


class of


inants which arise when linear SV40


DNA is cotransfected with circular SV40 and


formI DNAs


theseconditions, the

zy of


recombination is





to resultfrom the entry of the linear INAintoanaberrantrolling-circletype of


ip s

I 201 4828

. . I



4604'al 4334

1--270bp*1 Rec.40

f,-- 771bp i

I.-362bp-4 16-362 bp-l4

4926 9 44 4926 9 44

4182 4591 '41 82


!,- 410bp-I4

4591 '41-82


Rec. 16

FIG. 7. Schematicstructuresof theSV40-AAVrepeatunits of recombinants (Rec.) 16and40.Themapsof therepeatunitsfrom isolates 16and40arederivedfrom restrictioncleavage blot hybridization and nucleotide sequencing. The solid boxes denotetheSV40duplicated area,including the originofreplication.The shaded boxes denoteAAVinserts. Therepeatunit(771bp)ofisolate16wasreclonedinto the

HindIII site ofpBR322,as wastherepeat unitofisolate 40 (886 bp). Upper numbers denotetheSV40nucleotidesatSV40-AAV junctions; lowernumbersdenoteAAVnucleotides.The 771-bprepeatunitfrom isolate16consistsof410bpofAAV(nucleotides 4182to4591)and362 bpofSV40 (nucleotides4926to44).Therepeatunitfrom isolate40(886 bp)iscomposedof270bpof AAV (nucleotides 4334to4604)and 617bp ofSV40 (nucleotides4828to201). Symbols: 9,HindIII;P, PstI; i,BglI; Bal,BalI.









1- 886bp *886bp

4926 9

4 . A

ZZZZO0, I .__y





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40 44



4592 4586

4926 4930

SV40: ACCTCAGTTG_******** *


4190 4182 200202



4604 4602

4828 4835


SV40: ACAGCAAGCA[ ]** * *** * **


4340 4334 T T T C-G C-G A-T G*C C*G G*C G*C C-GGCCT G-CCGGA C-G G-C G*C G*C C*G C*G C*G G-C AA A 16/1 T / -T c A-T A*T AT C-G AG*C AG.CG G-CAC 16/2 \ C-G CoG A-T G-C C G G-C G&C G-C Co GGC CT

A *aas .


G*CCGGA C-G G*C G*C G-C C*G C G C G G*C A A A 40/1 cc T*A G*C GTAG A.T


CAT*AGT 40/2

FIG. 8. Sequenceof theSV40-AAV junctionsintherepeat units of recombinants 16 and 40. Nucleotidesequencesweredetermined accordingtothedideoxynucleotidemethod ofSangeretal.(30).The nucleotidesequencesof thecompleterepeat unitsweredetermined and are schematically summarized in Fig. 7. (A) The nucleotide sequencesof theparentalSV40and AAV DNAsarecomparedwith that of the recombinant DNA. The recombinant nucleotides are

written in boldface. Noteone ortwoshared bases in alljunctions. Asterisks denote nucleotides identicaltothose in the recombinant. (B) Secondarystructureof the AAVsequencesneartheSV40-AAV junctions. The arrows designate crossover points. In 40-1, the

sequenceatthejointwasslightly ambiguouswith respecttowhich of the two nucleotides indicated by the arrows represented the actualcrossoverpoint.Note that the AAVsequencesrepresent the 5'to3'complementsof thosereported bySrivastavaetal.(38).The terminalpalindromicsequenceinthe inverted repeatattherightend of the AAV 2genome extends from nucleotide 4551to nucleotide 4675. Only the internal portion of this sequence from nucleotide 4588tonucleotide 4638 is illustrated in the 16-1 and 40-1junctions.

(11). Possibly, the SV40origin regionor the AAV terminal repeat in the conformation in which it is released from the

virion,orboth, predisposetorecombinationinoradjacentto theoriginofreplicationinacircularSV40moleculeand, by

so doing, trigger a undirectional mode of DNA synthesis,

leading to a rolling-circle intermediate as opposed to the

more usual theta-type structures. It is not known whether therelatively specific site of therecombinationevent orthe presence of AAV terminal sequences at the joint in the recombinant is the critical factor leading to the tandem

structure. Inthisrespect, itwillbeof interesttoanalyzethe structureof thoseSV40-AAVrecombinantscontainingAAV

terminal sequences which arise from DNA cotransfectionto see ifthey tooexhibitareiterated structure.

