J. Mol. Biol. (1977) 112, 495-507

Detection of Long-range Sequence Order in Drosophila melanogaster Satellite D N A IV by a Photochemical Crosslinldng

Reaction and Denaturation Microscopy

Satellite DNA IV of Drosophila melanogaster has been isolated in an aetinomycin/ CsCI gradient and allowed to react with tritium-labeled 4,5',8-trimethylpsoralen (trioxsalen) in the presence of long wavelength ultraviolet light. Saturation experiments showed a limiting covalent binding of approximately one trioxsalen molecule per three base-pairs for the photochemical reaction. The buoyant density change of satellite IV (p = 1.705 g/cm s) after photoreaetion was found to be --0-182 (g/em3)/(trioxsalen/base.pair). To visualize directly the interstrand crosslinks, the photoehemically reacted satellite DNA was denatured and spread for electron microscopy. From 85% to 90% of the molecules examined have an appearance of long stretches of tandem loops with few observable double- stranded regions. The histogram of loop sizes in these denatured molecules shows a regular distribution of erosslinkable sites along satellite DNA IV with an interval of approximately 250 base-pairs, suggesting that a long-range periodicity of sequences exists in this satellite DNA. After extensive crosslinking, the observed loops still have sizes that are multiples of 250 base-pairs. These results are discussed in terms of the sequence of satellite DNA IV, the characteristics of the photochemical reaction, and theories of evolution of satellite DNA sequences.

To understand the evolution and function of satellite DNAs, detailed analysis of their sequence organization is essential (for a general review of satellite DNA, see Walker, 1971; Tartof, 1975). In Drosophila melanogaster nuclei there are four satellite DNA sequences tha t can be resolved and isolated in a var ie ty of density gradients (Trava- glini et at., 1968; Rae, 1970; Blumenfeld & Forrest, 1971; Gall et al., 1971; Peacock et al., 1973; Hears t et al., 1974; Endow et al., 1975; Shen et al., 1976). These satellite DNAs have been designated satellite I, I I , I I I and IV (Endow et al., 1975) in the order of their increasing buoyant densities in neutral CsCl: 1.672, 1.686, 1-688 and 1.705 g/cm 3, respectively. The sequences of satellite I, I I and IV have been analyzed by pyrimidine t rac t analysis (Peacock et al., 1973) and by a direct sequencing technique (Brutlag & Peacock, 1975; Endow et al., 1975). Unusually long pyrimidine tracts, ranging from 100 to over 1000 nucleotides in length, with a weight average molecular weight of 750 nucleotides, have been found and isolated from D. melanogaster by hydrolyzing its total DNA with formic aeid/diphenylamine (Birnboim et al., 1975; Birnboim & Sederoff, 1975; Sederoff et al., 1975). Over 90% of the polypyrimidines are derived from a specific region of different buoyant density from tha t of the bulk of the DNA. Birnboim & Sederoff (1975) concluded tha t the polypyrimidine/polypurine segments are clustered on the genome in sequences a t least 20,000 base-pairs long, and t ha t the polypyrimidines are on one s t rand with an occasional purine or group of purines. They observed an average of 33 purines for every 1000 pyrimidines in the pyrimidine-rich strand. All lines of evidence regarding the sequence and other properties of satellite DNA IV and the long polypyrimidine sequences suggest t ha t these two species axe derived from the same segments of DNA on the D. raelanogaster

495

496 C . - K . J . SHEN AND J . E . HEARST

genome. (1) They have similar buoyant densities in neutral CsC1 density gradients. (2) The major sequences in these two DNA components are

5' A-A-G 3' 5' A-G 3' G • . . , . . , and . .

3' T - T - C 5' 3' T-C 5' C

(3) Hybridization in situ showed that these two species are localized to the same positions on either metaphase chromosomes or polytene chromosomes of D. melano- gaster (Goldring et al., 1975 ; Sederoff et al., 1975).

