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Position of caesium ions in crystalline B-form DNA determined by synchrotron radiation diffraction
J. Mol. Biol. (1979) 134, 369-374
LETTERS
TO THE EDITOR
Position of Caesium Ions in Crystalline B-form DNA Determined by Synchrotron Radiation Diffraction Preliminary results The diffraction patterns of CsDNA taken with copper X-irradiation are considerably impaired because of the strong X-ray absorption by caesium ions. The use of high power synchrotron radiation of wavelength X = 1.2 A has yielded photographs suitable for intensity measurements. The structure of phage T2 CsDNA at 76% relative humidity is isomorphous to the crystalline B-form of LiDNA, and the disposition of cations appears to conform to the lo-fold screw symmetry of B-DNA. The structure factor amplitudes of 20 reflections in the diffraction pattern of phage T2 CsDNA are noticeably different from those of the same reflections in the LiDNA diffraction pattern, and the positions of the Cs + ions could thus be found. The best model has the cations located significantly close to dyad axes lying between the planes of successive nucleotide pairs. One of the two cations “belonging” to a nucleotide pair touches the surface of the narrow groove of the B-DNA double helix, while the other is on the wide groove side, rather far from its “own” DNA molecule.
The double helical structure of DNA is known to depend largely on the counterion bound to it. The B-form and the A-form may be observed for sodium, potassium and rubidium DNA salts (Langridge et al., 1957,196O). By contrast, the lithium ion does not allow DNA to adopt the A-conformation and thus confines the range of structures to the B-family (Marvin et al., 1961; Arnott & Selsing, 1975). The magnesium ion has a similar effect on the DNA structure; it also forbids the A-form (Skuratovskii $ Mokulskii, 1971; Skuratovskii & Bartenev, 1978). The mechanism of participation of the cation in the structural transformations of double helical DNA might be elucidated if the position of cations in the DNA structure could be revealed. Yet, X-ray analysis of the light DNA salts (magnesium, lithium, sodium) cannot yield this information, the electron “weight” of these cations being too small to make any noticeable contribution to the diffraction pattern. We studied the “heavy” caesium salt of calf thymus DNA and phage T2 DNA. Calf thymus DNA is a typical representative of the “normal” DNA class (with an approximately equal G + C and A + T content) and can be observed easily in both the B-form and the A-form. Phage T2 DNA is partly glucosylated, which prevents its sodium salt from adopting the A-form (Mokulskii et al., 1972). All attempts to study CsDNA with a conventional copper anode X-ray tube failed because of t,he strong X-ray absorption by the caesium ions (Skuratovskii et al., 1978).
On the one hand,
long
exposure
times
were
required;
on the other
hand,
the
specimens quickly deteriorated under the X-ray beam. Besides, CuKcr radiation (wavelength X = 1.54 A) makes caesium ions noticeably fluorescent, which creates an intensive background hindering the diffraction intensity measurements (Arnott et al., 1976). Considerable progress was made in the diffraction studies of &DNA by the use of 369 022%2836/79/300369-06
$02.00/06
0
1979 Academic
Press
Inc.
(London)
Ltd.
I.
370
YA.
SKURATOVSKII
AL.
ET
synchrotron radiation (wavelength /\ = 1.2 A) generated by the VEPP-3 storage ring (Institute of Nuclear Physics, Siberian branch, USSR Academy of Sciences, Novosibirsk). The X-ray absorption coefficient for h == 1.2 8, is about 2.1 times lower than in the case of h = 1.54 A, which, with the high power of a synchrotron radiation beam, allowed us to obtain quite informative X-ray photographs of CsDN14 in about one hour (Kapitonova et al., 1976; Mokulskaya et al., 1977). The structure of phage T2 CsDNA at certain relative humidities (see Table 1) happened to be isomorphous to the classic crystalline B-form of LiDNA (Langridge TABLE
Orthorhombic
lattice and molecular parameters
Reletive humidity
Lattice n
(%I 84 81 76 The (Amott
corresponding & Hukins,
1
22.450.4 22.7+0.3 22.61 0.3
31.2kO.6 30.61irO.4 31.OkO.3 values 1973).
