J . A m . Chem. SOC.1984, 106, 5671-5676
5671
Crystal Structure and Conformation of the Phosphotriester Adenosine 5 ’ 4 4 Diethyl phosphate). Possible Steric and Conformational Mechanisms for the Biochemical and Biological Effects Arising from Phosphate Alkylation Richard G . Brennan,+ Norman S. Kondo,$ and Muttaiya Sundaralingam*+ Contribution f r o m the Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53706, and the Department of Chemistry, University of the District of Columbia, Washington, D.C. 20008. Received December 12, 1983
Abstract: Phosphotriesterified oligonucleotides are often the major products resulting from the attack of mutagenic and carcinogenic alkylating agents on DNA and RNA. In order to elucidate the electronic and conformational perturbations arising from phosphate esterification, which may be the basis of its biochemical and biological effects, the X-ray structure of the triesterified nucleotide adenosine 5’-O-(diethyl phosphate) (Cl4HZ2NSO7P) was undertaken. The compound (FW = 403.33) crystallizes in the triclinic space group P1 ( Z = 1) with unit cell parameters of a = 6.799 ( l ) , b = 7.923 ( l ) , c = 9.003 (1) A, 01 = 86.86 ( l ) , p = 77.98 ( l ) , y = 77.85 (l)’, V = 463 A3,D,= 1.444 g ~ m - and ~ , DM = 1.45 g ~ m - ~The . structure was solved by heavy-atom methods and refined by the full-matrix least-squares technique to an R index of 0.039 ( R , = 0.051) using 1917 intensities. The D-ribofuranosyl ring is in a symmetrical twist conformation, C(2’)-endo-C( 1’)-exo (iT), with pseudorotational parameters P = 145.0 (2)’ and 7, = 39.4 (2)’. The adenine base is anti (69.0 (3)’) about the C(l’)-N(9) glycosyl bond, and the conformation about the exocyclic bond C(4’)-C(5’) is the preferred gauche’ (50.8 (3)’). Hydrogen bonding is centered about the ribosyl hydroxyls and the N(6) amino group of the base. The molecular packing is dominated by intermolecular base-alkyl stacking and alkyl-alkyl van der Waals interactions. The methyl group of one of the ethoxy groups is two-site disordered. Diethylation of the phosphate results in neutralization of the charge and geometric and conformational perturbations of the phosphodiester. All four P-O bonds are significantly shorter than those of the nonalkylated nucleotides. The three combinations of phosphcdiester linkages display the (g-,t), (gc,g-), and (t,t) conformations which are different from the familiar (g-,g-) conformation of right-handed polynucleotide helices. The lack of preference of the alkylated sugar phosphate backbone for the (g-,g-) phosphodiester conformation would tend to destack the bases and promote alkyl-base stacking. This will lead to sugar phosphate backbone configurations which would provide a mechanism for the biochemical and biological effects induced by phosphate alkylation.
Alkylation by many mutagenic and carcinogenic agents is not confined alone to the purine and pyrimidine bases of the nucleic acids. Phosphate alkylation can also be affected by methyl methanesulfonate and ethyl methanesulfonate a t neutral p H . ] The phosphodiester backbone is particularly susceptible to ethylation by the potent carcinogen ethylnitrosourea. The resulting phosphotriester product represents 60% of the total ethylation in TMV-RNA.* Similar results a r e observed both in vitro3 and in vivo4 when D N A is treated with ethylnitrosourea. R N A can be readily alkylated, but its sugar phosphate backbone forms unstable ethoxy linkages and undergoes chain ~ c i s s i o n . ~D N A , on the other hand, is able to form stable alkyl phosphotriesters6 which remain nearly unchanged after 72 h in cell culture.’ Although these alkyl groups are persistent, there is no evidence that mutations result. The biological and biochemical effects resulting from the alkylation of the phosphodiester backbone are not well understood but appear not to involve base mispairing.* Conformational perturbations in the sugar phosphate backbone, neutralization of the phosphate group, and the interference of the alkyl group with protein binding have often been invoked to explain these effects. To gain a detailed understanding of the conformational, electronic, and geometric perturbations resulting from alkylation of the phosphodiester backbone, we have determined the crystal and molecular structure of the first free (noncyclic) triesterified nucleotide adenosine 5’-O-(diethyl phosphate). On the basis of the conformational analysis of this compound and the observed crystal packing we suggest possible mechanisms which may explain the biochemical and biological effects resulting from phosphotriesterification.