Information about the evolution of satellite DNA IV may be obtained by a thorough understanding of the distribution of the purine residues on the polypyrimidine strand or tha t of the pyrimidines on the polypurine strand. We have used 4, 5', 8-trimethyl- psoralen (trioxsalen) to photochemically crosslink purified satellite DNA IV. As a result of its planar structure, psoralen can intercalate between the base-pairs of the DNA double helix (Dall'Aequa & Rodighiero, 1966) and, upon irradiation with long wavelength ultraviolet light (320 to 380 nm), cyclobutane bridges form between the 3, 4 or 4', 5' double bonds of the psoralen and the 5, 6 double bond of an adjacent pyrimidine base (Musajo et al., 1967). I t has also been reported that if the initial pyrimidine is added to the 4', 5' double bond of psoralen, a second pyrimidine can react eovalently with the 3, 4-psoralen double bond (Dall'Acqua et al., 1971). Thus, a covalent interstrand bridge forms when psoralen intercalates between two base-pairs (Cole, 1970,1971) in which the two pyrimidines are on opposite strands. These covalent interstrand crosslinks can be observed directly by completely denaturing the cross- linked DNA and then spreading it for electron microscopy. Non-crosslinked regions of the DNA appear as loops, while the positions of the interstrand bridges are deter- mined from the crossing points of the two strands of DNA. Examination of the cross- linking sites on satellite DNA IV has revealed the positions of the purines on the polypyrimidine strand or conversely the pyrimidines on the polypurine strand. We will show that the positions of most of the purines on the polypyrimidine strand are not random but occur between regular intervals of 250±50 pyridimides.

In order to purify satellite DNA IV, D. melanogaster DNA at a concentration of 120/~g/ml was centrifuged at 42,000 revs/min with an initial actinomycin D con- centration of 40 ~g/ml in a CsC1 solution of density 1.65 g/cm 3. After equilibrium was attained, the DNA solution was fractionated and the absorbance at 260 nm was measured for each fraction. The profile of A266nm (Fig. 1) is similar to tha t obtained by Peacock et al. (1973). The heavy peak at fractions 12 to 14 was pooled, extracted with n-butyl alcohol, and dialyzed against 0.01 M-Tris .HC1 (pH 8.0), 0.001 M-EDTA. This DNA component has a density of 1.705 g/cm 3 in neutral CsC1 density gradients (Fig. 2(a)). When banded in an alkaline CsC1 gradient (Fig. 2(b)), the two DNA strands separate with buoyant densities of 1.757 g/cm 3 and 1.750 g/cm 3 for the heavy and light strand, respectively. On the basis of its position in the actinomycin D/CsC1 density gradient, its buoyant density in neutral CsC1, and its strand separability in alkaline CsC1, it is concluded that the DNA component we have isolated is identical to the 1.705 g/cm 3 satellite DNA (Peacock et al., 1973) or satellite DNA IV (Endow et al., 1975) reported before. However, the possibility is not excluded tha t the satellite DNA IV we have is contaminated by a small amount ( < 10 %) of other D. melanogaster DNA sequences.

The isolated satellite DlqA IV was then allowed to react with [3H]trioxsalen. Since

L E T T E R S TO T H E E D I T O R 497

].2

I-I

I'0

0'9

o 0.8

0"7

0"6

~ 0"5 .Q <

0'4

0"5

0.2

0'1

i

0 2 4 6 8 I0 12 14 16 18 20 22 24 26 28 30

Frochon number

Fro. 1. Equilibrium profile of total nuclear DNA of D. rnelanogastcr in a preparative actinomycin D]CsC1 density gradient. D. melanogastcr DNA was isolated from 20 to 24-h old embryos as des- cribed previously (Hearst e¢ al., 1974), except tha t the purified nuclei suspended in 0.5 ~ -EDTA {pH 9.5} were first incubated at 50°C for 1 h in the presence of 0.1% Sarkosyl (Geigy) and 1 mg RNase]ml (Calbiochem; pancreatic, pretreated in 0.1 M-Tris.HC1 (pH 7-0) at 100°C for 10 min). Then 25 ml of 3 mg purified D. melanogaster DNA/ml was mixed with 1 ml of 1 mg actinomycin D (Calbiochem)]ml in 0"01 M-Tris.HC1 (pH 8.0), 0.001 M-EDTA, and 15 ml of 0.01 ~-Tris.HC1 (pH 8.0), 0.001 M-EDTA. 44.8 g of CsC1 (Reliable Chem. Co., technical grade) was added and the solu- tion was shaken at room temperature. After 10 rain, the solution was ultracentrifuged in a Ti60 rotor at 42,000 revs/min for 72 h at 20°C.

