Proc. Natl. Acad. Sci. USAVol. 82, pp. 3611-3615, June 1985Biochemistry

Crystal structure of Z-DNA without an alternatingpurine-pyrimidine sequence

(syn-ani conformation/ring pucker/intramolecular contacts/x-ray diffraction)

ANDREW H.-J. WANG*, REINHARD V. GESSNER*, Gus A. VAN DER MARELt, JACQUES H. VAN BOOMt,AND ALEXANDER RICH**Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; and tDepartment of Organic Chemistry, Gorlaeus Laboratory,University of Leiden, 2300 RA Leiden, The Netherlands

Contributed by Alexander Rich, February 8, 1985

ABSTRACT In left-handed Z-DNA, consecutive nucleo-tides along the chain alternate in the syn and anti conforma-tions. Purine residues form the syn conformation readily andup to now all Z-DNA crystal structures have sequences ofalternating purines and pyrimidines. However, we find thatd(C-G-A-T-C-G) with the cytosines brominated or methylatedon C-5 crystallizes as Z-DNA. The structure reveals thyminesin syn and adenines in anti conformations. This suggests thatZ-DNA may occur in sequences other than those with alternat-ing purine-pyrimidine sequence.

Double-helical DNA can exist both in right-handed and left-handed forms. The structure of right-handed B-DNA has beenknown since 1953 and an atomic resolution single-crystal x-raydiffraction analysis in 1979 showed that the DNA hexamerd(CpGpCpGpCpG) [(dC-dG)31 forms a left-handed helix calledZ-DNA (1). A variety of studies carried out on oligodeoxynu-cleotide single crystals (2-6) and on polynucleotides has shownthat Z-DNA can form in sequences with alternations ofpurinesand pyrimidines (see review in ref. 7). In the Z-DNA molecule,every other base adopts the syn conformation relative to thesugar, in contrast to B-DNA, where all of the bases are foundin the anti conformation. Purine nucleosides can adopt the synconformation as easily as they can adopt the anti conformation,while pyrimidine nucleosides do this less readily (8, 9). How-ever, we do not know whether pyrimidines can adopt the synconformation in DNA. It has been shown that negativesupercoiling can stabilize Z-DNA formation in plasmids (10,11). Studies of supercoiled plasmids suggested that segmentscan form Z-DNA without a strict alternation of purines andpyrimidines (12). Here we report that aDNA fragment with thesequence d(CpGpApTpCpG), where the cytosine residues aremodified either by methylation or bromination on the C-5position, crystallizes in the form of left-handed Z-DNA. Ex-amination of the crystal structure reveals that the two centralthymine residues adopt the syn conformation withintramolecular distances that are only slightly shorter than thoseseen with purine residues in the syn conformation. Two of thesix residues in this molecule no longer maintain an alternationof purines and pyrimidines and still it forms Z-DNA. Thissuggests that segments ofDNA may form left-handed Z-DNAwithout a strict adherence to the alternation of purines andpyrimidines. In addition, the presence of syn pyrimidines andanti purines in Z-DNA changes the external shape of themolecule.

Crystallization and Structure Solution

The oligonucleotides were synthesized by an improvedphosphate triester method in which either 5-bromo or 5-

