Abstract
Selective binding to nucleic acids and, more generally, to biopolymers, very often requires at a minimum the presence of specific functionalities and precise spatial arrangement. DNA can fold into defined 3D structures upon binding to metal centers and/or lanthanides. Binding efficiency can be boosted by modified nucleosides incorporated into DNA sequences. In this work the high selectivity of modified nucleosides towards copper (II) ions, when used in the monomeric form, is unexpectedly and drastically reduced upon being covalently attached to the DNA sequence in single-site scenario. Surprisingly, such selectivity is partially retained upon non-covalent (i.e. intercalation) mixture formed by native DNA duplex and a nucleoside in the monomeric form. Exploiting the electron spin properties of such different and rich binding mode scenarios, 1D/2D pulsed EPR experiments have been used and tailored to differentiate among the different modes. An unusual correlation of dispersion of hyperfine couplings and strength of the binding mode(s) is described.
Highlights
Metal ions play important roles in many ribozyme-mediated examples of scission and ligation reactions but their precise role in those reactions in not yet fully understood[1,2,3]
A crowded scenario of binding modes involves: (a) copper(II) free in solution, (b) the monomeric form of the nucleoside combined with Cu2+, (c) native DNA duplex combined with Cu2+, (d) covalently modified DNA sequence with one singly modified nucleotide combined with Cu2+, (e) native DNA sequence with non-covalently attached monomeric nucleoside, combined with Cu2+
The L2 monomer was analyzed by Continuous Wave (CW) and pulsed Electron paramagnetic resonance (EPR) spectroscopy
Summary
Metal ions play important roles in many ribozyme-mediated examples of scission and ligation reactions but their precise role in those reactions in not yet fully understood[1,2,3]. A crowded scenario of binding modes (and binding sites) involves: (a) copper(II) free in solution, (b) the monomeric form of the nucleoside combined with Cu2+, (c) native DNA duplex combined with Cu2+, (d) covalently modified DNA sequence with one singly modified nucleotide combined with Cu2+, (e) native (unmodified) DNA sequence with non-covalently attached (intercalation-type) monomeric nucleoside, combined with Cu2+ Those five different binding modes have been correlated to hyperfine spectroscopy (interactions electron-nuclei) to implement the core of such a fast and straightforward protocol, in order to confirm (or discard) the formation of a complex and to provide preliminary information on the nature of the nuclei that comprise the coordination sphere
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