( o ) Total D rne/onogoster DNA 1.701

Achnomycm D/CsCI gradient 12-14 regK)n

1"705 j

(b) 1,750 1"757 1"789

FIG. 2. Equilibrium profiles of D. melanogaster DNAs in the model E analytical ultracentrifuge. Buoyant densities of DNA in neutral CsC1 were determined according to Hearst & Schmid (1973). Micrococcus lysodeikticus DNA with a buoyant density of 1.733 g/cm 8 was used as a marker and a buoyant gradient constant of 9.35 × 10-lo g s~/cm 5 was used to calculate the buoyant densities. The alkaline CsC1 gradients were performed according to Peacock e¢ al. (1973). Buoyant densities were calculated relative to the marker M. lysodeikticus DNA which has a buoyant density of 1.789 g/cm s in alkaline CsCI density gradients. (a) Total D. melanogaster DNA and satellite DNA IV in neutral CsC1 density gradients. (b) Satellite DNA IV in an alkaline CsC1 density gradient.

498 C . - K . J . S H E N AND J . E . H E A R S T

the photoreac t ion be tween DNA and t r ioxsalen as well as the photodes t ruc t ion of

t r ioxsalen itself occurs dur ing the i r radia t ion (Wiesehahn et al., 1977; Isaaes et al.,

1977), i t is no t possible to achieve the sa tu ra t ion level of covalent b ind ing of t r ioxsalen

to DNA with only one addi t ion of the compound, even if the i r radia t ion is allowed to

cont inue for a long time. The m a x i m u m a m o u n t of t r ioxsalen t h a t can b ind covalent ly to satelli te DNA IV was de te rmined by i r rad ia t ing several samples o f the satell i te for

different t imes wi th repeated addi t ions of [3H]trioxsalen (2 /~g/ml) a t in tervals of 20 minutes . The results are shown in Figure 3. I t is observed t h a t a sa tu ra t ion level

is achieved after six addi t ions of t r ioxsalen and two hours of i r radiat ion. The l imi t ing

value of covalent b ind ing is one t r ioxsalen molecule for every two to four base-pairs.

4 0

35 o

c 30

~ 25

-~ 2c 8 o

D

2 .3 4 5 6 7

Number of odditione

Fie. 3. Covalent binding of 4,5',8-trimethylpsoralen to the satellite DNA IV of D. melanogaster. Purified satellite DNA IV was adjusted to a final eoncn of 10 ~g/ml in SSC (SSC is 0-15 M-NaC1, 0.015 M-sodium citrate, pH 8.0). Four portions of this solution were irradiated in the apparatus described by Wiesehahn et al. (1977) for 20, 60, 120 and 140 min with successive additions of 2 ~g [3H]trioxsalen/ml (Isaacs st al., 1977; spec. act. 63,000 cts/min per/~g) at intervals of 20 min. The intensity incident upon the samples between 320 nm and 410 nm was 25 mW/cm 2. After irradiation, the DNA samples were extracted twice with an equal volume of a chloroform/isoamyl alcohol mixture (24:1) and dialyzed against 0.01 M-Tris.HC1 (pH 8"0), 0-001 M-EDTA for 36 h with 3 changes of the buffer. This procedure is sufficient to remove more than 99% of the radio- activity in either a non-irradiated (DNA + [aH]trioxsalen) solution or a solution of 20 ~g [3H]- trioxsalen/ml in SSC alone that has been irradiated for 2 h. After dialysis, the radioactivity per unit volume was determined by counting 50 ~1 of the irradiated solutions in a scintillation fluid consisting of 1 ml water and 10 ml of a mixture of 1 1 Triton Xl00 (Rohm & Haas), 2 1 toluene (Mallinekrodt Chemical Works), and 12 g Omnifluor (New England Nuclear). The spec. act. of the [3H]trioxsalen has been determined in the same fluid. The amount of trioxsalen bound eovalently per mol base-pairs was determined from the absorbance of the solution at 260 nm and the radio- activity/unit volume.

