Poly 2-amino-6-N-methyladenylic acid: synthesis, characterization and interaction with polyuridylic acid

Structural transitions in poly(A), poly(C), poly(U), and poly(G) and their possible biological roles

The homopolynucleotide (homo-oligonucleotide) tracts function as regulatory elements at various stages of mRNAs life cycle. Numerous cellular proteins specifically bind to these tracts. Among them are the different poly(A)-binding proteins, poly(C)-binding proteins, multifunctional fragile X mental retardation protein which binds specifically both to poly(G) and poly(U) and others. Molecular mechanisms of regulation of gene expression mediated by homopolynucleotide tracts in RNAs are not fully understood and the structural diversity of these tracts can contribute substantially to this regulation. This review summarizes current knowledge on different forms of homoribopolynucleotides, in particular, neutral and acidic forms of poly(A) and poly(C), and also biological relevance of homoribopolynucleotide (homoribo-oligonucleotide) tracts is discussed. Under physiological conditions, the acidic forms of poly(A) and poly(C) can be induced by proton transfer from acidic amino acids of proteins to adenine and cytosine bases. Finally, we present potential mechanisms for the regulation of some biological processes through the formation of intramolecular poly(A) duplexes.

Template directed reactions of 2-aminoadenylic acid derivatives

The template-directed oligomerization of activated derivatives of 2-aminoadenylic acid (paA) on polyuridylic acid (poly(U)) in aqueous buffers was studied. The reaction differs from that of adenylic acid (pA) under identical conditions, in that only di- and tri-nucleotides are observed as substantial products rather than a longer sequence of oligomers. The reaction of paA also differs from that of pA in that it does not require Mg++, and is less susceptible to increased temperature. The relevance of these observations to the chemical evolution of polynucleotide replication is discussed. Improved syntheses of paA and its diphosphate are reported.

The interaction of 2,6,8-triaminopurine with poly(uridylic acid)

Equilibrium dialysis measurements have shown that poly(uridylic acid) binds 2,6,8-triaminopurine in a strongly cooperative manner to form a stable 2 : 1 complex at pH 7.8, 0.15 M Na+. The thermal dissociation of the complex has been characterized by ultraviolet absorbance versus temperature profiles. From the variation of Tm with the concentration of uncomplexed triaminopurine at this temperature, the partial molar enthalpy and entropy of formation of the complex have been calculated as --87 (+/- 2) kJ/mol of triaminopurine and --236 (+/- 7) J/mol of triaminopurine per K, respectively. In terms of Tm, the complex is approximately 4 degrees C more stable than the corresponding 2 : 1 complex of poly(U) with 2-aminoadenine. This stabilization is attributed to the existence of an additional hydrogen-bonding interaction, in the poly(U)-triaminopurine complex, between the 8-amino group of 2,6,8-triaminopurine and O(2) of the uracil moiety which is base paired with it in Hoogsteen fashion.

Infrared spectroscopy of polynucleotides in the carbonyl region in H2O solution: A.U systems

Strong absorbance of water at 1645 cm-1 has previously prevented dependable observation of infrared spectra of H2O solutions in the carbonyl region. We have obtained reliable spectra in pure water and in alcohol-water mixtures in this region and used them to study A.U polynucleotide interaction. Spectra in pure water were obtained by computer subtraction of solvent from that of solution measured in short path length cells. Mixed solvents, by diluting the water, permit use of longer cells and standard double-beam compensation methods. Poly(adenylic acid) in H20 solution has a strong NH2 deformation band at 1659 cm-1 coupled to an A ring vibration at 1605 cm-1. Poly(uridylic acid) has a broad band at approximately 1695 cm-1, predominantly C2 carbonyl stretch, an unresolved CR carbonyl band (probably near 1660 cm-1), and a ring vibration at approximately 1636 cm-1. The large changes these spectra undergo when helical structures are formed are discussed and compared with changes observed in D2O.

Poly(2-aminoadenylic acid): interaction with poly(uridylic acid)

Poly(2-aminoadenylic acid) forms both double and triple helices with poly(uridylic acid) [poly(U)]. The 2-amino group forms a third hydrogen bond, elevating the 2 leads to 1 transition temperature by 33 degrees C. The third strand, however, has about the same stability as poly(A)-2poly(U), as measured by Tm 3 leads to 2. This selective stabilization of the two-stranded helix results in a much greater resolution of the differnt thermal transitions than that observed in analogous polynucleotide systems. In contrast to other A, U systems 3 leads to 1 and 2 leads to 3 transitions are not observed under any conditions, and the triple helix always undergoes a 3 leads to 2 transition even at very high ionic strength. A 1:1 mixture of poly(2NH2A) and poly(U) exhibits no transient formation of 1:2 complex, unlike similar mixtures of poly(A) with poly(U) and poly(T). This difference is evidently due to a more rapid displacement reaction: [poly(2NH2A) + poly(2NH2A)-2poly(U) leads to 2 poly(2NH2A)-poly(U)] With poly(2NH2A) than with poly(A). We describe a method for establishing the combining ratios of polynucleotide complexes which used a computer to calculate the angles of intersection of mixing curves as explicit and continuous functions of the wavelength. The wavelength dispersions of the angles of intersection determine optimum wavelengths for establishing stoichiometry and can also provide reliable negative evidence that presumably plausible complexes are not formed. Analogous computer procedures have been developed to determine wavelengths which are selective for the formation of both 1:1 and 1:2 complexes. Infrared spectra of the 1:1 and 1:2 complexes resemble those of other A, U homoribopolynucleotide helices in having two and three strong bands, respectively, in the region of carbonyl stretching vibrations. CD spectra of the two complexes are unusual in having negative first extrema of moderate intensity. We attribute these extrema to intrastrand interactions of strong, well-resolved transitions at 278 nm (B2u) of the 2-aminoadenine residues. The CD spectra are correlated with those of other polynucleotide helices.

