Chain length-dependent association of distamycin-type oligopeptides with A·T and G·C pairs in polydeoxynucleotide duplexes

Zimmer, C.; Luck, G.; Birch-Hirschfeld, Eckhard; Weiß, R.; Arcamone, Federico; Guschlbauer, Wilhelm

doi:10.1016/0167-4781(83)90004-0

Cited by 25 publications

(10 citation statements)

References 23 publications

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“…It was also found that distamycin A interacted with the bases of only one strand of the duplex (9,17). While the results presented here show agreement with the A.Tspecific binding sites reported, they do not appear to support the further suggestion of a second mechanism of interaction with G.C base pairs at high concentrations of distamycin A (18). The increase in buoyant density of the A.T-rich species was 1.61%, while in the case of the A.T-poor species it was 0.89% at a ratio of 0.5moles of ligand per mole of DNA base pairs (Table 1).…”

Section: And Discussionsupporting

confidence: 77%

Effect of ligand binding on the buoyant density of DNA in Nycodenz gradients

Ford¹,

Rickwood²

1984

Nucl Acids Res

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The effect of ligand binding upon the buoyant density of DNA in Nycodenz gradients has been studied using DNAs of differing base compositions. The effect of both intercalating ligands (ethidium bromide and proflavin) and non-intercalating ligands (distamycin A, DAPI and netropsin) has been studied. The binding of intercalating ligands to DNA has essentially no effect on the buoyant density of DNA in Nycodenz gradients. The nonintercalating ligands were found to increase the buoyant density of DNA in a base specific manner. The increase in buoyant density can be interpreted in terms of disruption of the hydration shell of the DNA molecule caused by the binding of the ligand along the minor groove of the DNA helix.

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Section: And Discussionsupporting

confidence: 77%

Effect of ligand binding on the buoyant density of DNA in Nycodenz gradients

Ford¹,

Rickwood²

1984

Nucl Acids Res

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“…If the natural distamycin molecule is designated as Dst-3 (for its three pyrrole rings), synthetic analogues with as few as two or as many as seven pyrroles can be prepared. Comparative studies have been made of binding preferences of netropsin and Dst-2 through Dst-5 (23,(32)(33)(34). Although netropsin and Dst-2 apparently demand 4-base-pair sites containing only ART base pairs, the longer distamycin analogues become increasingly tolerant of occasional isolated G-C base pairs, particularly near the ends of a binding site.…”

mentioning

confidence: 99%

The molecular origin of DNA-drug specificity in netropsin and distamycin.

Kopka¹,

Yoon²,

Goodsell³

et al. 1985

Proc. Natl. Acad. Sci. U.S.A.

800

577

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X-ray analysis of the complex of netropsin with the B-DNA dodecamer of sequence C-G-C-G-A-A-T-TBrC-G-C-G reveals that the antitumor antibiotic binds within the minor groove by displacing the water molecules of the spine of hydration. Netropsin amide NH furnish hydrogen bonds to bridge DNA adenine N-3 and thymine 0-2 atoms occurring on adjacent base pairs and opposite helix strands, exactly as with the spine of hydration. The narrowness of the groove forces the netropsin molecule to sit symmetrically in the center, with its two pyrrole rings slightly non-coplanar so that each ring is parallel to the walls of its respective region of the groove. Drug binding neither unwinds nor elongates the double helix, but it does force open the minor groove by 0.5-2.0 A, and it bends back the helix axis by 8°across the region of attachment. The netropsin molecule has an intrinsic twist that favors insertion into the minor groove of B-DNA, and it is given a small additional twist upon binding. The base specificity that makes netropsin bind preferentially to runs of four or more ACT base pairs is provided not by hydrogen bonding but by close van der Waals contacts between adenine C-2 hydrogens and CH groups on the pyrrole rings of the drug molecule. Substitution of one or more pyrroles by imidazole could permit recognition of G'C base pairs as well, and it could lead to a class of synthetic "lexitropsins," capable of reading any desired short sequence of DNA base pairs.Netropsin and its close relative distamycin ( Fig. 1) are antiviral antitumor antibiotics that, although too toxic for clinical use, have received extensive study as the paradigms of base-specific yet non-intercalative DNA-binding drug molecules. First isolated from Streptomyces netropsis in 1951 (1, 2), netropsin exerts its biological activity by binding tightly to double-helical B-DNA, interfering with both replication and transcription (3, 4). It shows little or no affinity for single-stranded DNA or RNA or for double-stranded RNA or DNA-RNA hybrids (3-5), suggesting that it does not bind to the A helix. It also fails to bind to left-handed Z-DNA; in fact, binding of netropsin to DNA favors A-to-B and Z-to-B helix transitions (6, 7).Chemical protection studies (3,4,8) and Overhauser NMR experiments (9) indicate that netropsin does not intercalate between base pairs, but it binds within the minor groove of the intact double helix, using hydrogen bonds between netropsin amide NH and exposed adenine N-3 and thymine 0-2 on the floor of the minor groove. The drug molecule attaches to clusters of four or more A'T or ITC, but not to G-C, base pairs (3, 10, 11). Alternating A-T-A-T regions bind netropsin less well than continuous runs of A or T (12, 13). Binding involves both an electrostatic component from the two cationic ends and hydrogen bonds from the central three amide NH groups, although neither aspect is absolute- FIG. 1. The netropsin molecule can be regarded as being assembled from (left to right): guanidinium, amide, methylpyrrole, amide, methylpyrr...