Crosslinked DNA samples with one, three and seven addi t ions of t r ioxsalen were analyzed in the ul t racentr i fuge for their densit ies in neu t r a l CsC1. I t was found t h a t

the b u o y a n t dens i ty of satelli te D N A IV decreases u p o n covalent b ind ing of tr ioxsalen,

with values of 1-697, 1.663 and 1-646 g/cm 3 for each of the above three samples,

respectively. The plot of the b u o y a n t densities versus the a m o u n t of covalent ly bound t r ioxsalen per base-pair is a s t ra ight l ine (Fig. 4) with a slope of --0.182 (g/cm3)/(tri-

oxsalen/base-pair) .

LETTERS TO THE EDITOR

1.710 t

1.700

1-690

$ 1.680

~ 1.670

1.660 g m

1.650

1.640

499

0 0.10 0.20 0.30

Mol tnoxsalen bound/Mol bose-poirs

FIG. 4. Buoyant densities ofsatelllte DNA IV as a function of the amount of trioxsalen covalently bound per mol base-pairs. The least-squares method has been used to establish the linear plot.

Samples of satellite DNA IV tha t have reacted with trioxsalen to different extents were denatured at 37°C in 7 0 ~ formamide, 1.8 ~o formaldehyde and spread for electron microscopy (for details, see the legend to Fig. 5). The 37°C (formaldehyde ~ form- amide) denaturation has two advantages when it is compared to the 70°C (formalde- hyde alone) technique (Hanson et al., 1976) and the 37°C (glyoxal ~ formamide) method (Cech & Pardue, 1976): first, incubation at 37°C introduces fewer single- strand breaks than incubation at 70°C; secondly, formaldehyde reacts with all four bases (for a recent review, see McGhee & yon Hippel, 1975), while glyoxal reacts predominantly with guanine residues in nucleic acids (Hsu et al., 1973) and may result in incomplete denaturation of a simple sequence DNA.

When native satellite DNA IV was treated in this way, more than 95~/o of the molecules on the grids appeared as single-stranded DNA, indicating extensive strand separation for the non-crosslinked DNA molecules. On the other hand, the crosslinbed samples have completely different denaturation patterns. After denaturation, the majori ty of the crosslinked satellite DNA IV was found to consist of loops tandemly arranged on the molecules with very few double-stranded regions interspersed between the loops. At a binding ratio (r) of 0.04 trioxsalen molecules per base-pair, 20~/o to 30°/o of the molecules are single-stranded, while the rest are looped molecules (Fig. 5(a) and (b)) with the loop sizes ranging from less than a hundred to thousands of nucleotides. Decrease of the average size of the loops was observed when samples with higher binding ratios (0.21 and 0.33 trioxsalen molecules per base-pair, respec- tively) were spread under the denaturing conditions (Fig. 5(c)). Molecules having loops interspersed by long double-stranded regions were seen with a low frequency (1 to 2~/o) in the samples of high binding ratios (Fig. 5(d)). These long double-stranded regions could represent some DNA sequences tha t are much more densely crosslinked by trioxsalen than the bulk of satellite DNA IV. Adjacent to these double-stranded segments are non-crosslinkable regions, possibly the polypyrimidine/polypurine DNA.

Using the denaturation microscopy assay, about 10 to 15% of the DNA molecules in this satellite DNA IV preparation were cross-linl~ed much faster than the other 85 to 90%, and appeared completely double-stranded in denatured samples with binding ratios of 0.21 and 0.33. They may come from contamination by other satellite DNA sequences of D. melanogaster in the actinomycin D/CsCI gradient, because

500 C . - K . J . S H E N A N D J . E . H E A R S T

, I 0 0 0 b a s e s

I000 bases

FZG. 5. (a) and (b)

L E T T E R S T O T H E E D I T O R 501

I000 bases i i , , l l

F,o. 5. (o)

502 C.-K. J . S H E N AND J. E. H E A R S T

( d )

I000 bases i , ,

FIe. 5. Electron micrographs and tracings of crosslinked and denatured satellite DNA IV samples. [3H]trioxsalen crosslinked DNA (10 pl) was mixed with 70 pl of 99% formamide (MC & B manu- facturing Chemists), 5/~1 of 37% formaldehyde (Brothers Chemical Co.), 10/~1 of 0.1 M-Tris .HC1

