J . Phys. Chem. 1992, 96, 9612-9613
9612
(3) Suzuki, S.; Kawata, S.; Shiromaru, H.; Yamauchi, K.; Kikuchi, K.; Kato, T.; Achiba, Y. J . Phys. Chem. 1992, 96, 7159. (4) Hoinkis, M.; Yannoni, C. S.;Bethune, D. S.; Salem, J . R.; Johnson, R. D.; Crowder, M. S.;de Vries, M. S.Chem. Phys. Lett., in press. (5) Weaver, J. H.; Chai, Y.; Kroll, G. H.; Jin, C.; Ohno, T. R.; Haufler, R. E.; Guo, T.; Alford, J. M.; Concticao, J.; Chibante, L. P. F.; Jain, A.; Palmer, G.; Smalley, R. E. Chem. Phys. Lett. 1992, 190, 460. (6) Shinohara, H.; Sato, H.; Saito, Y.; Ohkohchi, M.; Ando, Y. J . Phys. Chem. 1992, 96, 3571. (7) Shinohara, H.; Sato, H.; Ohkohchi, M.; Ando, Y.; Kodama, T.; Shida, T.; Kato, T.; Saito, Y. Nature 1992, 357, 52. (8) Yannoni, C. S.; Hoinkis, M.; de Vries, M. S.; Bethune, D. S.;Salem, J. R.; Crowder, M. S.; Johnson, R. D. Science 1992, 256, 1191.
(9) Alvarez, M. M.; Gillan, E. G.; Holczer, K.; Kaner, R. B.; Min, K. S.; Whetten, R. L. J . Phys. Chem. 1991, 95, 10561. (10) Ross, M. M.; Nelson, H. H.; Callahan, J. H.; McElvany, S. W. J . Phys. Chem. 1992, 96, 5231. (1 1) Nagata, M.; Mizutani, M.; Bandow, S.;Kitagawa, H.; Maruyama, Y.; Kobayashi, Y.; Mitani, T. To be published. (12) Kimura, K.; Bandow, S.Bull. Chem. SOC.Jpn. 1983, 56, 3578. (13) Kikuchi, K.; Nakahara, N.; Wakabayashi, T.; Suzuki, S.;Shiromaru, H.; Miyake, Y.; Saito, K.; Ikemoto, I.; Kainosho, M.; Achiba, Y. Nature 1992, 357, 142. (14) Heath, J. R.; OBrien, S. C.; Zhang, Q.;Liu, Y.; Curl, R. F.; Kroto, H. W.; Tittel, F. K.; Smalley, R. E. J . Am. Chem. SOC.1985, 107, 7779.
Entropy-Volume Correlation with Hydration Changes in DNA-Ligand Interactions Dionisios Rentzeperis, Luis A. Merky,* Department of Chemistry, New York University, New York,New York 10003
and Donald W. Kupke Department of Biochemistry, University of Virginia, Charlottesville, Virginia 22908 (Received: August 25, 1992; In Final Form: October 6, 1992)
We report an apparent linear correlation between the entropy and the volume change for the association of the minor groove ligand, distamycin A, to synthetic polynucleotides of known sequence. The slope of the fitted line, ASo/AV', is significantly more shallow than that reported for the protonation of small organic acids and reflects, therefore, a smaller compression of the water dipoles arrayed as spine in the minor groove of the double helix prior to the release into the solvent during the binding process. The amount of releasable spine water is believed to be a function of the DNA sequence, thus giving rise to the observed linear correlation because other entropic effects appear nearly identical for these polynucleotides tested.