methyl deoxycytidine nucleosides were used as the startingmaterial (13). The purity of the oligomers was found to be>95% as judged by HPLC analysis. The crystallizationmixture contained 2.3 mM oligonucleotide, 33 mM sodiumcacodylate buffer (pH 7.0), 25 mM magnesium chloride, 25mM cobalt hexamine trichloride, and 25 mM calcium chlo-ride. Cobalt hexamine was used as it is known to stabilizeZ-DNA formation (14, 15). Crystal formation was induced byusing vapor-phase equilibration by equilibrating with 25%2-methyl-2,4-pentanediol at room temperature. After 3 weekscrystals began to appear in highly twinned clusters with amoderate yellow color. A triangular plate was placed in aglass capillary surrounded by a droplet of mother liquor forx-ray analysis. The brominated hexamer crystal was found tobe orthorhombic with space group P212121 and cell dimen-sions a = 18.3, b = 31.1, and c = 44.1 A. The methylatedderivatives crystallized as small quasihexagonal rods withmaximum dimensions of 0.1 mm. The space group and celldimensions of the methylated derivative were very similar tothose of the brominated derivative. Because the crystalfragments of the brominated derivative were larger, theywere used for data collection on a Nicolet P3 diffractometerout to a resolution of 1.54 A using the o-scan mode. The totalnumber of observable reflections with an intensity greaterthan 1.5 o(I) was 2386. The cell dimensions of this crystalwere similar to those that have been observed in otherorthorhombic single crystals ofDNA hexamer duplexes andso a set oftrial coordinates from an appropriate sequence wasgenerated from the (dC-dG)3 crystal structure (1). TheKonnert-Hendrickson refinement method was used and thestructure was refined to a final R value of 19.3% (16). In thecourse of this refinement, 88 water molecules were identifiedsolvating the oligonucleotide fragment. Although the crystalshad a yellow color, the cobalt hexamine could not be locatedunambiguously in the final Fourier map.

The Backbone Conformation of Z-DNA Is Independent ofNucleotide Sequence

In order to form the Z-DNA conformation in this sequence,we expected the two thymine residues to adopt the synconformation. This might be accomplished through a signifi-cant modification of the Z-DNA backbone. Instead, thebackbone was similar to that seen in the initial (dC-dG)3structure (1) as well as in the structures found in thed(m5C-G-T-A-m5C-G) (6). It appears that the thymine resi-dues comfortably adopted a syn conformation in the struc-ture. However, the outer surface features of the Z-DNAmolecule looked somewhat different. In Z-DNA, unlikeB-DNA, the base pairs are on the outer surface of themolecule. In this molecule there are irregularities where thepurines are in the anti conformation and the pyrimidines insyn. This can be readily seen in Fig. 1, which shows van derWaals diagrams of (dC-dG)3 and d(br5C-G-A-T-br5C-G).

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d(CGCGCG) d( CGAT'CG)

FIG. 1. A van der Waals diagram showing the structure ofd(C-G-C-G-C-G) and of d(br5C-G-A-T-br5C-G). The molecules areshown just as they appear in the crystal lattice with three moleculesstacked upon each other along the c axis. There is a continuity ofbasestacking although every sixth phosphate group is missing along thebackbone. A solid line going from phosphate to phosphate groupillustrates the zigzag nature of the nucleotide backbone and thegroove between them is shaded. The arrows point to the protrudingthymine groups in the syn conformation; otherwise, the similarity ofthe two molecules is evident. The phosphorus atoms are drawn asdotted concentric circles, oxygen atoms are shaded with interruptedcircles, nitrogen atoms are shaded with fine stippled circles, thebromine atom is drawn with solid circles, and carbon atoms aredrawn with smaller concentric circles.

These each show three molecules of the double-helicalhexamer as they are found in the crystal lattice. Bothstructures have a continuity of base stacking, so the moleculeappears as if it formed a continuous double helix even thoughevery sixth phosphate group is missing as the molecules arehexanucleoside pentaphosphates. A major difference be-tween the two structures is illustrated by the thymineresidues in the syn conformation that project away from theaxis of the molecule (indicated by arrows in Fig. 1). Theadenine residues in the anti conformation are positionedsomewhat closer to the axis of the molecule producing asurface indentation. The change in the conformation of thesetwo bases thus produces a significant irregularity in theexternal contour of the DNA due to changes in base se-quence. This is quite at variance with B-DNA in whichchanges in nucleotide sequence produce little modification inthe external form of the molecule. There is also a significantchange in the distribution of electronegative nitrogen andoxygen atoms on the Z-DNA surface with syn pyrimidinesand anti purines.A more detailed view is shown in the stereo diagram of Fig.