for
pnrameters h
calf
thymus
LiDNA
of phage
(A) c (the helical
T2 GWiVA h, axial
3.38 4: 0.03 3.37*0.02 3.37+0.02
33.7hO.6 33.7 10.4 33.6+0.3 sm’:
30.8
rise/residue (4
pitch)
.A: 22.5
il;
33.8
A sntl
3.38
a
et al., 1960; Arnott & Hukins, 1973). Calf thymus CsDNA at 76% and lower relative humidities gave typical diffraction patterns of the A-form, highly similar to those of thymus RbDNA (Wilkins, 1956). As in the case of RbDNA, a strong meridional reflection in the first layer-line indicates that the cation disposition does not conform to the characteristic ll-fold screw symmetry of individual DNA molecules in the A-form. No such reflection is present in the photographs of NaDNA in the A-form, probably just because Na + is too light to so manifest itself. As regards the diffraction photographs of phage T2 CsDNA, they contain no such indication to the effect that. the disposition of caesium ions does not conform to the lo-fold screw symmetry of individual B-DNA molecules, so in this respect the photographs of phage T2 CsDNA are no different from those of LiDNA (Fig. 1). The intensities of 20 independent reflections were measured and their structure factor amplitudes determined for CsDNA in the crystalline B-form. Our experiments were carried out in the medianal plane of the storage ring (the electron orbit plane) where synchrotron radiation is highly polarized (Kulipanov & Skrinskii, 1977), which was taken into account when structure factor amplitudes were determined. We also took into account the absorption factor (Skuratovskii et al.? 1978). Figure 2 presents a diagram comparing the structure factor amplitudes, obsFm. i.e. square-roots of diffraction intensities, of CsDNA with the structure factor amplitudes of the same reflections in the diffraction pattern of LiDNA (Arnott & Hukins, 1973), i.e. practically cation-free “pure” DNA (Li+ has only 2 electrons). Differences are observed in the centre of the pattern and in the periphery, which indicates a regular disposition of cations in the crystalline B-form structure. To find the position of caesium ions in the crystalline B-form structure, we searched for the minimum
LETTERS
FIG. 1. X-ray photographs from Langridge et al. (1960); length is 1.64 A) and of phage
TO
THE
EDITOR
371
of calf thymus LiDNA at 66% relative humidity (left, reproduced the fibre is somewhat inclined toward t,he X-ray beam; the waveT2 CsDNA at 76% relative humidity (right, the wavelength is 1.2 A).
(Arnott & Hukins, 1973), considering the structure of DNA itself to be identical to the model worked out in the same paper. If we assume that the disposition of cations conforms to the lo-fold screw symmetry of individual DNA molecules, then to determine the position of ions we only need to find the co-ordinates of two cations in the system of one nucleotide pair. We did not require the two cations to be related by dyad axes as the atoms of the DNA molecule itself. By varying the co-ordinates of cations within a range sufficient to examine the entire space in the unit cell free of the substance of DNA itself, we carefully studied the behaviour of R” in that space. All the time we kept a look-out for overlaps between cations or between cations and DNA atoms in the hard-sphere approximation. In this way we found the two deepest minima of R”, both of which fall into a range with no overlaps. R&, = 0*19, while the conventional crystallographic residual, The lowest is 0.16. The cylindrical polar co-ordinates of the R = %,sFm - cad’mll&d’mt two cations in the system of an individual nucleotide pair (Arnott & Hukins, 1972) are : r,=5.4311;~,=26”;2,=1.64~ r2 = 9.52 8; & = 197”; z2 = 0.52 A.
373
YA.
E!.!’ AL.
SKURATOVSKII
0.10 Reciprocal
&5 spmnq
o.io
3.25 a
(A-‘!
FIG. 2. A comparative diagram of structure factor amplitudes of the same reflections in the diffraction patterns of CsDNA and LiDNA. The filled bars are structure factor amplitudies of LiDNA, the open bars are those of CsDNA. The position of the reflection on the layer-line is in the centre of the common foot of the corresponding bars. The structure factor amplitude of the zero layer-line reflection closest to the pattern centre is so large in the case of LiDNA that it had to be truncated.