Considerable effort has been directed toward seeking relationships between the observed changes in volume to that of the entropy in aqueous media because both properties are functions of solution structure. Since most biochemical reactions involve changes in charge or partial charge, earlier emphasis2has dealt with the classic changes in electrostrictionj in which the intense electric field near small ions collapses the local water structure and reduces substantially the molar volume of nearby water molecules. This relatively large variation in the molar volume of water, -6 mL mol-', allows for useful measurements of the macroscopic volume change on small samples in dilute solutions4 for which entropy changes have been accessible. Theoretical developments for relating entropy to volume with small ions in water have been summarized.I An attempt to show a linear relation for the dissociation of small organic acids in water has been presented by Heplere5 Significant deviations from linearity, however, have been known for amino acids containing internal salt bridges and for the larger amines: The idea of structural or hydrophobic contributions to the volume change has received attention more recently,' and its importancein biosystems is now recognized. In the case of hydrophobic ions in water, the theory and procedures for separating classical electrostriction effects from those of structural hydration have been initiated.' In the present context, the features of structural hydration which have emerged are that the partial molar entropies and volumes are small or negative. The negative entropies upon solution of nonpolar moieties are interpreted as structure forming or of a strengthening of the water-water H bonds around such solutes; the negative volume changes are in part a result of their occupation of void or cavity spaces already extant in the structure of the water solvent. This has led to the conclusion that hydrophobic hydration
* To whom correspondence should be addressed.
occurs with an economy of space.' Systems involving larger biological structures for which both ionic and structural effects are manifest and which may show a potentially useful correlation between volume and entropy changes appear not to have been discovered. We have found an apparent linear correlation between entropy and volume changes for the association of the amphiphatic amine drug, distamycin A (Figure 1): which binds to the minor groove of five base pairs of DNA in the B conf~rmation.~ For these experiments we used either altemating-base heteropolymers or homopolymers of 100-200 base pairs per molecule. When this data is compared with the fitted line reported by HeplerIs drawn here as an association of protons to small organic acids, the two slopes, ASo/AVO, show a similar but divergent trend (Figure 2). The volume and entropy properties for the protonation of simple organic acids correlate approximately with the greater ordering and volume compression of water around the charged entities prior to the association. That is, the neutralization of opposing charges on small ions generates positive values for AVand AS. (Some examples showing negative values were cited by Hepler5for protonations involving no changes in formal charge.) In the case of the formation of distamycin A-DNA complexes, we observed a negative AV for all polymers but an entropy change, with compensating AH values, ranging almost equally from negative to positive over this span of samples. For the poly[d(AT)]-poly[d(AT)]and poly(dA).poly(dT) systems, seen as extremes of the fitted line in Figure 2, we have determined previously that the unligated poly(dA)*poly(dT)was much more hydrated, in agreement with previous ultrasound absorption studies.I0 In support of this view, we also reported a similar large difference in AVand A S when complexing netropsin (Figure l), a doubly-charged related ligand, to each of the above polymers.]' Both ligands fit tightly and lie deep in the minor groove, forming
0022-3654 I92 12096-9612S03 .OO/O , 1 0 1992 American Chemical Society I
,
-
The Journal of Physical Chemistry, Vol. 96, No. 24, 1992 9613
Letters
H2NvNHz
Distamycin A Figure 1. Structure of minor groove ligands: netropsin and distamycin
-10
-30
-20
-10
0
10
