Research Projects

Native DNA is a nonfluorescent biomacromolecule, but it becomes fluorescent by the appropriate structural induction of functional group/aryl substituents. Nucleobases Adenine (and cytosine) are electron donors, while guanine (and cytosine) are electron acceptors. Generally, electrons withdrawing group at Adenine/Cytosine and electron donating at thymidine/uridine/guanine enhance fluorescence because of the push-pull effect on intramolecular charge transfer. The conjugated aromatic systems, comprising donor and acceptor groups, are prone to exert a push-pull effect in the intramolecular charge transfer (ICT) and exhibit enhanced fluorescence. Also, the conjugation of the donor, the electron-rich aryl ring possessing an electron-donating group, to the cytosine/guanine derivative, exerts a push-pull effect, and the whole conjugated system becomes fluorescent. However, their vice-versa conjugations are non-fluorescent or weakly fluorescent. Most of the fluorescent nucleosides and their DNA are prepared through the conjugation of big benzenoid aromatic dyes/chromophores. However, nonbenzenoid aromatic scaffold Tropolone also occurs in plants, fungi, and bacteria as a constituent of Troponoid natural products that have a wide spectrum of bioactivity, such as antimicrobial and anti-tumor activities. Tropolone exhibits unique photophysical properties, including fluorescence (though low QY) and metal chelating properties with transition metal ions (Cu2+/Zn2+). Thus, the troponyl-DNA is lucrative, though it is challenging in synthesis. We hypothesized that tropolone DNA would bind with cellular Cu(II) and Zn(II) and metal and play a significant role in replication and transcription. In the repertoire of fluorescent DNA synthesis, recently we have begun to study the tropolonylated DNA and its photophysical and biochemical properties. Tropolone could be linked to nucleobases through a linker or without a linker. Previously, we have explored the tropolonyl-Ethyn-dU/ tropolonyl-triazole-dU DNA analogs that exhibit remarkable pH-dependent fluorescence after duplexation with complementary base-pairs, where Ethyn and triazole are linkers. Our previous studies have encouraged us to explore further tropolone-conjugated DNA for tuning fluorescence properties with all four nucleobases. Herein, we propose the direct arylation of nucleobases with 5-iodo-/bromo-/borate-Tropolone derivatives (ICT Acceptor) under Pd-catalyzed C(sp2)-H activation/Suzuki Miyaura coupling reaction conditions. These nucleosides would be derivatized into their respective phosphoramidites and triphosphates to incorporate into sequence-specific DNA. We propose the synthetic routes of all four tropolonyl-DNA nucleosides (see technical details). We would examine their photophysical properties. Expectedly, tropolonyl-dA/tropolonyl-dC analogues would be the best scenario for ICT because of an appropriate donor-acceptor combination and would exhibit strong fluorescence as compared to the other tropolonyl-dG/tropolonyl-dC nucleosides. Additionally, Tropolone's lipophilic properties would enhance the cell-permeability of tr-DNA irrespective of nucleobases. So we have planned to examine their cell permeability and cytotoxicity with normal and cancer cells. Next, its (tr-dA) phosphoramidite will be considered to incorporate in DNA oligo by DNA synthesizer for examining DNA duplex formation by CD. Next, it's (tr-dA) triphosphate would be tested as substrate for DNA polymerase-dependent DNA synthesis. All four tropolonyl-nucleosides (tr-dN) would exhibit metal chelating features owing to the tropolone group through primer extension methods. We also plan to incorporate tr-dN into DNA by enzymatically/photophysically that will generate a new type of functional DNA possessing fluorescence and metal chelating properties. Their outcome will provide a new avenue for nucleic acid research with tropolonyl functional nucleosides/DNA. This DNA will be a potential theranostic agent.