Magdalena Eriksson

Linear and circular dichroism of drug-nucleic acid complexes

Publisher Summary Polarized light spectroscopy offers possibilities to quickly characterize nucleic acids and their complexes with bound proteins or drug molecules, using a relatively small amount of sample. Linear dichroism (LD) provides structure information in terms of relative orientation between the bound drug molecule and the DNA molecular long axis, and also about the effects of ligand binding on the host. Circular dichroism (CD) may contribute additional structural details about such complexes. LD and CD, like other optical techniques, offer possibilities for rapid characterization of nucleic acid complexes using relatively small amounts of sample. The information that may be gained varies with the level of sophistication at which the measurements are carried out and interpreted. The presence of detectable LD thus, means that the ligand is bound to the oriented DNA, while the sign and amplitude of the LD signal contain information about the nature of the predominant binding mode. Use of complementary techniques, such as CD and fluorescence spectroscopy, may allow further conclusions regarding the structure and dynamics of DNA-ligand complexes. Nonchiral drug molecules (molecules that lack handedness and thereby optical activity) have no CD signal.

Interaction of ellipticine and an indolo[2,3b]-quinoxaline derivative with DNA and synthetic polynucleotides.

The non-covalent DNA interaction of the anticancer drug ellipticine (Scheme I, 1a) as well as an indolo[2,3-b]-quinoxaline derivative (Scheme I, 3b) with a dimethylaminoethyl side chain has been studied by light absorption, linear dichroism (LD) and fluorescence. Compound 3b (Scheme I) has antitumorigenic as well as antiviral activity. Both compounds bind to DNA or synthetic polynucleotides such as poly(dA-dT).(dA-dT) and poly(dG-dC).(dG-dC) by intercalation. In contrast to ellipticine, compound 3b (Scheme I) exhibits a significant binding specificity for alternating AT sequences. Its fluorescence is strongly enhanced in AT sequences and quenched in GC sequences. Fluorescence titrations evaluated as Scatchard plots show that both ellipticine and compound 3b (Scheme I) bind to the nucleic acids according to a non-cooperative neighbor exclusion model.

Sequence dependent N-terminal rearrangement and degradation of peptide nucleic acid (PNA) in aqueous solution

The stability of the PNA (peptide nucleic acid) thymine monomer ¿N-[2-(thymin-1-ylacetyl)]-N-(2-aminoaminoethyl)glycine¿ and those of various PNA oligomers (5-8-mers) have been measured at room temperature (20 degrees C) as a function of pH. The thymine monomer undergoes N-acyl transfer rearrangement with a half-life of 34 days at pH 11 as analyzed by 1H NMR; and two reactions, the N-acyl transfer and a sequential degradation, are found by HPLC analysis to occur at measurable rates for the oligomers at pH 9 or above. Dependent on the amino-terminal sequence, half-lives of 350 h to 163 days were found at pH 9. At pH 12 the half-lives ranged from 1.5 h to 21 days. The results are discussed in terms of PNA as a gene therapeutic drug as well as a possible prebiotic genetic material.

Observation of excimer formation in the covalent adducts of 9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene-7,8-diol with poly(dG-dC)

The covalent binding of 9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene-7,8-diol to alternating poly(dG–dC) results in extensive occurrence of excimers as shown by fluorescence spectroscopy; the origin is inferred to be close-lying pyrene chromophores bound to guanines in the minor groove of DNA.

Structure of Z-DNA in solution. A flow linear dichroism study

U.v. flow linear dichroism (L.D.) of the high-salt form of duplex poly(dG-dC)(‘Z-DNA’) shows that the reduced dichroism of Z-DNA is about twice as large as for B-DNA and the spectrum has the shape expected for Watson–Crick base-pairs oriented perpendicular to the helix; axis spectral features observed during the B→Z conversion are in qualitative agreement with a mechanism in which the base-pairs flip 180° around the glycosyl bonds.

Structure of a Covalent Complex Between Benzo(a)Pyrene Diol Epoxide and DNA

Abstract Flow linear dichroism and fluorescence spectroscopy show that the covalent (+)-anti-BPDE-DNA complex adopts two rapidly interchanging conformations. The binding introduces local flexibility in DNA facilitating further covalent attacks.

Structural properties of the covalent (+)-anti-BPDE-poly(dG-dC)(dG-dC) complex

The structure of the covalent (+)-anti-BPDE-poly(dG-dC) complex can be represented by two preferred orientations of the pyrene moiety; one at about 20 degrees relative to the helix axis and one at about 70 degrees, populated as 4:1. A rapid mobility of the BPDE may allow an exchange between the two orientations. The poly(dG-dC) structure becomes more flexible by (+)-anti-BPDE modification, seen as a shortened persistence length. This complex may be significant as a model for DNA interaction with covalently binding polyaromatic carcinogens.

The B - Z Transition in Poly [d(G-C) d(G-C)] After Covalent Binding of Anti- Benzo(a)Pyrenediolepoxide

(+)-anti-7,8-dihydroxy-9,10-oxy-7,8,9,10-tetrahydrobenzo(a)pyrene (BPDE) is a highly carcinogenic metabolite of benzo(a)pyrene (BP), which binds covalently and with high specificity to the exocyclic amino group of guanine in DNA (1) (Fig. 1).