2 in which the molecule is tilted 150 toward the reader so thatthe bases can all be seen. It is clear that the thymines are inthe syn conformation and adenines in anti. The adenineresidues are closer to the axis and the extent to which thethymine residues protrude can also be seen. Although theC-G base pairs are largely coplanar, the two A-T base pairshave dihedral angles of 110 and 120. It is not clear whether thisis intrinsic in the molecule or is a perturbation due to thebromine atom. The polarizable bromine atoms are seen tostack over the thymine rings and this may induce a slightchange in their orientation. The backbone of this Z-DNA

FIG. 2. A stereo diagram of the structure of d(br5C-G-A-T-br5C-G). Two molecules are seen in this diagram and the helical axis istipped 150 toward the viewer in order to show the disposition of thebases. The adenine residues in the anti position are very close to thehelical axis, while the thymine residues in the syn position areconsiderably removed. The COG base pairs are largely coplanar, butthere are 11° and 120 dihedral angles between the planes of theadenine and thymine residues.

molecule is similar to that seen in the (dC-dG)3 structure.Sugar rings along the chain have their 0-1' atoms orientedalternately either up or down as seen in all Z-DNA structures.

Changes in Base Stacking

In B-DNA the asymmetric unit is one nucleotide and thestacking between adjacent base pairs is somewhat similar, asthey lie over the helix axis of the molecule. Because there aretwo nucleotides in the asymmetric unit of Z-DNA, there aretwo different types of stacking interactions (7, 17). In the(dC-dG)3 crystal structure, CpG sequences were found to belargely sheared with the cytosines stacked over the cytosinesof the opposite strands and a rotation of only -9° betweenadjacent base pairs. In contrast to this, the GpC sequenceshad stacking between the bases on the same strand and a largerotation of -51° between each base pair (1).

Fig. 3 shows the stacking of successive base pairs in themolecule d(br5C-G-A-T-br5C-G). The nucleotides in the mol-ecule are numbered 1-6 along one strand and 7-12 along theother, so that br5Cl of one strand is hydrogen bonded to G12of the other. In Fig. 3a the base pair br5C1 G12 (solid lines)is shown projected over the base pair G2 br5C11 (open lines).The sequence ofthe molecules on the left strand is br5ClpG2.All of the molecules in the top row (Fig. 3a-c) have theconformation anti-p-syn for the dinucleotide sequence. Thisis in contrast to the second row (Fig. 3 d-f) in which themolecules have the sequence syn-p-anti in going from the 5'to 3' direction. The essential elements of the Z-DNA struc-ture are represented by the alternation of nucleoside confor-

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a b

(3--- T10

d

FIG. 3. Successive base pairs are viewed down the helix axis in order to show their stacking interactions. The base pair in solid lines is closerto the reader than the base pair drawn with open lines and the solid dot is the helical axis. The base pairs are identified by the symbols underthem, where C stands for br5C. Thus, in a the base pair br5C1 G12 lies above the base pair G2-br5C11. (a-c) Sequences in which the conformationis anti-p-syn, which means that the anti residue is on the 5' side of the phosphate and the residue in the syn conformation on the 3' side. (d-f)Sequences in which conformations are syn-p-anti. (f) The base pair G6 br5C7 as it stacks upon the base pair br5C1' G12' of the molecule below.

mations along the nucleotide chain rather than by the se-

quence of particular nucleotides.The three anti-p-syn sequences in the top row of Fig. 3 all

show a sheared orientation of the base pairs with somestacking in the center from opposite strands as described forthe (dC-dG)3 structure (1). These sequences pre also associ-ated with small changes in the twist angle. However, thereare some significant differences from the (dC-dG)3 due to theintroduction of thymine residues in syn and adenine residuesin anti conformation. Fig. 3 a and c show stacking inter-actions that are similar to those seen in the (dC-dG)3structure; the CpG base pairs are sheared so that the cytidineresidues stack over each other slightly in the center. Theguanine residues do not stack on bases but rather on the 0-1'atom of the furanose ring below them. However, in Fig. 3b,the two adenine residues in the anti conformation are foundto stack directly on top of each other with a greater stackinginteraction than that seen for the two central cytosineresidues in Fig. 3 a and c, while the thymine residues in Fig.3b are found to have very little stacking on one face. They arein weak van der Waals contact with the adjacent nucleotide,as the distance between the C-5' of adenosine and thethymine ring is near 3.5 A. It can also be seen that the bulkof the adenine ring is significantly closer to the axis of themolecule (solid dot) in Fig. 3b than are the cytosine rings inFig. 3 a and c, but the thymine rings are further away fromthe axis. The distances from the axis to the methyl group ofthe thymines T4 and T7 are 8.7 and 9.3 A, respectively. Theseatoms are the furthest removed from the axis of any baseatom in the molecule. In the (dC-dG)3 structure, the furthestbase atom was guanine C-8, which is 7.8 A away from the axis(15). However, ifa cytidine residue were in the syn conforma-tion, its apparent displacement would be less because of theabsence of the methyl group. The twist angles for the twobase pairs in Fig. 3 a and c are -13° and -12°, respectively,while for Fig. 3b it is just under -9°The lower row in Fig. 3 shows the stacking of the base pairs

