Modified guanines as constituents of smart ligands for nucleic acid quadruplexes
| Authors | |
|---|---|
| Year of publication | 2016 |
| Type | Article in Periodical |
| Magazine / Source | Chemistry - A European Journal |
| MU Faculty or unit | |
| Citation | |
| web | DOI: 10.1002/chem.201601608 |
| Doi | http://dx.doi.org/10.1002/chem.201601608 |
| Field | Physical chemistry and theoretical chemistry |
| Keywords | Density functional calculations; DNA recognition; G-quadruplexes; Nucleobases; pi interactions; stacking; hydrogen-bond cooperativity |
| Attached files | |
| Description | Repetitive guanine-rich nucleic acid sequences play a crucial role in maintaining the genome stability and cell live cycle and represent potential targets for regulatory drugs. Recently, it has been demonstrated that the guanine-based ligands with porphyrin core can be used as markers of G-quadruplex assemblies in the cell tissues. In this contribution we explore the model systems of the guanine-based ligands by methods of density-functional theory (DFT). We calculate the energy of formation for modified guanine tetrads as well as those for the modified tetrads stacked on the top of natural guanine tetrads. We decompose interaction energy to the contributions of hydrogen bonding, stacking, and ion coordination and the twist-rise potential energy scan is performed to find the individual local minima. The energy decomposition analysis reveals the impact of various substituents (F, Cl, Br, I, Me, NMe2) on individual energy terms. In addition, we analyze the cooperative reinforcement in forming the modified tetrads and stacked tetrads as well as the frontier orbitals participating in the hydrogen bonding framework involving HOMO-LUMO gap between the occupied sigma(HOMO) on the proton-accepting C=O and =N- groups and unoccupied sigma(LUMO) on the N-H groups. The investigated systems are demonstrated to have a potential in the ligand development mainly due to the stacking enhancement compared to natural guanine, a reference used. |
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