The second R,,, minimum are :
= O-38 (R = O-31) and the co-ordinates
of cations
for this
R"
r1 = 6.15 A; & = 25”; z1 = 1.33 A
r2 = 6.66 ii; & = 196” ; z2 = 0.66 A. The two dispositions are basically similar (cf. 4 or z) but the second can easily be rejected by the R-ratio of Hamilton’s significance test (1965). All contacts between cations and DNA atoms in the crystalline B-form unit cell (for the best disposition of cations) have not been studied in detail yet, but if their disposition is described in terms of interaction with an individual DNA molecule, the first of the two cations is deeply sunk in the narrow groove, so that its co-ordination sphere includes the base atoms (the situation is highly similar to that obtained for one of the Na+ ions in ApU crystals (Rosenberg et aE., 1973)). The pattern of interaction between such cations and DNA is more or less uniform : Figure 3 presents
LETTERS
TO
THE
EDITOR
373
FIG. 3. A view of 2 adjacent A.T pairs along the helix axis. The upper pair is shown by the thickest lines, the lower pair by the thin lines. At z = 0 the dyad belongs to the lower pair. The filled circles show non-hydrogen atoms located within 4.0 A of the caesium ion in the narrow groove (if not with the nucleotide sequence shown then with A and T rearranged). The shortest distances are (depending on the nucleotide sequence) 2.9 A to O-2 (T or C), 3.0 A to N-3 (A or G) and 3.1 A to N-2 (G). The distance to the nearest sugar O-5’ is 4.0 A.
their typical co-ordination. We can consider this cation to actually belong to its “own” DNA molecule. The other cation, located on the wide groove side, is rather far from its own DNA molecule; such cations show a variety of co-ordinations through the unit cell and belong rather to the crystal as a whole. Though the position of the two cations near the nucleotide pair changed independently during R” minimization, the cations “came by themselves” close to the molecular dyads lying between successive nucleotide pairs: for such a dyad in the same system 4 = 18” & 180”, z = 1.69 A (see Fig. 3). But if the cations were placed exactly on the dyad, i.e. if 4 were fixed at 18” (198”) and z at 1.69 A, then Rk,, becomes as large as 0.33 and such a disposition may be rejected by Hamilton’s (1965) test with a probability of greater than 95.5%. Therefore we do not think that the cations failed to find themselves exactly on the dyad axis because of some experimental inaccuracies. Perhaps the reason lies in the partial inadequacy of the usual assumptions made for DNA diffraction computations (Arnott & H&ins 1973; Arnott 1970). It might also be the presence of glucoside residues ; but, on the one hand, those residues, located in the wide groove of the B-DNA molecule, could hardly have any effect on the cation interactions in the narrow groove. On the other hand, the cation on the wide groove side is located far enough from the DNA molecule not to let the glucose easily “reach” it. Besides, the lo-fold screw symmetry shows that the disposition of cations is the same near glucose-free nucleotide pairs and those few where glucose is present. While computing CSlCF,
I.
374
YA.
SKURATOVSKII
ET
dL.
we did not take the glucoside residues into account, considering that their yuasirandom distribution along the DNA molecule should not significantly influence the value of structure factor amplitudes. It would be very good indeed if glucose did not interfere in any way, but the crystalline B-form is given only by the lithium salt of non-glucosylated DNAs, while the sodium, potassium, rubidium and caesium salts of these DNAs are in the A-conformation under the same conditions. We are grateful
to Mr D. Agrachyov
for his great
help in preparing
the manuscript.
I. YA. SKURATOVSKII
Institute of Molecular Genetics USSR Academy of Sciences Moscow 123182, USSR.
I,. I. VOLKOVA K. A. KAPITONOVA
V.N. Received
2 October
1978, and in revised
form
29 May
RARTENEV
1979.
