Sequence-specific fluorometric recognition of HIV-1 ds-DNA with zwitterionic zinc(II)-carboxylate polymers

Four water-stable zwitterionic zinc-carboxylate polymers are prepared by reacting N-carboxymethyl-(3,5-dicarboxy)-pyridinium bromide (H₃CmdcpBr) with zinc(II) nitrate in the presence of NaOH, through adjusting the solvents and ancillary ligands. With H₂O as the solvent and the absence of an ancillary ligand, a two-dimensional (2D) polymer network [Zn(Cmdcp)(H₂O)]_n (1) is formed. In a mixed H₂O/DMF solvent and with the presence of chelating ligands 2,2'-bipyridine (bipy), 1,10-phenanthroline (phen) and 2-(4-pyridyl)benzimidazole (pbz), a one-dimensional (1D) polymer of {[Zn₂(Cmdcp)(bipy)₂(H₂O)₅](NO₃)₂·3H₂O}_n (2), a mononuclear ionic species of [Zn(phen)(H₂O)₄][Cmdcp] (3), and a 2D polymer of {[Zn(Cmdcp)(pbz)][pbz]·7H₂O}_n (4) are accordingly formed. Compounds 1-4 are characterized by IR, elemental analyses and single crystal X-ray crystallography. Compound 2 strongly adsorbs single-stranded DNA (ss-DNA) probe (denoted as P-DNA) labeled with carboxyfluorescein (FAM) and quenches its fluorescence via a photo-induced electron transfer process. If, however, a double-stranded DNA (ds-DNA) of the human immunodeficiency virus 1 (HIV-1 ds-DNA) is further present, the P-DNA interacts with the major groove in HIV-1 ds-DNA via Hoogsteen hydrogen bonding to form a rigid triplex structure. This results in partial or complete fluorescence recovery depending on the concentration of HIV-1 ds-DNA. The findings are applied in fluorometric sensing of HIV-1 ds-DNA. The calibration plot is linear in the 0-60nM target DNA concentration range, with a 7.4nM detection limit (at a signal-to-noise ratio of 3). The assay is highly specific and not interfered by one base pair mutated for complementary target HIV-1 ds-DNA, complementary ss-DNA, single-base pair mutated for complementary ss-DNA, non-specific ss-DNA sequences, and higher-order dimeric G-quadruplexes.