Concerted Intercalation and Minor Groove Recognition of DNA by a Homodimeric Thiazole Orange Dye

Abstract

The thiazole orange dye TOTO binds to double-stranded DNA (dsDNA) by a sequence selective bis-intercalation. Each chromophore is sandwiched between two base pairs in a (5'-CpT-3'):(5'-ApG-3') site, and the linker spans two base pairs in the minor groove. We have used one- and two-dimensional NMR spectroscopy to examine the dsDNA binding of an analogue of TOTO in which the linker has been modified to contain a bipyridyl group (viologen) that has minor groove binding properties. We have investigated the binding of this analogue, called TOTOBIPY, to three different dsDNA sequences containing a 5'-CTAG-3', a 5'-CTTAG-3', and a 5'-CTATAG-3' sites, respectively, demonstrating that TOTOBIPY prefers to span three base pairs. The many intermolecular NOE connectivities between TOTOBIPY and the d(CGCTTAGCG):d(CGCTAAGCG) oligonucleotide in the complex shows that the bipyridyl-containing linker is positioned in the minor groove and spans three base pairs. Consequently, we have succeeded in designing and synthesizing a ligand that recognizes an extended recognition sequence of dsDNA as the result of a concerted intercalation and minor groove binding mode.

Exploring Base‐Pair‐Specific Optical Properties of the DNA Stain Thiazole Orange

“…Binding of cyanine dyes to nucleic acids has been widely investigated, and oxazole yellow and thiazole orange are probably amongst the most studied asymmetric cyanines. [7][8][9][10][11][12][13][14][15] The monomeric cyanines bind DNA in different ways; intercalation between base pairs, association to the minor groove as monomers, dimers, and higher aggregates, and probably also by interaction of positively charged dyes with the negatively charged ribosephosphate backbone. [7,9,10,46] A great deal of research has been devoted to the base-pair specificity of DNA binding.…”

“…However, the slow decay process also showed high hybridization-induced responses (decrease in decay time by 0.12-1.03 ns and increase in amplitude by factors of [4][5][6][7][8][9][10][11][12][13][14][15][16][17][18]. Although the fast decay process showed relatively little sensitivity to double-strand formation, it was this decay along with the slow decay process that exhibited the highest responsiveness to the presence of single-mismatched stacking partners.…”

Evaluation and Elucidation of DNA‐Containing Viologen Dendrimer Complex Formation

“…These viologens are inserted into the minor grooves of the DNA, findings that have been supported by AMBER force field and molecular dynamics (MD) calculations. [18,43] If the AMBER or MM+ calculations were initiated with one monomeric viologen 2 sandwiched in the minor groove, the N-P distances ranged from 0.44 to 0.52 nm in the AMBER force field, and from 0.47 to 0.65 nm in the MM+ force field. The viologens 2, which are placed close to the phosphate groups in the major groove, show smaller distances of around 0.33-0.38 nm in the AMBER force field and 0.40-0.46 nm in the MM+ force field (Figure 9, left).…”

Aptamer-based optical switch for biosensors

“…These so called "staining dyes" are nonfluorescent in solution but form a highly fluorescent complex with DNA by intercalating through the DNA double helix and thus have been widely used in dsDNA labeling, detecting, sizing, and DNAprotein study. [22][23][24] In this regard, it is worth noting that the non-covalent conjugation of a fluorophore to an aptamer may ultimately compromise the affinity of the aptamer to its ligand. 11 This new approach based on label-free aptamer and an intercalating dye would be useful for high-throughput screening in drug and environmental monitoring and further widely applicable for the analysis and study of proteins in biochemical and biomedical studies.…”