Thermostability of double-stranded deoxyribonucleic acids: the effects of covalent additions of a psoralen

Abstract

We have carried out a thermodynamic study on the effects of covalent additions of the psoralen derivative H M T , 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen, on the stability of double-stranded deoxyoligonucleotides. This was done with two systems. The first was a double-stranded D N A formed by two non-self-complementary oligonucleotides, 5'-GAAGCTACGAGC-3' and S-GCTCGTAGCTTC-3', where we site specifically placed an H M T molecule on the thymidine residue in oligonucleotide 5'-GAAGCT-ACGAGC-3' as either a furan-side monoadduct or a pyrone-side monoadduct. The second was a double-stranded D N A formed by a self-complementary oligonucleotide, 5'-GGGTACCC-3', where we placed an H M T molecule on the thymidine residue of each strand as a furan-side monoadduct or cross-linked the two strands with an H M T molecule linked to the two thymidines. We found that H M T cross-linking of the two strands stabilizes the double helix formed by 5'-GGGTACCC-3', as one might expect. Less predictable results were that the monoaddition of a psoralen stabilizes the double helix formed by the two non-self-complementary oligonucleotides by as much as 1.3 kcal/mol as a furan-side monoadduct and 0.7 kcal/mol as a pyrone-side monoadduct at 25 O C in 50 m M NaCl. In contrast, the monoaddition of a psoralen on each of the two thymidines in the double helix formed by 5'-GGGTACCC-3' destabilizes the helix by 1.8 kcal/mol at 25 OC in 1 M NaCl. This destabilization arises from an unfavorable enthalpy change (8.6 kcal/mol) and a favorable entropy change (23 cal/K.mol) due to the two H M T molecules at the centers of each strand. The measured hypochromicity on helix formation also suggests a substantial perturbation in stacking interactions when one H M T is added to each of the two thymidines in the double helix.

Minor Groove Orientation of the KWKK Peptide Tethered via the N-Terminal Amine to the Acrolein-Derived 1,N2-γ-Hydroxypropanodeoxyguanosine Lesion with a Trimethylene Linkage,

“…These robust catalytic efficiencies are observed on DNAs containing either abasic site-linked peptides (8,67) or γ-OH-PdG-linked peptides (6) even though these lesions stabilize, rather than destabilize duplex DNA. These data are similar to prior studies that investigated the structure−activity relationship of psoralen monoadducted DNAs and the UvrABC complex (68−70). Although the psoralen monoadduct stabilized the DNA duplex, the UvrABC system recognized and incised it with a very high efficiency, while in contrast, it was a very poor substrate for the human NER complex (70).…”

Recognition of DNA Adducts by Human Nucleotide Excision Repair

“…In comparison, BPDE-N 2 -guanine adducts exert more moderate effects on double-helical stability (16,17,24). Psoralen monoadducts, on the other hand, slightly increase helical stability (19,20,28), whereas anthramycin and CC-1065 adducts produce substantial increments in helical stability (21,22). Thus, an early subset of NER factors appears to be endowed with the capacity to sense thermodynamic parameters of double-stranded DNA and preferentially interact with those sites that exhibit unfavorable changes in free energy.…”

“…Melting temperature studies have shown that these bulky base adducts alter the thermodynamic characteristics of DNA in different ways. AAF adducts (14,15), BPDE adducts (16,17) and UV radiation products (18) destabilize the DNA double helix relative to nonmodified DNA, whereas 8-MOP (19,20), anthramycin (21), and CC-1065 adducts (22) stabilize the DNA duplex. In the predominant adduct formed by N-acetoxy-2-acetylaminofluorene (AAF-C 8 -guanine), the modified base is rotated out of the helix axis, and the duplex is locally denatured (14,23).…”

“…Modifications with psoralen induce helical distortion by unwinding the duplex and enhancing backbone flexibility (28) but fail to destabilize the secondary structure of DNA. On the contrary, thermostability measurements showed that both pyroneside and furanside monoadducts stabilize the helix by mediating stacking interactions between the psoralen moiety and the surrounding base pairs (19,20,28). Helix-stabilizing adducts were also obtained using anthramycin, a pyrrolo- [1,4]benzodiazepine antibiotic, and CC-1065, a composite compound consisting of three pyrroloindole subunits joined by amide linkages (Fig.…”

Melting of Cross-linked DNA. III. Calculation of Differential Melting Curves

“…Agents which give rise to interstrand linkage are potential antitumor drugs (9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21). Cross-linking strongly influences biological and physical properties of DNA molecule (22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35) and alters DNA structure and melting behavior (25,(37)(38)(39)(40)(41)(42). At the same time DNA conformation influences cross-link formation (36).…”