in the syn-p-anti sequence. Fig. 3fshows the stacking of thebottom C-G base pair ofone hexamer molecule with the upperG-C base pair of the hexamer molecule immediately below.The stacking of the bases at this position between the twomolecules is indistinguishable from the stacking of the GpCresidues within (4C-dG)3. However, significant differencesare seen in the sequences involving the A-T base pairs. In Fig.3 d and e, the stacking is shown for segments in which twopyrimidines are on one strand and two purines on the other.There is somewhat less stacking ofbases over each other thanis found in the GpC sequences of (dC-dG)3, which is similar

to Fig. 3f. The cytosine and thymine residues do not stackupon each other directly but T4 lies on top of the bromineatom of the C-5 residue (Fig. 3e), and the bromine atom ofC-li overlays T10 (Fig. 3d). Similarly, there is little stackingseen between the two purines G2 and A3 (Fig. 3d) and A9 andG8 (Fig. 3e). There is significantly less base stacking in thesyn-p-anti sequences. The twist angles of all of the sequencesare very similar to each other, averaging -49°

syn Conformation of Pyrimidine Nucleotides

All of the nucleotides in right-handed B-DNA are in the anticonformation while in Z-DNA every other base is in the synconformation (1). Purines are believed to form the synconformation with little strain and this fits with the observa-tion that Z-DNA formation is favored by sequences withalternations of purines and pyrimidines (7). The presentstructure shows that a Z-DNA conformation can form evenif the nucleotide sequences are out of alternation. Theconformation of several nucleotides in this structure is shownin Fig. 4, which illustrates the orientation of the furanose ringrelative to the base. The column on the left has syn nucleo-tides, including the two thymine residues, while the columnon the right shows anti conformations, including the twoadenine nucleotides. In the anti conformation, the atoms ofthe furanose ring are rotated so that they are no longer incontact with the atoms of the base. However, in the synconformation there are a number of "back" contacts-namely, contacts between atoms of the furanose ring and thebase. As seen in Fig. 4, the close contacts involve 0-2 ofpyrimidines T4 and T10 as well as N-3 of the purines in thesyn conformation. These contacts are listed in Table 1 for allof the nucleotides in the syn conformation.

It is of interest to compare the intramolecular contactsbetween the syn pyrimidine nucleosides T4 and T10 with thefour syn guanine nucleosides in Table 1. The distancesbetween 0-2 and the furanose 0-1' are slightly longer than thevan der Waals distance of 2.8 A. However, the contactsbetween 0-2 and C-2' or C-3' in the pyrimidines are slightlyshorter than those between N-3 and C-2' and C-3' for thepurines. The shortest distance (2.6 A) is found betweenthymine 0-2 and C-2' of T10 and distances similar to thathave been seen in pyrimidine nucleosides that have crystal-lized in the syn conformation (18, 19). These contacts aresensitive to slight changes in the rotation of the base about itsglycosyl bond. As mentioned above, the thymine rings are indirect van der Waals contact with bromine atoms on theadjacent nucleotide and it is possible these might perturb the

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T4, syn, x=59' A9, anti, x=-15W

T10, syn, X=75' A3, anti, X=-137-

G8, syn, X=64' C5, anti, x=-178'