mUmol Figure 2. Correlation between ASo and AVO (per mole base pair) for the association of the minor groove ligand distamycin A to polynucleotides of known sequence. Values taken in 10 mM sodium phosphate buffer, 1 mM Na,EDTA at p H = 7.0 and 20 OC, as described in ref 8. In the volume change experiments, we use equal volumes of each polynucleotide and of distamycin A at concentrations of 1-2 mM, both in the same solvent medium. In the calorimetric experiments: 1.4 mL of polynucleotide, 0.074.25 mM in phosphate, was titrated with a distamycin A solution, 0.3-1.5 mM. The numbered circles correspond to the following polynucleotides: 1, poly(dA)-poly(dT); 2, poly(dI).poly(dC); 3, poly(rA).poMdT); 4, poly [d(AG)I.poly [d(CT)I; 5 , p o W (AC)I*poly[d(GT)l; 6, p~l~[d(GC)I.pol~[d(GC)l; 7, poly[d(IC)I*poly[d(IC)]; 8, poly[d(AT)].poly[d(AT)]. The ASovalues are within h0.4 cal/mol base pair and AVO (10.5 mL/mol base pair). The solid line follows the linear regression equation: ASo = 8.60 0.53AVO, with a correlation coefficient of 0.82. The dotted line is Hepler’s ASo-AVO correlation (ref 5 ) for the protonation of small organic acids. AVO,
+
hydrogen bonds between the N-H protons of the ligands with the carbonyl and nitrogen atoms of the basepair edges facing the floor of the minor g r o o ~ e , ~ releasing *J~ any spine water into the bulk phase. The exposed hydrophobic groups of the ligand, in turn, may structure the surrounding water throughout the filled exterior of the minor groove of the duplex. We propose, as a working
hypothesis, that, upon filling up the minor groove, the distamycin A structures water around the outward-facing hydrophobic group leading to a volume contraction and a negative entropy change. On the other hand, release of compressed spine water will tend to increase the volume and entropy, the latter overwhelming the smaller ordering effect of the structured water surrounding the hydrophobic groups. Such could explain the data for the polymer systems on the right-hand quarter of our results in Figure 2; the polymers more toward the left side, having less water in the minor groove initially, will exhibit, upon binding, smaller opposing e f f m on the negative entropy and volume changes as conferred by the hydrophobic structuring. It is of interest also that poly[d(AT)].poly[d(AT)], which shows no distinctive spine water in the minor groove, presents, upon binding, a negative entropy change that is virtually equal and opposite in magnitude and sign from that of its isomer, poly(dA)*poly(dT). A similar equal but opposite entropic effect is seen for poly[d(IC)]-poly[d(IC)] compared with its isomer, poly(dI)*poly(dC).8 We argue that the variable amount of water filling the minor grooves of these polymers provides for the differences observed in the values and signs of AS upon binding to this ligand. The negative entropy changes resulting from hydrophobic structuring of water will also depend on the degree of penetration of the ligand and which may account for the observed scatter about the fitted line in Figure 2. Other entropy contributions (Le., release of counterions, combination of solutes and conformational changes, if any) are presumed to be identical for all examples. Thus, binding by poly[d(AG)].poly[d(CT)],and perhaps by the other three polymer systems in the central portion of this figure, should hold about half as much spine water as does poly(dA).poly(dT); that is, this amount of compressed water, leading to a positive AS when liberated, compensates for the reduced entropy generated by the other factors during the binding process. By this rationale, a linear slope, A S 0 / A P , as reported here, is to be expected for duplexes of uniform sequence. We propose that other examples of binding phenomena in biopolymer systems that show AH-AS compensation effects may be interpreted in terms of hydration differences as has been discussed e1~ewhere.I~ Acknowledgment. This work was supported by Grants GM42223 (L.A.M.) and GM34938 (D.W.K.) from the National Institutes of Health.
References and Notes (1) Conway, B. E. Ionic Hydration in Chemistry & Biophysics; Elsevier: New York, 1981. (2) Millero, F. J. Chem. Reu. 1971, 72, 147-176. (3) Drude, P.; Nernst, W. Z . Phys. Chem. (Munich) 1894, 15, 79-85. (4) Gillies, G.T.; Kupke, D. W. Rev.Sci. Instrum. 1988,59 (2), 307-313. (5) Hepler, L. G.J . Phys. Chem. 1965,69,965-967. (6) Kauzman, W.; Bcdanszky, A.; Rasper, J. J . Am. Chem. Soc. 1%2,84, 1777-1788. (7) Desnoyers, J. E. Phys. Chem. Liq. 1977, 7, 63-106. (8) Rentzeperis, D.; Kupke, D. W.; Marky, L. A. Biopolymers 1992,32, 1065-1075. (9) Schultz, P. G.;Dervan, P. B. J . Biomol. Struct. Dyn. 1984, I , 1133-1 147. (10) Buckin, V. A.; Kankiya, B. I.; Bulichov, N. V.; Lebedev, A. V.; Gukovsky, I. Y.; Chuprina, V. P.; Sarvazyan, A. P.; Williams, A. R. Nature 1989, 340, 321-322. (11) Marky, L. A.; Kupke, D. W. Biochemistry 1989, 28, 9982-9988. (12) Kopka, M. L.; Yoon, C.; Goodsell, D.; Pjura, P.; Dickerson, R. E. Proc. Natl. Acad. Sci. U.S.A. 1985,82, 1376-1380. (13) Coli, M.; Frederick, C. A,; Wang, A.-H.; Rich, A. Proc. Natl. Acad. Sci. U.S.A. 1985,84, 8385-8389. (14) Leikin, S.; Rau, D. C.; Parsegian, V. A. Phys. Reu. A 1991, 44, 521 2-521 8.