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“…It is known from equilibrium binding studies of distamycin analogues that homopolymer dA-dT sequences are preferred over alternating d(A-T) d(A-T) copolymer sequences (6, 7). The question arises whether G-C base pairs are permissible in the preferred binding sites of netropsin, distamycin, or higher oligo(N-methylpyrrolecarboxamide) homologs on DNA (6,7,23). P4E binds (5'-3') G-A-A-A-T-T, P5E binds A-G-A-A-A-T-T, and P6E binds T-A-G-A-A-A-T-T on the 381-bp fragment (Fig.…”

Section: Discussionmentioning

confidence: 99%

Sequence-specific recognition of B-DNA by oligo(N-methylpyrrolecarboxamide)s.

Youngquist¹,

Dervan²

1985

Proc. Natl. Acad. Sci. U.S.A.

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Four homologous oligopeptide-EDTA molecules, tri-, tetra, penta-, and hexa(N-methylpyrrolecarboxamide)-EDTA, in the presence of Fe(II), 02, and dithiothreitol, cleave 32P-end-labeled restriction fragments from plasmid pBR322 DNA at common locations rich in A-T base pairs that differ in the size of the binding site. From analysis of the cleavage patterns visualized by high-resolution denaturing gel electrophoresis, the oligopeptides with three, four, five, and six Nmethylpyrrolecarboxamide units, containing four, five, six, and seven amide NHs, bind sites of A-T-rich DNA consisting of five, six, seven, and eight contiguous base pairs, respectively. The general rule of n amides affording binding site sizes of n + 1 base pairs is consistent with the oligopeptides binding in the minor groove of right-handed DNA, with the amide NH groups forming bridges between the adjacent N-3 and 0-2 atoms of adenine or thymine on opposite strands of the DNA helix.Netropsin and distamycin A are antibiotics active against fungi, bacteria, and viruses. These di-and tripeptides show a marked preference for DNA rich in adenine (A) and thymine (T) and have binding sites four to six base pairs in size (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11). From a recent x-ray analysis of the complex of netropsin with the B-DNA dodecamer of sequence C-G-C-G-A-A-T-T-C-G-C-G, Dickerson and coworkers provide a molecular basis for the sequence-specific recognition of DNA by netropsin, and by extension, distamycin (12). They find that netropsin sits symmetrically in the center of the minor groove of right-handed DNA and displaces the water molecules of the spine of hydration (12). Each of its three amide NH groups forms a bridge between adjacent adenine N-3 or thymine 0-2 atoms on opposite helix strands (12). This explains recent solution data that distamycin analogues having n amides characteristically bind to n + 1 successive base pairs (13)(14)(15). Dickerson and coworkers suggest that the base specificity of netropsin for contiguous sequences of A-T base pairs in B-DNA is provided not by hydrogen bonding but by close van der Waals contacts between adenine C-2 hydrogens and CH groups on the pyrrole rings of the oligopeptide molecules (12). Because N-methylpyrrolecarboxamides could be used as recognition elements for the design of synthetic sequence-specific DNA-binding molecules, the question arises whether higher numbers of contiguous Nmethylpyrrolecarboxamides in synthetic oligopeptides would still fit the natural twist of the B-DNA helix (13-18).Affinity Cleaving. Attachment of DNA-cleaving moieties, such as EDTA-Fe(II) (19,20), to DNA-binding molecules followed by DNA cleavage pattern analysis using high-resolution denaturing gel electrophoresis is a useful method for determining the binding locations, site size, and orientation of small molecules on native DNA (14-18). The resulting cleavage patterns are simply the positive image visualized on an autoradiogram with respect to the negative image produced by cleavage inhibition patterns ("footprint...

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Chain length-dependent association of distamycin-type oligopeptides with A·T and G·C pairs in polydeoxynucleotide duplexes

Cited by 25 publications

References 23 publications

Effect of ligand binding on the buoyant density of DNA in Nycodenz gradients

Effect of ligand binding on the buoyant density of DNA in Nycodenz gradients

The molecular origin of DNA-drug specificity in netropsin and distamycin.

Sequence-specific recognition of B-DNA by oligo(N-methylpyrrolecarboxamide)s.

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