REFERENCES Arnott, S. (1970). Science, 16’7, 1694-1700. Arnott, S. & Hukins, D. W. L. (1972). Biochem. Biophys. Res. Commun. 47, 1504.~-1509. Arnott, S. & Hukins, D. W. L. (1973). J. Mol. BioZ. 81, 93-105. Arnott, S. & Selsing, E. (1975). J. Mol. Biol. 98, 265-269. Arnott, S., Chandrasekaran, R. & Leslie, A. G. W. (1976). J. Mol. Biol. 106, 735-748. Hamilton, W. C. (1965). Acta CrystaZEogr. 18, 502-510. Kapitonova, K. A., Mazanov, A. L., Mokulskaya, T. D., Mokulski, M. A. & Skuratovskii, Breidenstein I. Ya. (1976). Abstr. 10th Int. Congr. Biochem., p. 30, BrGnners Druckerei KG, Frankfurt am Mein. Kulipanov, G. N. & Skrinskii, A. N. (1977). Uspekhy Fiz. Nauk. 122, 369.-418. Langridge, R., Seeds, W. E., Wilson, H. R., Hooper, C. W., Wilkins, M. H. F. & Hamilton. L. D. (1957). J. Biophys. Biochem. Cytol. 3, 767-778. Langridge, R., Wilson, H. R., Hooper, C’. W., Wilkins, M. H. F. & Hamilton, I,. D. (1960). J. Mol. Biol. 2, 19-37. Marvin, D. A., Spencer, M., Wilkins, M. H. F. dz Hamilt,on, L. D. (1961). ./. Mol. Biol. 3, 547--565. Mokulskaya, T. D., Mokulskii, M. A., Nikitin, A. A., Skuratovskii, 1. Ya., Baru, S. E., Kulipanov, G. N., Sidorov, V. A., Skrinskii, A. N. & Khabakhpashev, A. G. (1977). Krystallographiya, 22, 744-752. Mokulskii, M. A., Kapitonova, K. A. & Mokulskaya, T. D. (1972). Mol. Biol. 6, 883--900. Rosenberg, J. M., Seeman, N. C., Kim, J. J. P., Suddath, F. L., Nicolas. H. B. &Rich, A. (1973). Nature (London), 243, 150-154. Skuratovskii, I. Ya. & Bartenev, V. N. (1978). Mol. Biol. 12, 1359-1376. Skuratovskii, I. Ya. & Mokulskii, M. A. (1971). Dokl. Akad. NaukSSSR, 200, 638-640. Skuratovskii, I. Ya., %pitonova, K. A. & Volkova, L. I. (1978). J. AppZ. Crystallogr. 11, 238-242. Wilkins, M. H. F. (1956). Cold Spring Harbor Symp. Quant. Biol. 21, 75-88.
Note Added in Proof: patterns.
Each
of the 20 intensities
was averaged
over the best, six diffractioll
LETTERS
TO THE EDITOR
Position of Caesium Ions in Crystalline B-form DNA Determined by Synchrotron Radiation Diffraction Preliminary results The diffraction patterns of CsDNA taken with copper X-irradiation are considerably impaired because of the strong X-ray absorption by caesium ions. The use of high power synchrotron radiation of wavelength X = 1.2 A has yielded photographs suitable for intensity measurements. The structure of phage T2 CsDNA at 76% relative humidity is isomorphous to the crystalline B-form of LiDNA, and the disposition of cations appears to conform to the lo-fold screw symmetry of B-DNA. The structure factor amplitudes of 20 reflections in the diffraction pattern of phage T2 CsDNA are noticeably different from those of the same reflections in the LiDNA diffraction pattern, and the positions of the Cs + ions could thus be found. The best model has the cations located significantly close to dyad axes lying between the planes of successive nucleotide pairs. One of the two cations “belonging” to a nucleotide pair touches the surface of the narrow groove of the B-DNA double helix, while the other is on the wide groove side, rather far from its “own” DNA molecule.
The double helical structure of DNA is known to depend largely on the counterion bound to it. The B-form and the A-form may be observed for sodium, potassium and rubidium DNA salts (Langridge et al., 1957,196O). By contrast, the lithium ion does not allow DNA to adopt the A-conformation and thus confines the range of structures to the B-family (Marvin et al., 1961; Arnott & Selsing, 1975). The magnesium ion has a similar effect on the DNA structure; it also forbids the A-form (Skuratovskii $ Mokulskii, 1971; Skuratovskii & Bartenev, 1978). The mechanism of participation of the cation in the structural transformations of double helical DNA might be elucidated if the position of cations in the DNA structure could be revealed. Yet, X-ray analysis of the light DNA salts (magnesium, lithium, sodium) cannot yield this information, the electron “weight” of these cations being too small to make any noticeable contribution to the diffraction pattern. We studied the “heavy” caesium salt of calf thymus DNA and phage T2 DNA. Calf thymus DNA is a typical representative of the “normal” DNA class (with an approximately equal G + C and A + T content) and can be observed easily in both the B-form and the A-form. Phage T2 DNA is partly glucosylated, which prevents its sodium salt from adopting the A-form (Mokulskii et al., 1972). All attempts to study CsDNA with a conventional copper anode X-ray tube failed because of t,he strong X-ray absorption by the caesium ions (Skuratovskii et al., 1978).
