Conditions for the stability of the alternative structures of duplex poly(dA‐dT)

Abstract

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...

Conformational transitions and hydration of poly d (A-T) � poly d (A-T) in fibers

“…Therefore the important effect of a tension applied to the fiber (Albiser et al 1988) must be taken into account in order to realize reversible transitions. The present result confirms, in a complementary way, those given in a recent study (Loprete and Hartman 1990) of non-oriented gels of poly d(A-T), poly d(A-T) where the D form could not be observed.…”

Selected deoxyoctanucleotides and their daunomycin complexes: Infrared absorption and vibrational circular dichroism spectra

“…The contour of this broad feature appears to reflect the conformation of the sugar-phosphate groups and may therefore provide some information about the structure of the backbone in favorable instances [21]. The shoulder at 1076 cm À1 in absorption, for which a corresponding VCD feature was definitively confirmed [21], was associated with the conformation of the sugar-phosphate groups in a C-structure in poly(dA-dC)Ápoly(dG-dT) and C and D structures in poly(dAdT)Ápoly(dA-dT) [44,45], i.e., the double helical structure of the oligomers in aqueous solution is not necessarily fixed in the canonical B-form. The absorption spectra reveal several additional distinct peaks, namely a group of more dominant peaks at 1054, 1022, 972, and 895 cm À1 , and a group of weaker side peaks, namely 1005, 965 and 945 cm À1 .…”

An A‐form of poly[d(A‐C)] · poly[d(G‐T)] induced by mercury (II) as studied by UV and FTIR spectroscopies

“…3b) shows bands at 1224, 1280, 1302 and 1323 cm-' and shoulders at 1208 and 1253 cm-'. This spectrum has some characteristics of a C-or a D-form [22,23]. The shoulder at 1208 cm-', for example, has been observed in the D-form of…”