Peptide nucleic acid–DNA duplexes: Long range hole migration from an internally linked anthraquinone

Bruce Armitage, Danith Ly, Troels Koch, Henrik Frydenlund, Henrik Ørum, Hans G. Batz, and Gary B. Schuster

PNAS
November 11, 1997

vol. 94

no. 23

12320-12325

Abstract

The
discovery that peptide nucleic acids (PNA) mimic DNA and RNA by forming
complementary duplex structures following Watson–Crick base pairing
rules opens fields in biochemistry, diagnostics, and medicine for
exploration. Progress requires the development of modified PNA duplexes
having unique and well defined properties. We find that anthraquinone
groups bound to internal positions of a PNA oligomer intercalate in the
PNA–DNA hybrid. Their irradiation with near-UV light leads to electron
transfer and oxidative damage at remote GG doublets on the
complementary DNA strand. This behavior mimics that observed in related
DNA duplexes and provides the first evidence for long range electron
(hole) transport in PNA–DNA hybrid. Analysis of the mechanism for
electron transport supports hole hopping.

 

Peptide nucleic acid (PNA) oligomers are DNA/RNA analogs (see Fig. 1) in which the natural sugar–phosphate backbone is replaced by a synthetic peptide backbone (1).
PNA oligomers that contain purine and pyrimidine nucleobases hybridize
with complementary DNA and RNA strands to form right-handed,
double-helical complexes according to the Watson–Crick rules of
hydrogen bond-mediated base pair formation (2). Although much has been learned about the structural (3) and thermodynamic (4)
factors involved in hybridization, little is known about the chemical
reactivity of PNA/DNA hybrids. It is crucial to understand how PNA/DNA
hybrids mimic the reactions and functions of duplex DNA. Of immediate
importance for their application as clinical diagnostic agents is
investigation of the conductivity of DNA and its PNA analogs (5, 6). 

DNA must balance the dual requirements of chemical stability and ease of transcription and replication (7).
It is clear that DNA is far from inert toward a variety of different
reactive species, particularly oxidizing agents. Oxidative damage to
DNA produced by normal metabolism, deep-UV laser irradiation (8), gamma rays (9), or pulse radiolysis (10) accumulates at guanine residues, an effect attributed to one-dimensional migration of a radical cation (“hole”) along the
DNA helix (11). Both the low oxidation potential and reactivity of the guanine radical cation contribute to the effectiveness of guanine
as a trap for the migrating hole. Because guanine lesions may be the major cause of mutations (12),
intense attention is focused on understanding the conductivity
properties of DNA to elucidate the mechanisms by which migration of
oxidative damage occurs (13). In this regard, the recent reports by Barton and coworkers are particularly important (14, 15).
They describe a system consisting of a rhodium complex that is
covalently linked to one end of a DNA duplex. Irradiation caused damage
to the DNA more than 30 Å from where the complex was presumed to
intercalate. This observation opens up exciting opportunities to study
the factors that control hole migration in nucleic acids.

Photosensitizers
often react with nucleic acids by single electron transfer to oxidize a
base. Recent findings reveal that the light-induced reactions of a
photosensitizer bound to duplex DNA by intercalation frequently
generate alkali-dependent cleavage sites selectively at the 5′-G of
G-purine doublets, with a strong preference for GG steps. These
photosensitizers include substituted anthraquinones (16, 17), naphthalimides (18, 19), a rhodium metal complex (14), and riboflavin (20). Breslin and Schuster (17)
demonstrated unambiguously that GG-selective, photoinduced damage of
DNA arises by an electron transfer pathway from an intercalated
anthraquinone. Time-resolved spectroscopy reveals that the excited
state of the quinone accepts an electron from a base in the DNA within
20 ps of excitation (21). The base radical cation (hole) can either recombine with the electron, be trapped by reaction with water and/or oxygen,
or migrate along the DNA helix to the lowest oxidation potential sites that serve as traps (22, 23).

We
prepared a series of PNA oligomers with anthraquinone derivatives (AQ)
covalently linked to internal positions. The ability of the quinone to
photosensitize DNA damage by electron transfer when bound to the duplex
by intercalation suggested it could serve a similar role in
PNA-containing duplexes. The inability of common intercalators to bind
to PNA (24)
required that the quinone chromophore be covalently linked to the PNA
backbone. The facile modification of PNA at internal residues as well
as the superior hybridization properties of PNA oligomers offer
distinct advantages relative to synthesis of modified DNA oligomers.
Irradiation of the anthraquinone in the hybrid duplex leads to long
distance hole migration and damage at GG sites in the DNA strand.
Additional experiments reveal the mechanism for hole migration by its
directional preference in the stacked base pairs of a PNA–DNA hybrid
duplex.