On the one hand,
long
exposure
times
were
required;
on the other
hand,
the
specimens quickly deteriorated under the X-ray beam. Besides, CuKcr radiation (wavelength X = 1.54 A) makes caesium ions noticeably fluorescent, which creates an intensive background hindering the diffraction intensity measurements (Arnott et al., 1976). Considerable progress was made in the diffraction studies of &DNA by the use of 369 022%2836/79/300369-06
$02.00/06
0
1979 Academic
Press
Inc.
(London)
Ltd.
I.
370
YA.
SKURATOVSKII
AL.
ET
synchrotron radiation (wavelength /\ = 1.2 A) generated by the VEPP-3 storage ring (Institute of Nuclear Physics, Siberian branch, USSR Academy of Sciences, Novosibirsk). The X-ray absorption coefficient for h == 1.2 8, is about 2.1 times lower than in the case of h = 1.54 A, which, with the high power of a synchrotron radiation beam, allowed us to obtain quite informative X-ray photographs of CsDN14 in about one hour (Kapitonova et al., 1976; Mokulskaya et al., 1977). The structure of phage T2 CsDNA at certain relative humidities (see Table 1) happened to be isomorphous to the classic crystalline B-form of LiDNA (Langridge TABLE
Orthorhombic
lattice and molecular parameters
Reletive humidity
Lattice n
(%I 84 81 76 The (Amott
corresponding & Hukins,
1
22.450.4 22.7+0.3 22.61 0.3
31.2kO.6 30.61irO.4 31.OkO.3 values 1973).
for
pnrameters h
calf
thymus
LiDNA
of phage
(A) c (the helical
T2 GWiVA h, axial
3.38 4: 0.03 3.37*0.02 3.37+0.02
33.7hO.6 33.7 10.4 33.6+0.3 sm’:
30.8
rise/residue (4
pitch)
.A: 22.5
il;
33.8
A sntl
3.38
a
et al., 1960; Arnott & Hukins, 1973). Calf thymus CsDNA at 76% and lower relative humidities gave typical diffraction patterns of the A-form, highly similar to those of thymus RbDNA (Wilkins, 1956). As in the case of RbDNA, a strong meridional reflection in the first layer-line indicates that the cation disposition does not conform to the characteristic ll-fold screw symmetry of individual DNA molecules in the A-form. No such reflection is present in the photographs of NaDNA in the A-form, probably just because Na + is too light to so manifest itself. As regards the diffraction photographs of phage T2 CsDNA, they contain no such indication to the effect that. the disposition of caesium ions does not conform to the lo-fold screw symmetry of individual B-DNA molecules, so in this respect the photographs of phage T2 CsDNA are no different from those of LiDNA (Fig. 1). The intensities of 20 independent reflections were measured and their structure factor amplitudes determined for CsDNA in the crystalline B-form. Our experiments were carried out in the medianal plane of the storage ring (the electron orbit plane) where synchrotron radiation is highly polarized (Kulipanov & Skrinskii, 1977), which was taken into account when structure factor amplitudes were determined. We also took into account the absorption factor (Skuratovskii et al.? 1978). Figure 2 presents a diagram comparing the structure factor amplitudes, obsFm. i.e. square-roots of diffraction intensities, of CsDNA with the structure factor amplitudes of the same reflections in the diffraction pattern of LiDNA (Arnott & Hukins, 1973), i.e. practically cation-free “pure” DNA (Li+ has only 2 electrons). Differences are observed in the centre of the pattern and in the periphery, which indicates a regular disposition of cations in the crystalline B-form structure. To find the position of caesium ions in the crystalline B-form structure, we searched for the minimum
LETTERS
FIG. 1. X-ray photographs from Langridge et al. (1960); length is 1.64 A) and of phage
TO
THE
EDITOR
371
of calf thymus LiDNA at 66% relative humidity (left, reproduced the fibre is somewhat inclined toward t,he X-ray beam; the waveT2 CsDNA at 76% relative humidity (right, the wavelength is 1.2 A).
