Chromomycin dimer-DNA oligomer complexes. Sequence selectivity and divalent cation specificity
- Columbia Univ., New York (USA)
This paper reports on a solution NMR characterization of the sequence selectivity and metal ion specificity in chromomycin-DNA oligomer complexes in the presence of divalent cations. The sequence selectivity studies have focused on chromomycin complexes with the self-complementary d(A1-A2-G3-G4-C5-C6-T7-T8) duplex containing a pair of adjacent (G3-G4){center dot}(C5-C6) steps and the self-complementary d(A1-G2-G3-A4-T5-C6-C7-T8) duplex containing a pair of separated (G2-G3){center dot}(C6-C7) steps in aqueous solution. The observed intermolecular NOEs establish that chromomycin binds as a Mg(II)-coordinated dimer (1 Mg(II) per complex) and contacts the minor-groove edge with retention of 2-fold symmetry centered about the (G3-G4-C5-C6){center dot}(G3-G4-C5-C6) segment of the d(A{sub 2}G{sub 2}C{sub 2}T{sub 2}) duplex. By contrast, complex formation is centered about the (G2-G3-A4-T5){center dot}(A4-T5-C6-C7) segment and results in removal of the two fold symmetry of the d(AG{sub 2}ATC{sub 2}T) duplex. These observations suggest a hierarchy of chromomycin binding sites, with a strong site detected at the (G-G) step due to the hydrogen-bonding potential of acceptor N3 and donor NH{sub 2} groups of guanosine that line the minor groove. The authors have measured the real-time proton to deuterium exchange kinetics of the aglycon C8-hydroxyl proton in the symmetric chromomycin-d-(A{sub 2}G{sub 2}C{sub 2}T{sub 2}) complex after dissolution in D{sub 2}O solution. The hydrogen exchange lifetimes in the absence of added catalysts decreases in the order NI(II) {much gt} Mg(II) > Zn(II) > Cd(II) complexes. These results establish that the divalent cation exchange does not occur through direct penetration of the cation into the complex but rather following dissociation of the divalent cation coordinated chromomycin dimer from its duplex binding site.
- OSTI ID:
- 5659431
- Journal Information:
- Biochemistry; (USA), Journal Name: Biochemistry; (USA) Vol. 29:49; ISSN 0006-2960; ISSN BICHA
- Country of Publication:
- United States
- Language:
- English
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Related Subjects
62 RADIOLOGY AND NUCLEAR MEDICINE
ADDUCTS
ALKALINE EARTH METAL COMPOUNDS
ANTI-INFECTIVE AGENTS
ANTIBIOTICS
AROMATICS
AZAARENES
BARYONS
CATIONS
CHARGED PARTICLES
CHEMICAL REACTIONS
CHEMICAL SHIFT
CROSS-LINKING
DNA
DNA ADDUCTS
DNA SEQUENCING
DRUGS
ELEMENTARY PARTICLES
FERMIONS
GUANOSINE
HADRONS
HEAVY WATER
HETEROCYCLIC COMPOUNDS
HYDROGEN COMPOUNDS
ION EXCHANGE
IONS
MAGNESIUM COMPOUNDS
MAGNETIC RESONANCE
MOLECULAR STRUCTURE
NUCLEAR MAGNETIC RESONANCE
NUCLEIC ACIDS
NUCLEONS
NUCLEOSIDES
NUCLEOTIDES
ORGANIC COMPOUNDS
ORGANIC NITROGEN COMPOUNDS
OVERHAUSER EFFECT
OXYGEN COMPOUNDS
POLYMERIZATION
PROTONS
PURINES
RESONANCE
RIBOSIDES
STRUCTURAL CHEMICAL ANALYSIS
WATER