Experimental Section A crystal of adenosine 5’-O-(diethyl phosphate), crystallized from water and air-dried, with dimensions 0.3 X 0.15 X 0.15 mm, was selected
‘University of Wisconsin. *University of the District of Columbia.
0002-7863/84/1506-5671$01.50/0
for intensity data collected on an Enraf-Nonius CAD4 diffractometer using Ni-filtered Cu Ka radiation ( A 1.5418 A). The unit cell parameters were refined by a least-square algorithm using 25 automatically centered reflections. A total of 2142 reflections were measured to a 28 value of 150°, of which 1917 unique reflections with intensities greater than 1.5a(Z)were used in the structural analysis. Three reflections monitored throughout data collection revealed negligible crystal decay. An absorption correction employing an empirical $ curve as well as Lorentz and polarization corrections was applied to the intensities.
Structure Determination and Refinement The structure was solved by the heavy-atom method, which revealed the five atoms of the phosphate group in the initial Patterson map. The remaining non-hydrogen atoms were located by subsequent Fourier syntheses. One of the methyl groups displayed a two-site disorder with each site having a 50% occupancy factor. The atomic positions for the non-hydrogen atoms were refined by full-matrix least-squares technique using anisotropic thermal parameters. Difference Fourier syntheses revealed 18 of the 22 hydrogen atoms which were submitted to full-matrix least-squares refinement using isotropic thermal parameters. The remaining hydrogen atoms were fixed from geometric considerations. The full-matrix least-squares refinement converged at R = xllFol - lFcll/ CIFol = 0.039 ( R , = 0.051).9 The function minimized was xw(lFol lFc1)2,where a modified counting statistics weighting scheme” was used with the weight of each reflection proportional to l/[u2(F) + (0.04F0)*].
( I ) Rhaese, H.-J.; Freese, E. Biochim. Biophys. Acra 1969, 190, 418-433. (2) Singer, B.; Fraenkel-Conrat, H. Biochemistry 1975, 14, 772-782. (3) Sun, L.; Singer, B. Biochemisrry 1975, 14, 1795-1802. (4) Singer, B.; Bodell, W. J.; Cleaver, J. E.; Thomas, G. H.; Rajewsky, M . F.; Thou, W. Nature (London) 1978, 276, 85-88. (5) Ludlum, D. B. Biochim. Biophys. Acta 1969, 174, 773-775. (6) Bannon, P.; Verly, W . Eur. J . Biochem. 1972, 31, 103-1 1 I . (7) Bodell, W . J.; Singer, B.; Thomas, G . H.; Cleaver, J. E. Nucleic Acids Res. 1979, 6 , 2819-2829. (8) Jensen, D. E.; Reed, D. J. Biochemisrry 1978, 17, 5098-5107. (9) R , = [CW(lFOl - IFc1)2/.EIFo1””2 (10) Stout, G . H.; Jensen, L. H . “X-ray Structure Determination. A Practical Guide”; McMillan: New York, 1968; pp 454-458.