L E T T E R S TO T H E E D I T O R 503

12

8

4

(a)

I (b) m I

'il lJ I 0 500 I000 1500 2000 2500 3000

LOOp size (nucleotides)

Fzo. 6. Histograms of the loop sizes of the trioxsalen crosslinked and denatured satellite DNA IV. (a) r = 0.04; (b) r = 0.21; (c) r ~ 0.33 (see text). The loop size is the average length of the 2 strands. The variation in the lengths of the 2 strands is less than 10 % for most of the loops ( > 80 %) measured. Percentage of double-strandedness : (a) 4.1% ; (b) 5.1%; (c) 8-0%. Number average loop size (nucleotides) : (a) 912; (b) 532; (c) 520. Number of loops in the sample: (a) 189; (b) 114; (c) 388.

satell i te D N A I, I I and I I I all show complete double-s t randedness unde r these de-

n a t u r a t i o n condit ions after b ind ing of t r ioxsalen to extents of r > 0.20 (Shen & Hearst , unpub l i shed results). Al te rna t ive ly , there m a y be a different D N A t h a t has

the same b u o y a n t dens i ty in bo th neu t r a l CsCl a n d ac t inomyc in D/CsC1 gradients as

satellite DNA IV. To fur ther inves t iga te the d i s t r ibu t ion of t r ioxsalen crosslinking sites in satell i te

D N A IV, photographs of looped molecules were t a ke n from the three crosslinked,

dena tu red samples (r = 0.04, 0.21 and 0.33), an d the sizes of the loops a nd the double-

s t randed regions were measured. The lengths were cal ibrated agains t circular single.

(pH 8"0), 0"01 •-EDTA, and 5 ~1 of 25 ~g single-stranded circular fd DNA/ml. After heating at 37°C for 45 min, the DNA was spread by the formamide isodenaturing procedures (Davis e~ al., 1971). 20 F1 of the denatured sample was mixed with 30 ~1 of water, 10 ~1 of 1 M-Tris .HC1 (pH 8.2), 0-1 M-EDTA, 40 ~1 of 99% formamide, and 5 ~d of 1 mg cytochrome e/ml. Then 50 ~1 of this hyperphase was spread onto an 81 cm 2 h.~ophase containing 17% formamide and 0.01 M-Tris .HCl (pH 8-5), 0-001 M-EDTA. DNA was picked up on parlodion-coated copper grids (Pelco), stained in uranyl acetate, ~nd shadowed with 80% Pt/20% Pd. Grids were examined in a Philips electron microscope and lengths of DNA molecules were measured as described previously (Shen & Hearst, 1976). (a) and (b) r = 0-04; (c) and (d) r = 0.33 (see text).

33

504 C . - K . J. SHEN AND J. E. HEARST

stranded fd DNA. Figure 6 shows the loop size distributions of the three samples. I t also shows the double-strandedness and the number average loop size. Note tha t the 10 to 15% extensively crosslinked molecules mentioned above were not included in these measurements. The sample with r = 0.04 has a distribution of multiple peaks centered approximately at 250, 500, 750, 1000 nucleotides, etc. (Fig. 6(a)), suggesting that the crosslinking sites are regularly distributed in satellite DNA IV at intervals of 250 base-pairs. The tandemness of the basic units was supported by the fact tha t as r was increased to 0-21, the proportion of the larger loops decreased while tha t of the loops with sizes of 250 and 500 nucleotides increased (Fig. 6(b)). Interestingly, this bimodal distribution of loop sizes persists even at the saturation level of trioxsalen binding (r = 0.33), where a number average loop size of 520 nucleotides is obtained (Fig. 6(c)). Because of the resolution limit of the protein monolayer spreading tech- nique, however, it is not certain whether each crossing point results from only one crosshnk or whether some of the crossing points contain several crosslinks clustered within a short region that cannot be resolved in the electron microscope.

The above results demonstrated tha t trioxsalen can react covalently with D. melanogaster satellite DNA IV to a saturation level of one trioxsalen molecule per three base-pairs. Since the denaturation patterns of trioxsalen-saturated satellite DNA IV molecules showed mostly loops with a number average loop size of 520 nucleotides, only about 0"6% of the covalently bound trioxsalen exists in the form of interstrand crosslinks. This low fraction of crosslinks is very different from the result obtained when trioxsalen reacts with a complex DNA such as the mainband DNA of D. melanogaster, where at least 15~/o of the covalently bound molecules are interstrand diadducts (data not shown). The much lower proportion of crosslinl~s in satellite DNA IV results from the polypyrimidine/polypurine nature of satellite IV.