FIG. 4. The position of the deoxyribose ring is shown relative tothe bases for a number of residues. The bases are drawn as if theywere lying on a horizontal surface and the sugars are seen to adoptdifferent positions around the glycosyl bond that is in the plane of thebases but extending away from the reader. All of the residues on theleft are in the syn conformation and those on the right are in the anticonformation and the angle of rotation (X) is indicated. The closestcontacts between the base and the sugar are found in the synconformations between 0-2 of pyrimidines or N-3 of purines and thevarious atoms 0-1', C-2', and C-3' of the sugar ring.

glycosyl angle. However, the important general observationis that the intramolecular contacts for the thymine residues inthe syn conformation are only slightly shorter than thosefound for the guanine residues in the syn conformation.The base to sugar "back contacts" are sensitive to the

pucker of the furanose rings. In general, adoption of a C-3'endo conformation in the syn nucleotides removes unfavor-able short contacts. The sugar pucker and the glycosyltorsional angles are listed in Table 2 for all of the residues. Itcan be seen that nucleosides T4 and T10 both adopt puckersthat are the C-3' endo type, while the adenine residues in theanti conformation A3 and A9 both adopt puckers of the C-2'endo type. In the original (dC-dG)3 Z-DNA structure, all ofthe cytosine residues were anti and had the C-2' endoconformation, while the guanine residues were all syn andwere found in the C-3' endo conformation (except for endeffects). However, all of the values fall in a fairly tight range,with a distribution of angles encompassing <300 in the syn

group and only a slightly greater spread for the anti conforma-tions.

Table 1. Close contacts of nucleotides in the syn conformation:Distances between the furanose atoms and guanine N-3 or

thymine 0-2

Base Atom 0-1' C-2' C-3'

G2 N-3 3.1 3.4 3.2T4 0-2 3.0 3.0 3.1G6 N-3 3.5 3.2 4.1G8 N-3 3.4 3.0 3.3T10 0-2 3.2 2.6 3.2G12 N-3 3.6 3.2 4.4

Table 2. Sugar pucker and X angles in d(br5C-G-A-T-br5C-G)Pucker

Residue By distance Type X, degrees

antibr5C1 C-3' exo C-2' endo -136

A3 C-2' endo C-2' endo -137br5C5 C-1' exo C-2' endo -178br5C7 C-2' endo C-2' endo -152

A9 C-2' endo C-2' endo -150br5ClW C-1' exo C-2' endo -163

synG2 C-3' endo C-3' endo 59T4 C-4' exo C-3' endo 59G6 C-3' exo C-2' endo 78G8 C-4' exo C-3' endo 64T10 C-3' endo C-3' endo 75G12 C-2' endo C-2' endo 84

The sugar puckers are listed by the maximum distance of anindividual atom from the plane of the four remaining atoms as wellas by the type of sugar pucker-i.e., C-2' endo or C-3' endo.

DISCUSSIONZ-DNA is a higher energy form of the double helix (7). Theconversion of right-handed B-DNA to left-handed Z-DNA isaccompanied by rotation about the glycosyl bonds of everyother residue from an anti to a syn conformation. Sincepurine residues can adopt the syn conformation more readilythan pyrimidines (8), Z-DNA formation is favored in se-quences with alternations of purines and pyrimidines. How-ever, we find that a molecule without an alternating sequenceappears to be able to crystallize as Z-DNA. An importantpoint is how much additional energy is required for thisprocess. If the energy difference is small, then such se-quences may form Z-DNA readily with a number ofbases outof purine pyrimidine alternation. Until recently there havebeen no measurements for estimating the likelihood offorming Z-DNA in nucleotide sequences that do not alternatein purines and pyrimidines. The present structure allows usto make some qualitative estimates.Two factors stabilize the higher energy Z-DNA in biologi-

cal systems. In negatively supercoiled DNA, the energy ofnegative supercoiling is used to stabilize Z-DNA formation(7). Likewise, Z-DNA binding proteins can stabilize theZ-DNA conformation in a complex (7). In experimentscarried out with negatively supercoiled plasmid pBR322, a14-base-pair sequence of alternating purines and pyrimidineswith 1 base pair out of alternation was identified as a site ofZ-DNA formation (12). In the present work, a chemicallymodified hexanucleotide with 2 of 6 base pairs out ofpurine-pyrimidine alternation forms Z-DNA in a singlecrystal lattice.The present structure shows that the backbone can ac-

commodate Z-DNA formation in a nonalternating purine-pyrimidine sequence. The root-mean-square (rms) deviationof the backbone of the present structure compared to the(dC-dG)3 structure is only 0.45 A. This is in contrast to thebases that deviate significantly in their position in theout-of-alternation segments.