(Arnott & Hukins, 1973), considering the structure of DNA itself to be identical to the model worked out in the same paper. If we assume that the disposition of cations conforms to the lo-fold screw symmetry of individual DNA molecules, then to determine the position of ions we only need to find the co-ordinates of two cations in the system of one nucleotide pair. We did not require the two cations to be related by dyad axes as the atoms of the DNA molecule itself. By varying the co-ordinates of cations within a range sufficient to examine the entire space in the unit cell free of the substance of DNA itself, we carefully studied the behaviour of R” in that space. All the time we kept a look-out for overlaps between cations or between cations and DNA atoms in the hard-sphere approximation. In this way we found the two deepest minima of R”, both of which fall into a range with no overlaps. R&, = 0*19, while the conventional crystallographic residual, The lowest is 0.16. The cylindrical polar co-ordinates of the R = %,sFm - cad’mll&d’mt two cations in the system of an individual nucleotide pair (Arnott & Hukins, 1972) are : r,=5.4311;~,=26”;2,=1.64~ r2 = 9.52 8; & = 197”; z2 = 0.52 A.
373
YA.
E!.!’ AL.
SKURATOVSKII
0.10 Reciprocal
&5 spmnq
o.io
3.25 a
(A-‘!
FIG. 2. A comparative diagram of structure factor amplitudes of the same reflections in the diffraction patterns of CsDNA and LiDNA. The filled bars are structure factor amplitudies of LiDNA, the open bars are those of CsDNA. The position of the reflection on the layer-line is in the centre of the common foot of the corresponding bars. The structure factor amplitude of the zero layer-line reflection closest to the pattern centre is so large in the case of LiDNA that it had to be truncated.
The second R,,, minimum are :
= O-38 (R = O-31) and the co-ordinates
of cations
for this
R"
r1 = 6.15 A; & = 25”; z1 = 1.33 A
r2 = 6.66 ii; & = 196” ; z2 = 0.66 A. The two dispositions are basically similar (cf. 4 or z) but the second can easily be rejected by the R-ratio of Hamilton’s significance test (1965). All contacts between cations and DNA atoms in the crystalline B-form unit cell (for the best disposition of cations) have not been studied in detail yet, but if their disposition is described in terms of interaction with an individual DNA molecule, the first of the two cations is deeply sunk in the narrow groove, so that its co-ordination sphere includes the base atoms (the situation is highly similar to that obtained for one of the Na+ ions in ApU crystals (Rosenberg et aE., 1973)). The pattern of interaction between such cations and DNA is more or less uniform : Figure 3 presents
LETTERS
TO
THE
EDITOR
373
FIG. 3. A view of 2 adjacent A.T pairs along the helix axis. The upper pair is shown by the thickest lines, the lower pair by the thin lines. At z = 0 the dyad belongs to the lower pair. The filled circles show non-hydrogen atoms located within 4.0 A of the caesium ion in the narrow groove (if not with the nucleotide sequence shown then with A and T rearranged). The shortest distances are (depending on the nucleotide sequence) 2.9 A to O-2 (T or C), 3.0 A to N-3 (A or G) and 3.1 A to N-2 (G). The distance to the nearest sugar O-5’ is 4.0 A.
their typical co-ordination. We can consider this cation to actually belong to its “own” DNA molecule. The other cation, located on the wide groove side, is rather far from its own DNA molecule; such cations show a variety of co-ordinations through the unit cell and belong rather to the crystal as a whole. Though the position of the two cations near the nucleotide pair changed independently during R” minimization, the cations “came by themselves” close to the molecular dyads lying between successive nucleotide pairs: for such a dyad in the same system 4 = 18” & 180”, z = 1.69 A (see Fig. 3). But if the cations were placed exactly on the dyad, i.e. if 4 were fixed at 18” (198”) and z at 1.69 A, then Rk,, becomes as large as 0.33 and such a disposition may be rejected by Hamilton’s (1965) test with a probability of greater than 95.5%. Therefore we do not think that the cations failed to find themselves exactly on the dyad axis because of some experimental inaccuracies. Perhaps the reason lies in the partial inadequacy of the usual assumptions made for DNA diffraction computations (Arnott & H&ins 1973; Arnott 1970). It might also be the presence of glucoside residues ; but, on the one hand, those residues, located in the wide groove of the B-DNA molecule, could hardly have any effect on the cation interactions in the narrow groove. On the other hand, the cation on the wide groove side is located far enough from the DNA molecule not to let the glucose easily “reach” it. Besides, the lo-fold screw symmetry shows that the disposition of cations is the same near glucose-free nucleotide pairs and those few where glucose is present. While computing CSlCF,
I.
