Bifunctional molecules having a DNA intercalator or DNA groove binder linked to ethylene diamine tetraacetic acid, their preparation and use to cleave DNA

• US 4,942,227 A
• Filed: 01/23/1987
• Issued: 07/17/1990
• Est. Priority Date: 01/11/1982
• Status: Expired due to Fees

• Current Assignee: California Institute of Technology
• Original Assignee: California Institute of Technology
• Inventors: Hertzberg, Robert P., Dervan, Peter B.
• Primary Examiner(s): Rollins, John W.
• Assistant Examiner(s): Wilson, James O.
• Application Number:
  US07/006,442
• Time in Patent Office: 1,271 Days
• Field of Search: 536/27, 536/28, 536/29, 514/44
• US Class Current: 536/25.4
• CPC Class Codes: C07D 207/34 with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached to ring carbon atoms
• CPC Class Codes: C07D 221/12 Phenanthridines

Abstract

Bifunctional molecules having a DNA intercalator or DNA groove binder linked to ethylene diamine tetraacetic acid such as compounds having the formula: ##STR1## wherein R is methyl or ethyl. Also, the method of cleaving DNA by contact with one of the above-identified molecules in the presence of ferrous ion and oxygen.

The process of preparing said molecules by the reaction of P-carboxy methidium halide, p-carboxy ethidium halide, or other DNA intercalator or DNA groove binder with 1-3-diaminopropane followed by condensation with ethylenediamine tetraacetic acid.

Distamycin-EDTA.Fe(II)(DE.FE(II)) contains EDTA attached to the amino terminus of the groove binder tripeptide (tris-N-methylpyrrolecarboxamide). De.Fe(II) cleaves DNA contiguous to a five base pair A+T rich sequence. This is a novel and unique molecule and superior in sequence specificity to the naturally occurring antitumor compound used in man, bleomycin which cleaves DNA at a two base pair recognition site. EDTA-distamycin-Fe(II)(ED.Fe(II)) contains EDTA attached to the carboxy terminus of the groove binder tripeptide, tris-N-methylpyrrolecarboxamide. ED.Fe(II) cleaves DNA contiguous to a five base pair A+T rich sequence. Penta-N-methylpyrrolecarboxamide-EDTA.Fe(II)(P5E.Fe(II)) cleaves on opposite strands at the six base pair recognition level in a catalytic reaction. This is the first designed synthetic molecule that approximates the double strand sequence specific cleavage of DNA(4-6 bp recognition level) by the natural substance restriction enzymes, tools which make possible recombinant DNA manipulations. P5E.Fe(II) cuts DNA at sequences not available by the naturally occurring restriction enzymes.

The dimers, bis(EDTA-distamycin.Fe(II)) and EDTA-bisdistamycin.Fe(II) which double strand cleave DNA at the eight base pair recognition level (A+T rich).

Claims

1. The process of cleaving double stranded DNA by contact with a compound having the formula:

##STR15## wherein the above formula, R is methyl or ethyl, in the presence of effective DNA cleavage promoting amounts of ferrous ion and oxygen.

2. The process of cleaving double stranded DNA by contact with distamycin ethylenediamine tetraacetic acid wherein ethylenediamine tetraacetic acid is tethered to the amino terminus of the N-methylpyrrole tripeptide moiety of the distamycin in the presence of effective DNA cleavage promoting amounts of ferrous ion and oxygen.

3. The process of cleaving double stranded DNA by contact with ethylenediamine tetraacetic acid distamycin wherein ethylenediamine tetraacetic acid is tethered to the carboxy terminus of the N-methylpyrrole tripeptide moiety of the distamycin in the presence of effective DNA cleavage promoting amounts of ferrous ion and oxygen.

4. The process of cleaving double stranded DNA by contact with penta-N-methylpyrrole-carboxamide ethylenediamine tetraacetic acid in the presence of effective DNA cleavage promoting amounts of ferrous ion and oxygen.

5. The process of cleaving double stranded DNA by contact with bis(ethylenediamine tetraacetic acid distamycin) in the presence of effective DNA cleavage promoting amounts of ferrous ion and oxygen.

6. The process of cleaving double stranded DNA by contact with ethylenediamine tetraacetic acid-(bisdistamycin) in the presence of effective DNA cleavage promoting amounts of ferrous ion and oxygen.

7. The process of cleaving double stranded DNA by contact with methidiumpropyl ethylenediamine tetraacetic acid in the presence of effective DNA cleavage promoting amounts of ferrous ion and oxygen.

8. The process of cleaving double stranded DNA by contact with ethidiumpropyl ethylenediamine tetraacetic acid in the presence of effective DNA cleavage promoting amounts of ferrous ion and oxygen.