X-ray-structure of a cytidylyl-3',5'-adenosine-proflavine complex: a self-paired parallel-chain double helical dimer with an intercalated acridine dye.

Abstract

The non-self-complementary dinucleoside monophosphate cytidylyl-3',5'-adenosine (CpA) forms a basepaired parallel-chain dimer with an intercalated proflavine.The dimer complex possesses a right-handed helical twist. The dimer helix has an irregular girth with a neutral adenine-adenine (A-A) pair, hydrogen-bonded through the N6 and N7 sites (C1'... C1' separation of 10.97 A), and a triply hydrogen-bonded protonated cytosine-cytosine (C-C) pair with a proton shared between the base N3 sites (C1'... C1' separation of 9.59 A). The torsion angles of the sugar-phosphate backbone are within their most preferred ranges and the sugar puckering sequence (5' -3') is C3'-endo, C2'-endo. There is also a second proflavine molecule sandwiched between CpA dimers on the 21-axis. Both proflavines are necessarily disordered, being on dyad axis, and this suggests possible insights into the dynamics of intercalation of planar drugs. This structure shows that intercalation of planar drugs in nucleic acids may not be restricted to antiparallel complementary Watson-Crick pairing regions and provides additional mechanisms for acridine mutagenesis.The genetic molecules DNA and RNA are targets for various chemical agents that possess carcinogenic and mutagenic properties. The molecular modes of interactions of these agents with the nucleic acid and the effects they produce on the molecular geometry and conformations of DNA and RNA have been a subject of considerable interest (1-4). X-ray diffraction studies of DNA fibers (2, 5) and of co-crystals of self-complementary dinucleoside monophosphate (6, 7) with the dye proflavine have provided important insights on the stereochemistry of intercalation of proflavine into nucleic acids. Because the known single-crystal complexes, in which the dye is intercalated between the base pairs, involve self-complementary chains, it was of interest to investigate whether similar complexes can be formed between dyes and non-self-complementary nucleic acid fragments. Also, it has been demonstrated that proflavine causes a direct inhibition of protein synthesis (8,9) and that it impairs the enzymic aminoacylation of tRNA (10). Binding studies led to the conclusion that proflavine inhibition of protein synthesis results from strong binding of proflavine to tRNA (11,12). The evidence for intercalation of proflavine in tRNA was, however, indirect (11,12). The binding of proflavine to yeast tRNAPhe was studied by x-ray crystallography after diffusing proflavine into pregrown crystals of yeast tRNAPhe (13). Intercalation of proflavine in helical stems was not found; instead, the binding sites involve electrostatic and hydrogen bonding interactions with the polynucleotide sugar-phosphate backbone (14, t).Here, we report the crystal and molecular structure of an intercalated proflavine in a novel self-paired right-handed parallel-chain double helical dimer of cytidylyl-3',5'-adenosine (CpA). The dinucleoside monophosphate CpA was chosen not only because it constitutes the end portion of the invariant CCA t...

Structure of the Parallel Duplex of Poly(A) RNA: Evaluation of a 50 Year‐Old Prediction

“…This base pairing pattern has been previously observed for the dinucleotide monophosphate of CpA. [15] An additional hydrogen bond forms between the oxygen atom of the phosphate group of one strand and the second hydrogen atom of the amino group from the opposite strand (Figure 1 A). Therefore, the A-A base pairing is mediated by four hydrogen Table 1: Data collection and refinement of the (rA) 11 duplex structure.…”

Principles of Nucleic Acid Structure

“…If this sequence is reversed, either no crystals are formed or the complex adopts a nonhelical structure (1110). The same pyrimidine-3',S'-purine sequence was found even in the non-l _ __ complementary CpA·proflavin complex formed by a parallel double helix with drug intercalated between A-A and C-C base-pairs (1109).…”

“…Only such systems will be considered here-other systems with non-intercalative drug-base stacking and non-Watson-Crick base-pairs are not treated (1108)(1109)(1110). In all cases (except daunomycin intercalated into a hexadeoxynucleotide (Section 16.3), the DNA or RNA component is a dinucleoside monophosphate.…”

A naturally occurring, noncanonical GTP aptamer made of simple tandem repeats

“…6) is also consistent with a triple helix, 21 - 24 although a high-resolution structure will be needed to confirm this hypothesis. A second known example of a stable structure formed by an RNA containing only cytidine and adenosine is a dimer formed by two molecules of CA and an intercalated proflavine molecule 38 . Like the proposed fold of the omega sequence, the structure of this dimer contains parallel strands.…”