374
YA.
SKURATOVSKII
ET
dL.
we did not take the glucoside residues into account, considering that their yuasirandom distribution along the DNA molecule should not significantly influence the value of structure factor amplitudes. It would be very good indeed if glucose did not interfere in any way, but the crystalline B-form is given only by the lithium salt of non-glucosylated DNAs, while the sodium, potassium, rubidium and caesium salts of these DNAs are in the A-conformation under the same conditions. We are grateful
to Mr D. Agrachyov
for his great
help in preparing
the manuscript.
I. YA. SKURATOVSKII
Institute of Molecular Genetics USSR Academy of Sciences Moscow 123182, USSR.
I,. I. VOLKOVA K. A. KAPITONOVA
V.N. Received
2 October
1978, and in revised
form
29 May
RARTENEV
1979.
REFERENCES Arnott, S. (1970). Science, 16’7, 1694-1700. Arnott, S. & Hukins, D. W. L. (1972). Biochem. Biophys. Res. Commun. 47, 1504.~-1509. Arnott, S. & Hukins, D. W. L. (1973). J. Mol. BioZ. 81, 93-105. Arnott, S. & Selsing, E. (1975). J. Mol. Biol. 98, 265-269. Arnott, S., Chandrasekaran, R. & Leslie, A. G. W. (1976). J. Mol. Biol. 106, 735-748. Hamilton, W. C. (1965). Acta CrystaZEogr. 18, 502-510. Kapitonova, K. A., Mazanov, A. L., Mokulskaya, T. D., Mokulski, M. A. & Skuratovskii, Breidenstein I. Ya. (1976). Abstr. 10th Int. Congr. Biochem., p. 30, BrGnners Druckerei KG, Frankfurt am Mein. Kulipanov, G. N. & Skrinskii, A. N. (1977). Uspekhy Fiz. Nauk. 122, 369.-418. Langridge, R., Seeds, W. E., Wilson, H. R., Hooper, C. W., Wilkins, M. H. F. & Hamilton. L. D. (1957). J. Biophys. Biochem. Cytol. 3, 767-778. Langridge, R., Wilson, H. R., Hooper, C’. W., Wilkins, M. H. F. & Hamilton, I,. D. (1960). J. Mol. Biol. 2, 19-37. Marvin, D. A., Spencer, M., Wilkins, M. H. F. dz Hamilt,on, L. D. (1961). ./. Mol. Biol. 3, 547--565. Mokulskaya, T. D., Mokulskii, M. A., Nikitin, A. A., Skuratovskii, 1. Ya., Baru, S. E., Kulipanov, G. N., Sidorov, V. A., Skrinskii, A. N. & Khabakhpashev, A. G. (1977). Krystallographiya, 22, 744-752. Mokulskii, M. A., Kapitonova, K. A. & Mokulskaya, T. D. (1972). Mol. Biol. 6, 883--900. Rosenberg, J. M., Seeman, N. C., Kim, J. J. P., Suddath, F. L., Nicolas. H. B. &Rich, A. (1973). Nature (London), 243, 150-154. Skuratovskii, I. Ya. & Bartenev, V. N. (1978). Mol. Biol. 12, 1359-1376. Skuratovskii, I. Ya. & Mokulskii, M. A. (1971). Dokl. Akad. NaukSSSR, 200, 638-640. Skuratovskii, I. Ya., %pitonova, K. A. & Volkova, L. I. (1978). J. AppZ. Crystallogr. 11, 238-242. Wilkins, M. H. F. (1956). Cold Spring Harbor Symp. Quant. Biol. 21, 75-88.
Note Added in Proof: patterns.
Each
of the 20 intensities
was averaged
over the best, six diffractioll