Sequence specificity of mutagen-nucleic acid complexes in solution: Intercalation and mutagen-base pair overlap geometries for proflavine binding to dC-dC-dG-dG and dG-dG-dC-dC self-complementary duplexes

Abstract

The complex formed between the mutagen proflavine and the dC-dC-dC-dG and dG-dG-dC-dC self-complementary tetranucleotide duplexes has been monitored by proton high resolution nuclear magnetic resonance spectroscopy in 0.1 M phosphate solution at high nucleotide/drug ratios. The large upfield shifts (0.5 to 0.85 ppm) observed at all the proflavine ring nonexchangeable protons on complex formation are consistent with intercalation of the mutagen betweenbase pairs of the tetranucleotide duplex. We have proposed an ap roximate overlap geometry between the proflavine ring and nearest neighbor base pairs at the intercalation site from a comparison between experimental shifts and those calculated for various stacking orientations. We have compared the binding of actinomycin D, propidium diiodide, and proflavine to self-complementary tetranucleotide sequences dC-dC-dG-dG and dGdC-dC-dC by UV absorbance changes in the drug bands between 400 and 500 nm. Actinomycin D exhibits a pronounced specificity for sequences with dG-dC sites (dG-dG-dC-dC), while propidium diiodide and proflavine exhibit a specificity for sequences with dC-dG sites (dC-dC-dG-dG). Actinomycin D binds more strongly than propidium diiodide and proflavine to dCdG-dC-dG (contains dC-dG and dG-dC binding sites), indicative of the additional stabilization from hydrogen bonding and hydrophobic interactions between the pentapeptide lactone rings of actinomycin D and the base pair edges and sugar-phosphate backbone of the tetranucleotide duplex. The cationic acridine dyes form two types of complexes with nucleic acids dependent on the nucleotide to dye ratio (1). At high nucleotide/dye ratios, there is a red shift which has been attributed to intercalation of the dye between nucleic acid base pairs (2). At low nucleotide/dye ratios, there is a blue shift in the visible spectrum of the dye which is attributed to stacking of dye aggregates along the sugar-phosphate backbone (1). The published optical studies include a quantitative analysis of the binding of proflavine to polynucleotides and transfer RNA (3, 4), to DNA (5, 6), and to bacteriophage (7, 8).The 2:2 complexes of 9-aminoacridine with the dinucleoside phosphates adenylyl-(3'-5')-uridine (9) and 5-iodocytidylyl-(3'-5')-guanosine (10) have been solved by x-ray crystallography. The adenine bases form Hoogsteen type hydrogen bonds to the uracil bases in the former crystal structure (9), and the base pairs are stacked parallel to each other with the 9-aminoacridine sandwiched between them. The cytosine-bases form Watson-Crick type hydrogen bonds to the guanosine bases in the latter crystals (10), with one 9-aminoacridine stacked on the exterior and the other molecule intercalated into the dinucleoside duplex.Alden and Arnott have put forward a model based on stereochemical principles for the intercalation of proflavine (Fig. 1) into B-DNA (11). The model proposes a change in the torsion angles about C4'-C5' and 04-P backbone bonds to a trans conformation and a change in sugar pucker to C3' endo-(3...

Proton nuclear magnetic resonance study of the self-complementary hexanucleotide d(pTpA)3 and its interaction with daunomycin

“…Since only one daunomycin resonance was observed for each proton monitored, the daunomycin exchange rate must be rapid. This has also been noted for other synthetic nucleotide duplex-drug systems (Patel & Canuel, 1977;Patel, 1979). The daunomycin chemical shifts observed therefore represent an average of the chemical shifts of the free drug and the complexed drug.…”

“…figure 4: Temperature dependence of the adenine H(2) chemical shifts in 1 M NaCl, 10 mM phosphate, and 1 mM EDTA, pH 6.8, in the absence (•) and presence ( ) of daunomycin (daunomycin/nucleotide ratio of 0.06). but such shifts have been reported for a variety of oligonucleotides (Borer et al, 1975;Patel & Canuel, 1977;Patel, 1977Patel, , 1979 and polynucleotides (Patel & Canel, 1978).…”

“…The small chemical shift of the aromatic protons of daunomycin accompanying denaturation of the drug-hexanucleotide complex (Figure 8B) is somewhat unexpected. Aromatic protons of other drugs have typically shown up to 0.8-ppm upfield shifts accompanying intercalation (Patel & Canuel, 1977), and this has been attributed largely to ringcurrent contributions from adjacent base pairs (Giessner- Prettre & Pullman, 1976). However the low-field aromatic proton of daunomycin exhibits only a 0.08-ppm upfield shift.…”

Modulation of platinum antitumor drug binding to DNA by linked and free intercalators

“…This result can be explained in terms of the known sequence preference, pyr(3'-5')pur > pur(3'-5')pur » pur(3'-5')pyr, for intercalation to dinucleoside phosphates Krugh & Reinhardt, 1975; Reinhardt & Krugh, 1978;Kastrup et al, 1978). NMR studies suggested that this pyr(3'-5')pur sequence would also be favored by the acridines, proflavin (Patel, 1977;Patel & Canuel, 1977), and 9-aminoacridine (Young & Kallenbach, 1981). Several theoretical analyses have indicated such a sequence preference to be an intrinsic property of the lower energy required to open up a pyr(3'-5')pur base pair to form an intercalator binding site, and that it is not significantly dependent on a particular intercalator (Ornstein & Rein, 1979;Miller et al, 1980;Nuss et al, 1979).…”

Theoretical studies of drug-dinucleotide interactions. Empirical energy function calculations on the interaction of ethidium, 9-aminoacridine, and proflavin cations with the base-paired dinucleotides GpC and CpG

“…9-Aminoacridine (major) has the N+ group pointing in toward the nucleoside; 9-aminoacridine (minor) has the N+ group pointing away from the nucleoside. 7 The first seven angles refer to the first dinucleoside phosphate, the second to its H-bonded partner. 8 Our torsional angles are related to those of Sundaralingham32 in the following way: our = Sundaralingham's + 120; ce = 360 -\ = 360 -\ = 360 -': ft = 360 -; c = 360 -'; ' = ' -180. endo) deoxyribose sugar ring puckering of BDNA is altered to a mixed sugar puckering of the type C3,-endo(3,-5')C2/endo.…”