7-Amino actinomycin D bound to single-stranded hairpin DNA enhanced by loop sequence-dependent luminescent Eu3+ and Tb3+ binding

Exploring the Thermodynamics of 7-Amino Actinomycin D-Induced Single-Stranded DNA Hairpin by Spectroscopic Techniques and Computational Simulations

NMR studies have indicated that the anti-tumor therapeutic agent actinomycin D (ACTD) can induce seemingly single-stranded DNA (ssDNA) oligomer 5'-CCGTT₃GTGG-3' to form a hairpin structure with tandem GT mismatches at the stem region next to a loop of three stacked thymine bases. In an effort to uncover the preference of binding sequence and to elucidate the thermodynamics properties of the binding, a combination of spectroscopic techniques and computational simulation studies was performed with d(CCGTT_nGTGG) and d(CCGAA_nGAGG) (denoted as GTT_n and GAA_n, respectively; n = 3, 5, and 7) sequences. In the presence of 7-amino actinomycin D (7AACTD), all the six oligomers formed stable hairpin structures. The GTT₅-7AACTD/GAA₅-7AACTD hairpin structure was more stable than the corresponding GTT_n-7AACTD and GAA_n-7AACTD (n = 3, 7). No significant ΔG difference was observed between GTT_n-7AACTD and GAA_n-7AACTD complexes with the same loop length. In agreement with the 7AACTD-induced hairpin stability results, the binding affinity of GTT_n and GAA_n with 7AACTD increased from n = 3 to n = 5 and then decreased when n is 7. Moreover, GTT_n and GAA_n with the same loop length showed comparable binding affinities to 7AACTD. Furthermore, molecular dynamics simulations found that van der Waals interactions between GTT_n/GAA_n and 7AACTD were the primary attractive forces for 7AACTD binding, and the electrostatic interactions between the carbonyl groups of 7AACTD and bases in the hairpin were the major unfavorable forces. These findings furthered our understanding that 7AACTD is sensitive to the loop size and sequence as well as tandem GT/GA mismatches of their deoxyribonucleic acid (DNA) targets. A deep understanding of the thermodynamics and the molecular recognition mechanism of 7AACTD with ssDNAs would further the development of ACTD-like antitumor agents.

Significant FRET between SWNT/DNA and rare earth ions: a signature of their spatial correlations

Significant acceleration of the photoluminescence (PL) decay rate was observed in water solutions of two rare earth ions (REIs), Tb and Eu. We propose that the time-resolved PL spectroscopy data are explained by a fluorescence resonance energy transfer (FRET) between the REIs. FRET was directly confirmed by detecting the induced PL of the energy acceptor, Eu ion, under the PL excitation of the donor ion, Tb, with FRET efficiency reaching 7% in the most saturated solution, where the distance between the unlike REIs is the shortest. Using this as a calibration experiment, a comparable FRET was measured in the mixed solution of REIs with single-wall nanotubes (SWNTs) wrapped with DNA. From the FRET efficiency of 10% and 7% for Tb and Eu, respectively, the characteristic distance between the REI and SWNT/DNA was obtained as 15.9 ± 1.3 Å, suggesting that the complexes are formed because of Coulomb attraction between the REI and the ionized phosphate groups of the DNA.