Thedifference instructurebetween group A and B

recom-binants raises thequestionof whether botharethe results of

equivalent initial recombination events. The similarity in

kinetics and dependence on initial DNA concentrations observed after both cotransfectionand coinfection(13) sug-gestequivalence,eventhoughthestructuresof these

recom-binants are


different. Many


cycles of the recombinant molecules take place before the

recombi-nant is isolated, cloned, and




the infectious-center assay detects


those recombinant

structures which retaina functional SV40



replica-tion and which are of the right size to be encapsidated. Although there is no reason to assume that the conditions

required for amplification of the group B structures are


different from those


for group A

struc-tures, it is not known to what extent the


and selected groups of recombinants represent the initial popu-lations of recombinantstructures.To examine this




DNA molecules within a few hours of coinfection or cotransfec-tion and tocharacterize the spectrum of recombinant struc-turesthatarefound.

The fourSV40-AAV


that were


mani-fest some


features. The AAV terminal

palin-drome was inserted


nearthe SV40




as if it were a


site for recombination. This may reflect the more open


of this



transcriptional complexes (31).



were notidentical with respecttothe SV40 nucle-otidesorAAVnucleotides involved atthecrossover




of the AAV terminal inverted repeat was

involved in the two recombinants


and a small


could beformedatthe second end of the AAV insert (junctions 16-2 and40-2). Theseresults may






structureofthe DNAnearthe





recombination. Short


(5to 10





AAVDNAs wereobservedat or nearthecrossover





short, homologous



appears to be






with nucleotide


tests indicate that


appearwithtwice the

frequency expected

on a


random basis

(D. Dorsett,



and E.


unpublished data).ThefourSV40-AAV

junctions sequenced

thus share some features which fit the



modelofGutaiand Nathans


andwhicharein agreement with the analyses of Bullock et al. (5) of



DNA-host cell DNA


Six of the seven group B recombinants contain the


terminus of the AAVgenome. Whether this is


is unclear. If the biaswere




suggest some


property ofthe


end of the genome. A similar

on November 10, 2019 by guest




representation of right terminal sequences was noted in

AAV-defective interfering particle genomes (33).

Of special interest is the resemblance of the structure of thegroup B recombinants to the structure of the integrated

copies of the AAV genome found in latently infected cells (7). In the lattercase, thejunction between AAVDNA and cell DNA also involved the AAV terminal sequences, and

the integrated viral DNAwaspresentas alinear head-to-tail tandem repeat. The terminal repeat has been suggested to servenotonlyarole in integration butalso tofunction asa primer for DNA replication (1, 38). The AAV genome has recently been cloned into pBR322 (28) as a biologically activemolecule, sothat ithasbeen possible tocharacterize the requirements for the terminal sequences. Three points

have emerged from these studies. (i) The sequence is re-quiredforrescue orreplication from the integrated state or both(20,29,34). (ii) Thesequencehasanextensive capacity

forselfrepair (29, 34). (iii) As longasthe overall conforma-tion ofthe terminalstructureismaintained,thesequence can be discretelyaltered without loss ofbiologicalactivity (22).


We thank Tamar Koch and Bernard Danovitch for technical assistanceand Rachel Ben-Levyfor helpwiththe DNA sequencing. We alsothankDale Dorsett and Yosef Shaul for their valuable advice

and helpwith thecomputeranalysis of DNAsequences.

Partofthis work was supported by U.S.Public Health Service



22251from theNational Institutesof Health. LITERATURECITED

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on November 10, 2019 by guest



FIG.1.combinantproducingtransferredAAVundigestedwithintively.withundigestedexposednatesSV40stainRestriction mapping,before cloning, of SV40-AAVre-DNAinisolatesderivedfromsinglerecombinant-cells.DNAsof isolates4and5(seethetext),eitheror digested with restri
FIG.2.electrophoresis,T,arethanSV40-AAVisolatesisolate Pvull;Retention of SV40sequencesin SV40-AAVrecombinants
FIG. 3.40.4675).enzymesdigestedizeddesignateSV40(A)tovirusOnlywere completion. Restriction mapping (before cloning) of isolates 38 and DNAs of isolates 38 and 40 were digested with restriction and fractionated on agarose gels, and the blot was hybrid- with
Fig. 8A,follows.repetitive


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