By remelting of renatured strands (Peacock et al., 1973; Endow et al., 1975) and from sequencing data (Brutlag & Peacock, 1975; Endow et al., 1975; S.ederoff et al., 1975), satellite DN.4 IV has been shown to be an homogeneous, highly repetitive DNA with less than 10% sequence heterogeneity. The major portion of this satellite is composed of a pentameric repeating unit

5' A-A-G-A-G 3' • • • • •

3' T-T-C-T-C 5'

This polypyrimidine/polypurine satellite DNA is most likely to have been generated by amplification of the short basic repeating unit through mechanisms such as saltatory replications which have been proposed for the evolution of satellite DNA (Walker, 1971). Our electron microscope data indicate tha t some sequence hetero- geneity, if not all, has been introduced into the homogeneous array of satellite IV during its evolution in a non-random fashion. One simple explanation for the occur- rence of trioxsalen crosslinking sites on satellite IV would be tha t the continuity of the polypyrimidine/polypurine was destroyed by base mutation, insertion, or other mechanisms that brought a purine or a short cluster of purines into the polypyrimi- dine strand. This would generate potentially crosslinkable sites on satellite DNA IV. According to the denaturation patterns of the trioxsalen-saturated sample, modifica- tion of the homogeneity of satellite DNA IV has occurred with a frequency of at least once for every 520 base-pairs. In fact, the weight average loop size (710 nucleotides) is very close to the weight average length of the polypyrimidines isolated from

L E T T E R S TO THE EDITOR 505

D. me ,negater (Birnboim & Sederoff, 1975). More importantly, most of the trioxsalen crosslinking sites have been introduced into satellite DNA IV in a non-random fashion, with regular intervals of 250 and 500 base-pairs. Thus a high order periodicity in the sequence of this satellite DNA exists.

From the distribution of cleavage sites of restriction enzyme EcoRI, Botchan (1974) has shown tha t bovine satellite DNA I consists of a basic repeating unit of 1400 ( t 5 0 ) base-pairs which is also internally repetitious. These results have been explained in terms of the evolution of the satellite DNA. Such long-range periodicity in satellite sequences has since been found in several eukaryotes by using restriction enzymes: guinea pig satellite I I I (HSrz et al., 1974), mouse satellite DNA (Southern, 1975) and D. me ,negater satellite DNA I H (Manteuil etal., 1975; Shen etal., 1976). We have treated satellites of D. me,negater with several different restriction enzymes and found tha t none of them cut satellite IV (Shen et al., 1976). The data presented in this s tudy indicate tha t satellite DNA IV may have evolved through two main stages. The first stage was the replication of the short repeating unit up to a length of 250 base-pairs; after sequence divergence including the insertion of purines at a single locus in the polypyrimidine, this 250 base-pairs-long unit was amplified to generate the long stretches of satellite IV. Alternatively, the purines could have been intro- duced into an original, perfectly repeating pentamer of pyrimidines and restricted by unknown mechanisms to positions every 250±50 base-pairs. During or after the above two stages, base mutations and/or unequal crossing-over could have occurred, intro- ducing more random heterogeneity into the array of satellite IV.

About 20 to 30O/o of the loops remain having a length of 500 nucleotides even after extensive cross]inking of satellite DNA IV. There is no indication that these loops are clustered on some of the molecules, while the 250 nucleotides-long loops are clustered on others. I f most of the trioxsalen crosslinking sites were generated in satellite IV with a uniform spacing of 250 base-pairs as suggested above, the "500- nucleotide loops" could occur as a result of the modification and/or elimination of some of the crosslinking sites. On the other hand, Dall 'Acqua etal. (1971) have reported tha t only when the first pyrimidine is added to the 4', 5' double bond of the psoralen is it possible for the absorption of a second photon to ~duce reaction with a second pyrimidine to form the pyrimidine-trioxsalen-pyrimidine diadducts. So if the trioxsa- len reacts with one pyrimidine at a crosslinking site at its 3, 4 double bond, the second pyrimidine on the opposite strand of the adjacent base-pair will not react with the compound and no crosslink is formed. The third possible mechanism for the blocking of the crosslinking sites is illustrated by Figure 7. Crosslinking could happen if trioxsalen intercalates into space b or c and then photoreacts with the pyrhnidines. However, if trioxsalen molecules get into spaces a and d, they are likely to block the crosslinking reactions at b, c either by preventing the intercalation of other trioxsalen molecules into spaces b, c (site exclusion mechanism, Crothers, 1968; La t t & Sober,