0 1984 American Chemical Society
J. Am. Chem. Soc.. Vol. 106, No. 19, 1984
5612
Brennan, Kondo, and Sundaralingam
Table I. Atomic Parameters for Adenosine 5'-O-(Diethyl phosphate). Fractional Positional Parameters Are Multiplied by lo4 for Non-Hydrogen Atoms and lo3 for Hydrogen Atoms
B, = $'3LEjBijaia,
atom
X
Y
2
B , or B
multiplicity
P
2.65 (2) -7 (0) 39 (0) 4 (0) -1769 (3) -271 (2) 3.54 (4) O(1) 13 (3) 453 (4) 376 (3) 1560 (2) 4.27 (5) O(2) 233 (9) 2848 (4) 6.17 (12) -767 (6) C(9) C(10-1) 7.45 (34) 0.50 -1023 (22) 43 (16) 4169 (10) 787 (23) C(10-2) -209 (15) 4062 (1 1) 12.18 (33) 0.50 879 (4) -1078 (3) 1638 (4) O(3") 4.25 (5) 1630 (7) -2516 (5) 7.03 (12) 1397 (8) C(12) 3371 (8) 1829 (7) -3442 (5) 6.38 (11) (313) -2067 (3) -156 (3) 1302 (3) 3.97 (5) O(5') -4034 (4) 3.06 (5) 496 (3) 842 (3) C(5') -5498 (3) 1218 (3) 2.39 (4) 2426 (3) C(4') 2545 (2) 2.85 (4) -4831 (3) 2851 (2) O(4') 195 (2) 2.17 (4) -5654 (3) 4037 (3) C(3') -7761 (3) 305 (2) 3.17 (3) 4803 (2) O(3') 2.06 (4) -4510 (3) 5176 (3) 887 (2) C(2') 691 (2) 2.85 (4) -5186 (3) 6954 (2) O(2') -4958 (3) 2554 (2) 4658 (3) 2.07 (4) (71') 3411 (2) 2.42 (4) -3488 (3) 4982 (3) N(9) 4577 (4) 3.02 (5) -1369 (4) 2999 (3) C(8) 4960 (3) 3.23 (5) -451 (3) 4044 (3) N(7) 2.37 (4) -2044 (3) 5190 (3) 5669 (3) C(5) 2.08 (4) 4830 (2) 5681 (3) -3930 (3) C(4) 2.76 (4) 5703 (2) 6283 (3) -5785 (3) N(3) 2.85 (5) 6999 (3) 6890 (4) -5598 (3) C(2) 2.60 (4) 7507 (2) 6965 (3) -3886 (3) N(1) 2.35 (4) 6600 (2) 6352 (3) -2054 (3) C(6) 3.38 (5) 7079 (2) 6418 (3) -334 (3) N(6) 109 (3) 1.6 (5) H1 (C-5') -379 (4) -6 (3) -43 (4) 3.6 (7) H2(C-5') -437 (6) 47 (5) 155 (4) 2.9 (6) H(C-4') 209 (4) -686 (5) -76 (3) 1.2 (4) H(C-3') 386 (3) -503 (4) 3.7 (7) 580 (5) -796 (6) H(0-3') 21 (4) 2.6 (6) H(C-2') 476 (4) -288 (5) 44 (3) -18 (3) 2.4 (6) 721 (4) -472 (5) H (0-2') 311 (3) 2.2 (5) 525 (4) H(C-1') -614 (5) 2.6 (6) -79 (5) 202 (4) H(C-8) 408 (4) 794 (4) 3.5 (7) 694 (5) -47 (6) Hl(N-6) 3.9 (8) 654 (4) 617 (5) H2(N-6) 69 (6) 3.1 (6) 775 (4) -682 (6) H(C-2) 726 (4) 5.4 (10) 253 (5) -164 (6) Hl(C-9) -4 (7) 4.0 (0) 319 (0) -104 (0) 151 (0) H2(C-9)' -271 (6) 6.3 (12) 229 (7) H1 (C-12) 30 (8) 14.4 (29) -283 (13) 62 (14) 85 (15) H2(C-12) 11.3 (22) -440 (10) 238 (10) 328 (13) H1 (C-13) -307 (12) 14.6 (31) 262 (12) 428 (16) H2(C-13) 4 0- ( 0 ) -342 (0) H31C-13)" 437 (0) 63 (0) ., "The atomic coordinates of these hydrogen atoms were fixed from geometric considerations. No hydrogen atoms were assigned to the C(10-1) or C(10-2) methyl carbon atoms \
I
\ - I
The maximum values of the shift over error ratios were
