DNA sequence specificity of triplex‐binding ligands

Abstract

We have examined the ability of naphthylquinoline, a 2,7-disubstituted anthraquinone and BePI, a benzo[e]pyridoindole derivative, to stabilize parallel DNA triplexes of different base composition. 1Fluorescence melting studies, with both inter-and intramolecular triplexes, show that all three ligands stabilize triplexes that contain blocks of TAT triplets. Naphthylquinoline has no effect on triplexes formed with third strands composed of (TC) n or (CCT) n , but stabilizes triplexes that contain (TTC) n . In contrast, BePI slightly destabilizes the triplexes that are formed at (TC) n (CCT) n and (TTC) n . 2,7-Anthraquinone stabilizes (TC) n (CCT) n and (TTC) n , although it has the greatest effect on the latter. DNase I footprinting studies confirm that triplexes formed with (CCT) n are stabilized by the 2,7-disubstituted amidoanthraquinone but not by naphthylquinoline. Both ligands stabilize the triplex formed with (CCTT) n and neither affects the complex with (CT) n . We suggest that BePI and naphthylquinoline can only bind between adjacent TAT triplets, while the anthraquinone has a broader sequence of selectivity. These differences may be attributed to the presence (naphthylquinoline and BePI) or absence (anthraquinone) of a positive charge on the aromatic portion of the ligand, which prevents intercalation adjacent to C + GC triplets. The most stable structures are formed when the stacked rings (bases or ligand) alternate between charged and uncharged species. Triplexes containing alternating C + GC and TAT triplets are not stabilized by ligands as they would interrupt the alternating pattern of charged and uncharged residues.Keywords: anthraquinone; molecular beacon; naphthylquinoline; triple helix; triplex-binding ligand.The formation of intermolecular DNA triple helices offers a means for designing agents which can bind to specific DNA sequences [1][2][3][4][5][6]. In this approach, a third strand oligonucleotide binds in the major groove of duplex DNA, forming specific hydrogen bond contacts with substituents on the purines of the duplex base pairs. In these structures the third strand can run either parallel or antiparallel to the duplex purine strand. Parallel triplexes, which have been most widely studied, consist of TAT and C + GC triplets, while the antiparallel motif contains GGC and AAT or TAT triplets. Although triplex-forming oligonucleotides bind to their duplex targets with considerable sequence selectivity, their binding may not be strong. Several strategies have therefore been used to improve their affinity, including the use of base and backbone analogues [7][8][9][10], and tethering DNA binding agents such as acridine [11,12] or psoralen [13] to the end of the oligonucleotide. An alternative strategy uses ligands which bind selectively to triplex (not duplex) DNA and which therefore perturb the equilibrium in the direction of triplex formation. Several such ligands have been described (reviewed in [14]) including 3-methoxy-7H-8-methyl-11 [(3¢-amino) [27,28]. Although most studies with the...

A model for triple helix formation on human telomerase reverse transcriptase (hTERT) promoter and stabilization by specific interactions with the water soluble perylene derivative, DAPER

“…To increase the stability of anti-parallel triplexes [12,34], we have studied the water soluble perylene derivative DAPER (Figure 1c). Studying G-quadruplex stabilizing drugs [35,36], we have previously shown that DAPER is able to selectively bind to G-quadruplex structures with respect to duplex, on account of G-quadruplex larger aromatic area and higher charge density [37][38][39].…”

DNA Major Groove Binders: Triple Helix-Forming Oligonucleotides, Triple Helix-Specific DNA Ligands and Cleaving Agents

“…The only ligand that can stabilize triple helices in the absence of blocks of TႧAxT triplets is amidoanthraquinone. This is most likely due to the absence of a positive charge on the aromatic portion of the ligand [131]. It would be interesting to use competition dialysis to compare the binding of particular ligands to various triple-stranded structures containing a variety of binding sites.…”

A small molecule that induces assembly of a four way DNA junction at low temperature

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