Structure-function relationships of phenoxazine nucleosides for identification of mismatches in duplex DNA by fluorescence spectroscopy

The effects of the flanking sequence on the mismatch-detection capabilities of the fluorescent nucleoside phenoxazine (tC(O)) were examined in a systematic fashion, and compared to the previously reported fluorescent, phenoxazine-based nucleoside Ç(f) . We see some similarities for the two fluorescent nucleosides, for example, the emission intensity of the C-mismatched duplex is always the highest, and a three-peak pattern in the spectrum emerges when the fluorosides are base-paired with A. However, phenoxazine was only able to distinguish a mismatch from the fully base-paired duplex in 11 out of 16 flanking sequences, and was able to identify each of the mismatches in six of those sequences. Therefore, tC(O) shows poorer discrimination of mismatches than was previously reported for Ç(f) , which could be used to identify all base-pairing partners in all immediately flanking sequences, albeit in some cases by using mercuric ions to selectively quench the emission of the T-mismatched duplex. The mercuric titration might resolve the overlap of fluorescence curves of tC(O) in some flanking sequences, but not for 5'-d(CtC(O) G) and 5'-d(TtC(O) A) due to overlap of A-mismatch and G-match fluorescence curves. A pH titration was performed on Ç(f) , tC(O) and a N5-methylated derivative of tC(O) , which showed that the emergence of the three-peak pattern is associated with the de-protonation of N5 in the fluorosides. We also show that neither the α- nor β-anomer of the phenothiazine nucleoside (tC) was able to detect a mismatch in any of the flanking sequences examined.

Comparison of a nucleosidic vs non-nucleosidic postsynthetic "click" modification of DNA with base-labile fluorescent probes

The azides 1 and 2 bearing a phenoxazinium and a coumarin fluorophore, respectively, were applied in postsynthetic "click"-type bioconjugation and coupled to oligonucleotides modified with alkyne groups using two alternative approaches: (i) as a nucleotide modification at the 2'-position of uridine and (ii) as a nucleotide substitution using (S)-(-)-3-amino-1,2-propanediol as an acyclic linker between the phosphodiester bridges. The corresponding alkynylated phosporamidites 3 and 6 were used as DNA building blocks for the preparation of alkyne-bearing DNA duplexes. The base pairs adjacent to the site of modification and the base opposite to it were varied in the DNA sequences. The modified duplexes were investigated by UV/vis absorption spectroscopy (including melting temperatures) and fluorescence spectroscopy in order to study the different optical properties of the two chromophores and to evaluate their potential for bioanalytical applications. The sequence-selective fluorescence quenching of phenoxazinium 1 differs only slightly and does not depend on the type of modification, meaning whether it has been attached to the 2'-position of uridine or as DNA base surrogate using the acyclic glycol linker. The 2'-chromophore-modified uridine still recognizes adenine as the counterbase, and the duplexes exhibit a sufficient thermal stability that is comparable to that of unmodified duplexes. Thus, the application of the 2'-modification site of uridine is preferred in comparison to glycol-assisted DNA base surrogates. Accordingly, the coumarin dye azide 2 was attached only to the 2'-position of uridine. The significant Stokes shift of approximately 100 nm and the good quantum yields make the coumarin chromophore a powerful fluorescent label for nucleic acids.

Synthetic incorporation of Nile Blue into DNA using 2'-deoxyriboside substitutes: Representative comparison of (R)- and (S)-aminopropanediol as an acyclic linker

The Nile Blue chromophore was incorporated into oligonucleotides using "click" chemistry for the postsynthetic modification of oligonucleotides. These were synthesized using DNA building block 3 bearing an alkyne group and reacted with the azide 4. (R)-3-amino-1,2-propanediol was applied as the linker between the phosphodiester bridges. Two sets of DNA duplexes were prepared. One set carried the chromophore in an A-T environment, the second set in a G-C environment. Both were characterized by optical spectroscopy. Sequence-dependent fluorescence quenching was applied as a sensitive tool to compare the stacking interactions with respect to the chirality of the acyclic linker attachment. The results were compared to recent results from duplexes that carried the Nile Blue label in a sequentially and structurally identical context, except for the opposite chirality of the linker ((S)-3-amino-1,2-propandiol). Only minor, negligible differences were observed. Melting temperatures, UV-vis absorption spectra together with fluorescence quenching data indicate that Nile Blue stacks perfectly between the adjacent base pairs regardless of whether it has been attached via an S- or R-configured linker. This result was supported by geometrically optimized DNA models.

Fluorescent color readout of DNA hybridization with thiazole orange as an artificial DNA base

A fluorescent chameleon: A single thiazole orange (TO) dye, when used as an artificial DNA base shows the typical green emission, whereas the interstrand TO dimer exhibits an orange excimer-type emission inside duplex DNA (see picture).

Pathways of excess electron transfer in phenothiazine-tethered DNA containing single-base mismatches

The effects of local structural disorder on excess electron transfer (EET) in DNA were investigated by evaluating photoinduced electron transfer in phenothiazine (PTZ)-modified oligodeoxynucleotides bearing single-base mismatches. Unexpectedly, more efficient electron transfer was observed for the mismatched duplexes than for the complementary DNA, suggesting that distraction of hydrogen bond interaction at the mismatch site enables electron injection or hopping beyond the mismatch sites. It was also anticipated that water accessibility of the mismatched nucleobases could affect EET because protonation of the electron-captured pyrimidine intermediates became competitive to EET, especially at the mismatch sites.

Thiazole orange and Cy3: improvement of fluorescent DNA probes with use of short range electron transfer

Thiazole orange was synthetically incorporated into oligonucleotides by using the corresponding phosphoramidite as the building block for automated DNA synthesis. Due to the covalent fixation of the TO dye as a DNA base surrogate, the TO-modified oligonucleotides do not exhibit a significant increase of fluorescence upon hybridization with the counterstrand. However, if 5-nitroindole (NI) is present as a second artificial DNA base (two base pairs away from the TO dye) a fluorescence increase upon DNA hybridization can be observed. That suggests that a short-range photoinduced electron transfer causes the fluorescence quenching in the single strand. The latter result represents a concept that can be transferred to the commercially available Cy3 label. It enables the Cy3 fluorophore to display the DNA hybridization by a fluorescence increase that is normally not observed with this dye.