Conformation of the synthetic DNA poly(amino²dA-dT) duplex in high-salt and aqueous alcohol solutions

Abstract

It has previously been demonstrated by other workers that the duplex of a synthetic DNA poly(amino2dA-dT) undergoes a salt-induced conformational isomerization. We show in the present work using circular dichroism that the same isomerization is induced in poly(amino2dA-dT) by various alcohols. The isomerization was originally identified as the B-to-Z and then B-to-A conformational transition of DNA but we demonstrate that the high-salt or alcohol conformation of poly (amino2dA-dT) is the non Z-DNA zig-zag double helix we have previously observed with poly(dA-dT) and called X-DNA. X-DNA is a cesium cation specific conformation of poly(dA-dT) while no similar cation specificity is observed with poly(amino2dA-dT). Thus it appears that the extra amino group attached to A and cesium cations make the same thing; they probably dehydrate the double helix minor groove and relieve its conformational variability. Poly(amino2dA-dT) is exceptionally stable in X-DNA and conditions inducing it are mild, which opens the door to assess its molecular structure.

Conformational Isomerizations of the Poly(dA-dT) and Poly(amino2dA-dT) Duplexes Involving the Unusual X-DNA Double Helix: A Fourth Derivative Spectrophotometric Study

“…Poly(amino 2 dA-dT) was synthesized and characterized as described in detail previously (19). The polynucleotides were dissolved in 10 mM potassium phosphate pH 7.4 and extensively dialyzed following the procedure described elsewhere (11).…”

Circular dichroism of polynucleotides: Interactions of NiCl2 with poly(dA‐dT)·poly(dA‐dT) and poly(dG‐dC)·poly(dG‐dC) in a water‐in‐oil microemulsion

“…The prominent CD maximum recorded for 20.0 mM nickel concentration at temperatures intermediate between room and melting, suggests the formation of either an A-form of polyAT or C(1) aggregates, [61][62][63][64][65][66][67] both exhibiting a strong CD maximum, at 260 nm for the canonical A-form of polyAT 65 and at about 280 nm for the C(1) form obtained in the ethanol (33.6%)-NaClO 4 (0.61 M) solvent at 267 K. 63 However it is well known that the A-form of polyAT can be obtained only at low temperatures 61 and that the B-to-A transition is inhibited by even very low concentrations of nickel. 63 A typical feature of the A-form, in addition, is a strong CD minimum in the region 210-220 nm.…”

“…63 In microemulsion, the region below 230 nm cannot be explored, but the appearance of our spectra would suggest, instead, the growth of a strong positive band in that spectral region, in analogy with what has been reported for the C(1) aggregates. 63,67 It is, therefore, reasonable to assign the first temperature-induced conformational change to the transition from a B-family double helix to a C(1) compact form of polyAT, while the second thermal process can be identified as the melting of the C(1) aggregates to yield the denatured polynucleotide.…”

Replication, Transcription and Nuclease Digestion of the Unusual X-DNA Double Helix of Poly(amino2dA-dT)

“…eHJdATP ( Poly(amino 2 dA-dT} and poly(dA-dT} were prepared as described earlier (5,8). prepared in mixtures of 5 ml final volumes that were composed as before ( 5,8) except for eH]dTTP (21.2 mCi/mmol i.e., 47 dpm/pmol) was applied in place of dTTP.…”

“…prepared in mixtures of 5 ml final volumes that were composed as before ( 5,8) except for eH]dTTP (21.2 mCi/mmol i.e., 47 dpm/pmol) was applied in place of dTTP. Synthesis, isolation and purification of the polymeric products were carried out as earlier (5,8) except for Bio-Gel P-150 gel filtration column chromatography was used for separation of the high molecular weight products. Finally 8.8 OD 260 units of poly(amino 2 dA-eH]dT) and 11.7 units of poly(dA-eH]dT) were obtained and characterized by thermal melting.…”