ABSTRACT Since the origin of first aminoglycosides antibiotics, streptomycin, isolated by Selman Waksman about 60 years ago, a number of aminoglycosides antibiotics were discovered to treat different infections. Neomycin class aminoglycosides were found to originally target the A site 16S rRNA in the 30S subunit of the ribosome within the Gram-negative bacteria. In addition to its antibacterial effect, aminoglycosides were also found to binding to various other viral RNA structures such as TAR and RRE of HIV, Group I introns and hammerhead ribozyme, implying its potential to be used as antiviral reagent. Furthermore, previous studies in our laboratory discovered a new class of targets, triple helix nucleic acids for aminolgycosides. Aminoglycosides, especially neomycin, shows potent stabilization effect of poly(dA)2poly(dT), poly(rA)2poly(rU), short-mixed-base oligomers, an intramolecular 12-mer triplex, DNA/RNA hybrid duplexes/triplexes and even G-tetraplex. The binding infidelity of aminoglycosides induces a variety of problems such as drug resistance and adverse side effects, thereby diminishing their therapeutic application. Increase of aminoglycoside antibiotics binding selectivity has become imperative. Chemical derivatization, either modifying a specific functional group or conjugating them with other ligands, has developed quickly in the past decade to improve aminoglycosides selectivity and expand them for a new therapeutic application. Aminoglycosides dimer, intercalator-neomycin conjugate and minor groove binder-neomycin conjugate were synthesized and studied by our laboratory. Primary study showed that the binding selectivity was achieved, for example, a neomycin dimer favors an AT-rich duplex at nanomolar scale. However, in order to understand better the aminoglycosides binding selectivity and achieve the different therapeutic applications, a comprehensive picture of aminoglycosides binding to a variety of nucleic acids is a requirement. Unfortunately, this study is still in lack. This work considers the neomycin class aminoglycosides, especially neomycin which has the most amino groups (6) relative to other aminoglycosides. The binding to a broad range of nucleic acids will be considered, and these targets include single strand RNA, AT/GC rich duplexes, TAT DNA triplex oligomer and polymer, AU rich RNA duplex and triplex, hybrid duplexes, G-tetraplex, polydC intercalating tetraplex, and A site 16S rRNA. The common thread of those structures that neomycin favorably binds to lies in their propensity toward an A-type conformation. The more A like the conformation is, the more favorably neomycin binds to it. The complete thermodynamic and kinetic studies of aminoglycosides interaction with various nucleic acids were conducted mainly via techniques including UV thermal denaturation, circular dichroism, fluorescence, differential scanning calorimetry, isothermal titration calorimetry, and surface plasmon resonance
