The occurrence of alternative structures for the lithium, sodium, and potassium salts of poly(dG-dC) was determined as a function of hydration using IR spectra of nonoriented gels. Poly(dG-dC).K with added KCl (r = 0.56 where r is the moles of KCl per mole of nucleotide residue) gave results essentially identical to the much studied poly(dG-dC).Na with added NaCl (r = 0.56). Both gave a sharp transition from a unique B structure (hereafter designated B*) to the Z structure upon dehydration. Poly(dG-dC).Li with added LiCl (r = 0.36) assumed the B* structure at high hydration but made a broad transition to the C structures as hydration was lowered. We believe this is the first clear evidence of the C structure for poly(dG-dC). No other structures (A, D, or Z) were observed at any hydration in nonoriented gels. Poly(dG-dC).Na with added ZnCl2 (r = 0.2) existed as a mixture of the B* and Z structures in maximally hydrated gels. A broad, incomplete transition to a higher mole fraction of Z structure occurred upon dehydration. Zn2+ promotes the Z structure for poly(dG-dC) and appears to bind to guanine residues. Poly(dG-dC).Na with added MgCl2 or CaCl2 (r = 0.2) assumed the normal B* structure at maximum hydration with no hint of Z structure. Slight dehydration produced a very sharp transition to the Z structure. Both Mg2+ and Ca2+ are strong promoters of the Z structure but do not bind to cytosine or guanine residues.

We show that the lithium salt of calf-thymus DNA can assume the C structure in nonoriented, hydrated gels. The transitions between the B and C structures showed little hysteresis and none of the metastable structural states which occur in oriented gels. Therefore crystal-lattice forces are not needed to stabilize the C structure. The occurrence of the alternative structures of the Li, Na and K salts of poly(dA-dC).poly(dG-dT) was measured as a function of hydration for nonoriented gels. Poly(dA-dC).poly(dG-dT).Li exists in the B structure at high hydrations and in the C structure at moderate hydrations with no A or Z structure at any hydration tested. The Na salt of poly(dA-dC).poly(dG-dT) exists in the B structure at high hydration, as mixtures of B and C at moderate hydrations and in the A structure at lower hydrations. The potassium salt behaves similarly except that mixtures of the C and A structures exist at lower hydrations. ZnCl2 and NaNO3, which promote the Z structure in duplex poly(dG-dC), promote the C structure in poly(dA-dC).poly(dG-dT). Information contained in the sequence of base pairs and not specific ionic interactions appear to determine the stability of the alternative structures of polynucleotides as hydration is changed.

SYNOPSISThe alternative structures of the lithium, sodium, potassium, and rubidium salts of poly(dAd T ) were studied using ir spectra of hydrated, nonoriented gels. Poly (dA-dT) Na existed as the B structure a t high hydration and as the A structure a t moderate hydration. A disordered state occurred a t low hydration. No hint of the C, D, or other structures was observed a t any hydration for nonoriented gels containing NaCl up to 0.56 moles NaC1/ mole of nucleotide residue. Poly (dA-dT) -Li existed as the B structure a t high hydration, made a gradual transition to the C structure a t moderate hydration, and became disordered at low hydration. Poly (dA-dT) K and poly( dA-dT) -Rb existed as the B structure a t high hydration and as the presumptive D structure at lower hydration. The addition of Zn ( 11) to poly(dA-dT)-Na produced a gradual transition from the B to the C structure upon dehydration. The addition of NaN03 to poly (dA-dT) * Na gave only the A and B structures, and not the C or Z structures that are promoted by NO, in other base sequences. The D N A secondary structure stabilized by a given ion is determined by a specific base sequence and not simply by the properties of the ion INTRODUCTIONThe nature of the alternative structures of poly (dAdr) and the conditions for the stability of these structures have received much study (reviewed in Ref'. 1 ) . Crystallographic studies of oriented gels of poly ( dA-dT) have demonstrated the existence of the A, B, C, and D structures depending on the counterion to the polymer, the salt content of the gel, and the hydration (or water activity) of the Raman studies have confirmed the existence of the B structure in ~o l u t i o n s~~~~ and the A structure in partially oriented and unoriented gels.' Nuclear magnetic resonance spectra of solutions of poly (dA- Biopolymers, Vol. 30, 753-761 (1990) ('CC OOOS-:~525/90/7-80753-09 $04.00* To whom correspondence should be addressed.nonoriented 16*17 gels, have been assigned to the A, B, C, and D structures of poly (dA-dT) . Although the existence of the A, B, C, and D structures of poly (dA-dT ) has been broadly supported, the stabilizing conditions for these structures are less certain. We have therefore made a systematic survey of the structures that exist and the conditions for stability for the Li, Na, K, and Rb salts of poly(dA-dT) using nonoriented gels in which shifts in equilibrium due to crystal-lattice forces should be minimized.A brief review of the salient results for the conditions of stability of alternative structures of poly (dA-dT) follows.Davies and Baldwin first observed the diffraction patterns of the sodium, lithium, and ammonium salts of poly (dA-dT) using hydrated oriented gels.' They found the A and B structures for the Na and Li salts of poly(dA-dT), respectively. A C-like structure and a new structure, which they called D, were observed for poly (dA-dT) * NH4. Samples of poly (dA-dT) -Na containing ca. 0.2 moles of NaCl per mole of nucleotide (hereafter designated r = 0.2) also gave the D s...

Infrared spectroscopy was used to study the structures and transitions in hydrated gels of double-helical poly(dG-dC) complexed with the metal carcinogens Cd(II) and Ag(I). For one Cd(II) per ten nucleotides (r = 0.1), the B structure was stable at high and moderate hydrations with D2O and the B and Z structures coexisted at low hydrations. For poly(dG-dC) with Cd(II) at r = 0.2 to 0.35, the Z structure was stable at high hydrations (94% r.h. for r = 0.2). At a given value of hydration, H2O gave a higher content of Z structure than D2O. Cd(II) most likely binds to guanine residues at N7 in both the B and Z forms of poly(dG-dC) but binding to guanine N3 can not be excluded. It is unlikely that Cd(II) binds to cytosine residues at the r values studied and the cytosine residues did not protonate at N3 as Cd(II) bound to guanine residues. Poly(dG-dC) with Ag(I) at r = 0.2 to 0.36, existed in a B-family structure which is different from the B-family structure of the type I complex of Ag(I) and calf-thymus DNA. Poly(dG-dC) with Ag(I) did not assume the Z structure at lower hydrations even though NO3- was present in the sample. Ag(I) differs from other soft-metal acids which promote the Z structure. Ag(I) most likely binds to the guanine N7 or N3 and not to cytosine residues. Cytosine residues did not protonate at N3 as Ag(I) was bound to guanine.(ABSTRACT TRUNCATED AT 250 WORDS)

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