This structure raises a number of questions. For example,there is a stabilizing stacking of adenine A3 on adenine A9and to what extent does this interaction compensate for theloss of stacking of thymine residues? Also, what is therelative energetic contribution of one base pair out of alterna-tion versus two? Finally, do AT base pairs form out-of-alternation Z-DNA structure more easily than do O0C basepairs? In this structure there is a modification in the externalshape of the molecule in the region that is out of

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purine-pyrimidine alternation. Such sequence-dependentshape changes are not seen in B-DNA. An irregular shape onthe surface of Z-DNA suggests the possibility that this locusmight be easily recognized, for example, by a protein or othermolecule binding to its surface.

Previously, it had been shown that there are two conforma-tions of phosphate groups in Z-DNA-namely, Zj and Z11(20). In the present structure, the phosphate P-5 is in the Z11conformation and the other nine are all in the Z1 conforma-tion. The P-5 phosphate has the Z11 conformation becausethere is a magnesium ion complexed to the N-7 of guanine-6in a manner similar to that seen in the (dC-dG)3 structure (20).In the (dC-dG)3 structure, the water molecules are highlyorganized in the deep helical groove. The Z-DNA crystalstructure of the hexanucleotide d(C-G-T-A-C-G) has beenreported in which the cytosine residues are modified bymethylation or bromination ip the C-5 position (6). The watermolecules in the helical groove are disordered near the ANTbase pairs. In the present structure the organization of thewater is different from that seen in (dC-dG)3. Several of thewater molecules are now found in the plane of the base pairsthat, in the structures above, were found between the basepairs. This may reflect the fact that the A-T base pairs haveadenine N-3 near the axis of the molecule and, unlike the 0-2of pyrimidines, adenine N-3 favors hydrogen bonding towater in the plane of the base. No large segments ofdisordered water molecules were found in the groove of thepresent structure.A few crystallographic studies have been carried out of

pyrimidine residues that crystallize in the syn conformation(18) (see review in ref. 19). They are usually associated withsome modification of the pyrimidine that favors the synconformation. For example, substitution of a cyano group onthe C-6 position of uridine yields a molecule that crystallizesin the syn conformation (19). The distances between the 0-2and the furanose ring atoms in that modified 6-cyanouridinestructure are similar to those seen in the present structure. Asin most of the pyrimidines that crystallize in the syn confor-mation, the pucker of the furanose rings is suitably adjustedto minimize close contacts with the base.

In the present structure, Z-DNA stabilization has beenenhanced by including either methyl groups or bromineatoms on the 5 position of cytosine. In addition, cobalthexamine has been included in the crystallization mixture.We have previously reported the structure of the cobalthexamine complex of (dC-dG)3 (15). Cobalt hexamine stabi-lizes that molecule by making 5 hydrogen bonds to the outerpart of the molecule to the guanine residue and a neighboringphosphate. The positions occupied by cobalt hexamine in the(dC-dG)3 crystal lattices are no longer available in the presentstructure since they are now occupied by the A-T base pairs.Although the crystals are yellow no cobalt hexamine wasidentified in the lattice, probably due to disordering. How-ever, crystallization is not essential since studies of anoligonucleotide without purine-pyrimidine alternation yieldNMR data demonstrating Z-DNA with syn thymines insolution.At present, the potential for Z-DNA formation has been

sought in DNA sequences by searching out segments thathave alternations of purines and pyrimidines. Crystallizationof this out-of-alternation sequence suggests that Z-DNA

might occur more widely, including some sequences thatcontain base pairs out of purine-pyrimidine alternation. Thismakes it more difficult to recognize potential Z-DNA seg-ments by simply scanning nucleotide sequences. Nonethe-less, alternations ofpurines and pyrimidines are still the mostlikely for forming Z-DNA. We may now define Z-DNA as aleft-handed double helix held together by Watson-Crick basepairs in which the bases alternate in anti and syn conforma-tions. This definition of Z-DNA can be applied to anynucleotide sequence that may form Z-DNA. The extent towhich significant segments of Z-DNA form with base pairsout of purine-pyrimidine alternation remains to be deter-mined experimentally.