Complexes of poly(adenylic acid) with complementary monomers

The interaction of a number of potentially complementary monomers with poly(A) has been investigated by equilibrium dialysis, optical rotatory dispersion and ultraviolet absorption measurements. Experiments were conducted at pH 7.0, 0.15 M Na+, where poly(A) exists as a random coil with some degree of base-stacking, and at pH 6.0, 0.15 M Na+, where poly(A) adopts the protonated double-helical acid form structure below 15 degrees C. Binding isotherms show that, at 3.5 degrees C, poly(A) forms a 1 : 1 complex with xanthine at pH 6, and a 2:1 complex at pH 7, while oxoformycin forms a 1:1 complex with poly(A) at both pH 6 and pH 7. Poly(A) forms a complex, tentatively assigned 1:1 stoichiometry, with 8-azaxanthine at pH 6, but no complexing occurs at pH 7. The complexes have been characterized by their optical rotatory dispersion and ultraviolet spectra, their thermal stabilities, and their rates of formation at low temperature. All the complexes are laevorotatory at long wavelengths (greater than 300 nm) and unplex formation at low temperature is a slow process requiring many hours for completion. The complexes of poly(A) with 3-methylxanthine have been reinvestigated and shown to undergo normal helix-coil transitions; the anomalous melting behaviour noted previously [Biopolymers, 10, 21 -- 33 (1971)] has been explained. From a comparison of optical rotatory dispersion spectra, it is concluded that the poly(A) with 3-methylxanthine have similar structures, which are quite different from the structures of the corresponding complexes with 7-methylxanthine. The structures and properties of the poly(A) - monomer complexes are discussed, and compared with those of other polynucleotide - monomer complexes. No significant interaction was observed between poly(A) and hypoxanthine, allopurinol, 6,8-dihydroxypurine, 1-methylxanthine, 9-methylxanthine, theophylline, theobromine or 3,9-dimethylxanthine.

Poly(8-aminoguanylic acid): formation of ordered self-structures and interaction with poly(cytidylic acid)

Poly(8-aminoguanylic acid) has in neutral solution a novel ordered structure of high stability. The 8-amino group permits formation of three hydrogen bonds between two residues along the "top", or long axis, of the purines. The usual hydrogen bonding protons and Watson-Crick pairing sites are not involved in the association. The bonding scheme has a twofold rotation axis and is hemiprotonated at N(7). Poly(8NH2G) is converted by alkaline titration (pK = 9.7) to a quite different ordered structure, which is the favored form over the range approximately pH 10-11. The bonding scheme appears to be composed of a planar, tetrameric array of guanine residues, in which the 8-amino group does not participate in interbase hydrogen bonding. Poly (8NH2G) does not interact with poly(C) in neutral solution because of the high stability of the hemiprotonated G-G self-structure. Titration to the alkaline plateau, however, permits ready formation of a two-stranded Watson-Crick helix. In contrast to the monomer 8NH2GMP, poly(8NH2G) does not form a triple helix with poly(C) under any conditions. The properties of the ordered structures are interpreted in terms of a strong tendency of the 8-amino group to form a third interbase hydrogen bond, when this possibility is not prevented by high pH.

H nuclear magnetic resonance study of restricted internal rotation of N-6,N-6-dimethyladenine in aqueous solution

Kinetics of internal rotation about the C(6)-N(6) bond of N-6,N-6-dimethyladenine (M2-6A) was investigated by -1H nuclear magnetic resonance line-shape analysis of the methyl resonances (220 MHz). Rates of rotation were determined for M2-6A deuterated at N(1) and for neutral M2-6A. Activation parameters for monodeuterated M2-6A at 22 degrees are Ea = 13.8kcal/mol, log A = 12.6, incrementG++=14.9 kcal/mol, incrementH++ = 13.1 kcal/mol, incrementS++ = minus 5.8 eu; for neutral M2-6A: Ea = 15.5 kcal/mol, log A = 14.9, incrementG++ = 12.6 kcal/mol, incrementH++ = 14.9 kcal/mol, incrementS++ =7.8 eu. Vertical stacking of bases interferes with internal rotation of the dimethylamino group.