Fluorescent Sequence-Specific dsDNA Binding Oligomers

Sequence-specific detection methods for double-stranded DNA (dsDNA) that obviate the need for denaturation would provide useful tools for bioorganic chemistry and genetics.¹ Previous efforts, such as molecular beacons² or peptide nucleic acid–thiazole orange (PNA-TO) conjugates,³ require harsh denaturation conditions for hybridization to single-stranded DNA.^2–4 Previous efforts from our laboratory for the sequence-specific detection of dsDNA have focused on pyrrole–imidazole (Py-Im) polyamide–fluorophore conjugates, such as tetramethylrhodamine (TMR) or thiazole orange (TO), that bind in the minor groove of DNA.^5–7 TMR fluorescence was shown to be quenched when the fluorophore was covalently linked to the ring nitrogen of a pyrrole recognition element within a polyamide.⁵ Remarkably, fluorescence was restored in a sequence-dependent manner upon binding to dsDNA.⁵ Similarly, polyamide–TO intercalator conjugates also demonstrate fluorescence enhancement in the presence of match dsDNA.⁶

Having established Py-Im polyamide–dye conjugates as a suitable platform for sequence-specific fluorescent dsDNA detection,^5,6 we sought to develop a new class of fluorescent DNA binders wherein the fluorescent moiety is an integrated part of the recognition modules. We report here the design of sequence-specific fluorescent dsDNA-binding oligomers (Figure 1) which incorporate multiple 6-5 fused dimer recognition modules⁸ and show a marked fluorescent enhancement upon excitation at 340 nm in the presence of dsDNA. Oligomer O1 contains the chlorothiophene-benzimidazole (Ct-Bi-), pyrrole-imidazopyridine (-Py-Ip-), and imidazole-hydroxybenzimidazole (-Im-Hz-) recognition modules, whereas oligomer O2 contains imidazole-imidazopyridine (Im-Ip-) and two pyrrole-benzimidazole (-Py-Bi-) modules. The binding affinities of O1 and O2 targeted to two biologically important sequences, 5′-ATACGT-3′ (O1) and 5′-WGGGGW-3′ (O2), were determined to be K_a = 1.6 × 10⁹ M⁻¹ and 2.6 × 10⁹ M⁻¹, respectively, by quantitative DNase I footprinting.^9–11

Figure 1.

Structure of oligomers. (a) Oligomer O1 containing Ct-Bi-, -Py-Ip-, and -Im-Hz- recognition modules. (b) Oligomer O2 containing Im-Ip-and two -Py-Bi- recognition modules.

A library of dsDNA hairpins containing six base-pair match and mismatch binding sites for O1 and O2 was used to investigate their emission properties (Figure 2). The dsDNA library for O1 and O2 contained match sites (1 and 8, respectively), single base-pair (bp) mismatch sites (2–5 and 10–12, respectively), double bp mismatch sites (6 and 13, respectively), and full mismatch sites (7 for both oligomers). The dsDNA 9 contains the 4-G match site of oligomer O2; however, the flanking sequence has been changed to emphasize the effect on binding. The presence of G · C bp under the tail is expected to lower the binding affinity of O2 as compared to that of dsDNA 8.¹²

Figure 2.

Design of dsDNA library. (a) dsDNA sequences used for O1. (b) dsDNA sequences used for O2.

Oligomers O1 and O2, (1 μM concentration) were each incubated with an increasing concentration (1 nM to 1 μM) of dsDNA, and their emission spectra were recorded after excitation at 340 nm. The oligomers exhibited a marked increase in fluorescence upon addition of dsDNA containing their match site 1 and 8, respectively (Figures 3 and 4).¹³ Oligomer O1 showed a moderate decrease in fluorescence intensity in the presence of dsDNA 2, but proved to be much more sensitive to the incorporation of single base-pair mismatches at the alternate positions in dsDNAs 3–5 (Figure 4a). The incorporation of multiple base-pair mismatches in dsDNAs 6 and 7 showed a significant diminution in fluorescence intensity for O1. Oligomer O2 exhibited a similar trend in sequence specificity, with a moderate decrease in fluorescence intensity observed upon incorporation of single base-pair mismatches (9–12) and a more significant decrease with multiple mismatches (13 and 7, Figure 4b).

Figure 3.

Fluorescence emission spectra of O1 and O2 (1 μM) after 12 h incubation with their match binding site dsDNA (λ_Ex = 340 nm). (a) Data for compound O1. (b) Data for compound O2. The emission was shown to plateau beyond 1 equiv DNA. (See Supporting Information for plots.)

Figure 4.

Plot of dsDNA concentration versus normalized fluorescence for each dsDNA. (a) Data for compound O1. (b) Data for compound O2.

Sequence-specific DNA binding molecules containing a fluorescent switch integrated as part of the recognition modules provides a method to detect DNA sequences without denaturation and in the absence of conjugation to a dye molecule. Fluorescent oligomers may be useful as site-specific chromosome paints for telomeric and centromeric repeats14a,b and could provide insight into cellular trafficking of DNA binding compounds.