This research was supported by grants from the National Institutesof Health, the American Cancer Society, National Aeronautics andSpace Administration, the Office of Naval Research, the NationalScience Foundation, as well as the Netherlands Organization for theAdvancement of Pure Research (ZWO). R.V.G. was supported by agrant from Studienstiftung des Deutschen Volkes.

1. Wang, A. H.-J., Quigley, G. J., Kolpak, F. J., Crawford,J. L., van Boom, J. H., van der Marel, G. & Rich, A. (1979)Nature (London) 282, 680-686.

2. Drew, H., Takano, T., Tanaka, S., Itakura, K. & Dickerson,R. E. (1980) Nature (London) 286, 567-573.

3. Crawford, J. L., Kolpak, F. J., Wang, A. H.-J., Quigley,G. J., van Boom, J. H., van der Marel, G. & Rich, A. (1980)Proc. Natl. Acad. Sci. USA 77, 4016-4020.

4. Drew, H. R. & Dickerson, R. E. (1981) J. Mol. Biol. 152,723-736.

5. Fujii, S., Wang, A. H.-J., van der Marel, G., van Boom, J. H.& Rich, A. (1982) Nucleic Acids Res. 10, 7879-7892.

6. Wang, A. H.-J., Hakoshima, T., van der Marel, G., vanBoom, J. H. & Rich, A. (1984) Cell 37, 321-331.

7. Rich, A., Nordheim, A. & Wang, A. H.-J. (1984) Annu. Rev.Biochem. 53, 791-846.

8. Haschemeyer, A. E. V. & Rich, A. (1%7) J. Mol. Biol. 27,369-384.

9. Davies, D. B. (1978) Progress in NMR Spectroscopy(Pergamon, Oxford), Vol. 12, pp. 135-186.

10. Singleton, C. K., Klysik, J., Stirdivant, S. M. & Wells, R. D.(1982) Nature (London) 299, 312-316.

11. Peck, L. J., Nordheim, A., Rich, A. & Wang, J. C. (1982)Proc. Natl. Acad. Sci. USA 79, 45604564.

12. Nordheim, A., Lafer, E. M., Peck, L. J., Wang, J. C., Stollar,B. D. & Rich, A. (1982) Cell 31, 309-318.

13. van der Marel, G., van Boeckel, C. A. A., Wille, G. & vanBoom, J. H. (1981) Tetrahedron Lett. 22, 3887.

14. Behe, M. & Felsenfeld, G. (1981) Proc. Natl. Acad. Sci. USA78, 1619-1623.

15. Gessner, R., Quigley, G. J., Wang, A. H.-J., van der Marel,G., van Boom, J. H. & Rich, A. (1984) Biochemistry 24,237-240.

16. Hendrickson, W. A. & Konnert, J. (1979) in BiomolecularStructure, Conformation, Function and Evolution, ed.Srinivasan, R. (Pergamon, Oxford), pp. 43-57.

17. Wang, A. H.-J., Fujii, S., van Boom, J. H. & Rich, A. (1983)Cold Spring Harbor Symp. Quant. Biol. 47, 33-44.

18. Saenger, W. & Scheit, K. H. (1970) J. Mol. Biol. 50, 153-169.19. Yamagata, Y., Kobayashi, Y., Okabe, N., Tomita, K., Sano,

T., Inoue, H. & Ueda, T. (1983) Nucleosides Nucleotides 2,335-343.

20. Wang, A. H.-J., Quigley, G. J., Kolpak, F. J., van der Marel,G., van Boom, J. H. & Rich, A. (1981) Science 211, 171-176.

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