2 I I I I I I I I I

Pu Pu Pu Pu Py Pu Pu Pu Pu py py pyOpybpuCpydpy PY PY

_ _ _ I I I I I I I I I _ _ _

I 5

FIe. 7. Drawing of a satellite DNA IV segment in which a purine has been introduced into the polypyrimidine strand.

506 C.-K. J . SHEN AND J. E. HEARST

1968) or by reacting with the pyrimidines 1 and 3, leaving no more available reactive bonds on pyrimidines 1 and 3. Similar arguments can be made to explain the possible blocking of crosslinl~able sites where a short cluster of purines have been inserted into the polypyrimidine strand. I t is not possible a t present to make conclusions about what mechanisms are responsible for the appearance of the 500-nucleotide loops.

As can be seen in Figure 6(b) and (c), more than 2 0 ~ of the loops measured have loop sizes other than 2504-50 and 500-~50 nucleotides. This indicates either tha t a t least some of the base mutat ions have introduced purines into the polypyrimidine strand a t intervals different from 250:L50 base-pairs or t ha t unequal crossing-over events (Smith, 1976) have occurred in satellite IV tha t are out of register with respect to those crosslinkable sites spaced a t 250±50 base-pairs.

We thank Leroy F. Liu for his generous supply of fd DNA. This work was supported by the American Cancer Society grant no. NP-185, by the National Institutes of Health grant no. GMll l80 and by the National Science Foundation grant no. GB36799. One author (C.-K. J. S.) has been supported by the Earle C. Anthony Fellowship from the University of California.

Department of Chemistry University of California Berkeley, Calif. 94720, U.S.A.

C ~ - K u N JAMES SHEN JOHN E. HEARST

Received 25 October 1976, and in revised form 14 January 1977

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Birnboim, H. C. & Sederoff, R. R. (1975). Cell, 5, 173-181. Birnboim, H. C., Straus, N. A. & Sederoff, R. R. (1975). Biochemistry, 14, 1643-1647. Blumenfeld, M. & Forrest, H. S. (1971). Prec. Nat. Acad. Sci., U.S.A. 68, 3145-3149. Botchan, M. R. (1974). Nature (London), 251,288-292. Brutlag, D. L. & Peacock, W. J. (1975). In The Eukaryote Chromosome (Peacock, W. J.

& Brock, R. I)., eds), pp. 35-45, Australian National University Press, Canberra. Cech, T. R. & Pardue, M. L. (1976). Prec. Nat. Aead. ~ci., U.S.A. 73, 2644-2648. Cole, R. S. (1970). Biochim. Biophys. Acta, 217, 30-39. Cole, R. S. (1971). Biochim. Biophys. Acta, 254, 30-39. Crothers, D. M. (1968). Biopolymers, 6, 575-584. Dall'Aequa, R. & Rodighiero, G. (1966). Re. Accad. Naz. Lintel, 40, 411-422. Dall'Acqua, R., Marciani, S., Ciauatta, L. & Rodighiero, G. (1971). Z. Naturforsch. 26b,

561-569. Davis, R. W., Simon, M. & Davidson, N. (1971). In Methods in Enzymology (Grossman, L.

& Moldave, K., eds), pp. 413-428, Academic Press, New York. Endow, S. A., Polan, M. L. & Gall, J. G. (1975). J. Mol. Biol. 96, 665-692. Gall, J. G., Cohen, E. H. & Polan, M. L. (1971). Chromosoma, 33, 319-344. Goldring, E. S., Brutlag, D. L. & Peacock, W. J. (1975). In The Eukaryot~ Chromosome

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