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Highly fluorescent guanosine mimics for folding and energy transfer studies.

ABSTRACT: Guanosines with substituents at the 8-position can provide useful fluorescent probes that effectively mimic guanine residues even in highly demanding model systems such as polymorphic G-quadruplexes and duplex DNA. Here, we report the synthesis and photophysical properties of a small family of 8-substituted-2'-deoxyguanosines that have been incorporated into the human telomeric repeat sequence using phosphoramidite chemistry. These include 8-(2-pyridyl)-2'-deoxyguanosine (2PyG), 8-(2-phenylethenyl)-2'-deoxyguanosine (StG) and 8-[2-(pyrid-4-yl)-ethenyl]-2'-deoxyguanosine (4PVG). On DNA folding and stability, 8-substituted guanosines can exhibit context-dependent effects but were better tolerated by G-quadruplex and duplex structures than pyrimidine mismatches. In contrast to previously reported fluorescent guanine analogs, 8-substituted guanosines exhibit similar or even higher quantum yields upon their incorporation into nucleic acids (? = 0.02-0.45). We have used these highly emissive probes to quantify energy transfer efficiencies from unmodified DNA nucleobases to 8-substituted guanosines. The resulting DNA-to-probe energy transfer efficiencies (?(t)) are highly structure selective, with ?(t)(duplex)?< ?(t)(single-strand) < ?(t)(G-quadruplex). These trends were independent of the exact structural features and thermal stabilities of the G-quadruplexes or duplexes containing them. The combination of efficient energy transfer, high probe quantum yield, and high molar extinction coefficient of the DNA provides a highly sensitive and reliable readout of G-quadruplex formation even in highly diluted sample solutions of 0.25 nM.

SUBMITTER: Dumas A

PROVIDER: S-EPMC3159459 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature

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Highly fluorescent guanosine mimics for folding and energy transfer studies.

Dumas Anaëlle A Luedtke Nathan W NW

Nucleic acids research 20110506 15

Guanosines with substituents at the 8-position can provide useful fluorescent probes that effectively mimic guanine residues even in highly demanding model systems such as polymorphic G-quadruplexes and duplex DNA. Here, we report the synthesis and photophysical properties of a small family of 8-substituted-2'-deoxyguanosines that have been incorporated into the human telomeric repeat sequence using phosphoramidite chemistry. These include 8-(2-pyridyl)-2'-deoxyguanosine (2PyG), 8-(2-phenylethen ...[more]

PMID: 21551219

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Project description:Photophysical data and orbital energy levels (from electrochemistry) were compared for molecules with the same BODIPY acceptor part (red) and perpendicularly oriented xanthene or BODIPY donor fragments (green). Transfer of energy, hence the photophysical properties of the cassettes, including the pH dependent fluorescence in the xanthene-containing molecules, correlates with the relative energies of the frontier orbitals in these systems. Intracellular sensing of protons is often achieved via sensors that switch off completely at certain pH values, but probes of this type are not easy to locate inside cells in their "off-state". A communication from these laboratories (J. Am. Chem. Soc., 2009, 131, 1642-3) described how the energy transfer cassette 1 could be used for intracellular imaging of pH. This probe is fluorescent whatever the pH, but its exact photophysical properties are governed by the protonation states of the xanthene donors. This work was undertaken to further investigate correlations between structure, photophysical properties, and pH for energy transfer cassettes. To achieve this, three other cassettes 2-4 were prepared: another one containing pH-sensitive xanthene donors (2) and two "control cassettes" that each have two BODIPY-based donors (3 and 4). Both the cassettes 1 and 2 with xanthene-based donors fluoresce red under slightly acidic conditions (pH < ?6) and green when the medium is more basic (>?7), whereas the corresponding cassettes with BODIPY donors give almost complete energy transfer regardless of pH. The cassettes that have BODIPY donors, by contrast, show no significant fluorescence from the donor parts, but the overall quantum yields of the cassettes when excited at the donor (observation of acceptor fluorescence) are high (ca. 0.6 and 0.9). Electrochemical measurements were performed to elucidate orbital energy level differences between the pH-fluorescence profiles of cassettes with xanthene donors, relative to the two with BODIPY donors. These studies confirm energy transfer in the cassettes is dramatically altered by analytes that perturb relative orbital levels. Energy transfer cassettes with distinct fluorescent donor and acceptor units provide a new, and potentially useful, approach to sensors for biomedical applications.

Project description:This paper concerns the development of water-compatible fluorescent imaging probes with tunable photonic properties that can be excited at a single wavelength. Bichromophoric cassettes 1a-1c consisting of a BODIPY donor and a cyanine acceptor were prepared using a simple synthetic route, and their photophysical properties were investigated. Upon excitation of the BODIPY moiety at 488 nm the excitation energy is transferred through an acetylene bridge to the cyanine dye acceptor, which emits light at approximately 600, 700, and 800 nm, i.e., with remarkable dispersions. This effect is facilitated by efficient energy transfer that gives a "quasi-Stokes" shift between 86 and 290 nm, opening a huge spectral window for imaging. The emissive properties of the cassettes depend on the energy-transfer (ET) mechanism: the faster the transfer, the more efficient it is. Measurements of rates of ET indicate that a through-bond ET takes place in the cassettes 1a and 1b that is 2 orders of magnitude faster than the classical through-space, Förster ET. In the case of cassette 1c, however, both mechanisms are possible, and the rate measurements do not allow us to discern between them. Thus, the cassettes 1a-1c are well suited for multiplexing experiments in biotechnological methods that involve a single laser excitation source. However, for widespread application of these probes, their solubility in aqueous media must be improved. Consequently, the probes were encapsulated in calcium phosphate/silicate nanoparticles (diameter ca. 22 nm) that are freely dispersible in water. This encapsulation process resulted in only minor changes in the photophysical properties of the cassettes. The system based on cassette 1a was chosen to probe how effectively these nanoparticles could be used to deliver the dyes into cells. Encapsulated cassette 1a permeated Clone 9 rat liver cells, where it localized in the mitochondria and fluoresced through the acceptor part, i.e., red. Overall, this paper reports readily accessible, cyanine-based through-bond ET cassettes that are lypophilic but can be encapsulated to form nanoparticles that disperse freely in water. These particles can be used to enter cells and to label organelles.

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Highly fluorescent guanosine mimics for folding and energy transfer studies.

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Highly fluorescent guanosine mimics for folding and energy transfer studies.

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