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NMR and Paramagnetic Ion Substitution Locates a Modified‐Nucleoside Dependent Metal Binding Site in DNA: Molecular Dynamics, Surface Charge and H 2 O Ordering
Author(s) -
Agris Paul F.,
Stuart John W.,
Guenther Richard,
Basti Mufeed M.
Publication year - 1996
Publication title -
magnetic resonance in chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.483
H-Index - 72
eISSN - 1097-458X
pISSN - 0749-1581
DOI - 10.1002/(sici)1097-458x(199612)34:13<s87::aid-omr49>3.0.co;2-y
Subject(s) - chemistry , dna , stereochemistry , nuclear magnetic resonance spectroscopy , molecular dynamics , nucleoside , crystallography , titration , computational chemistry , inorganic chemistry , biochemistry
The NMR‐derived structure, dynamics and metal binding of a unique 17‐residue DNA stem and loop hairpin were determined. The hairpin binds one Mg 2+ ion and is a biologically active DNA analogue of the yeast tRNA Phe anticodon domain only when two naturally occurring modified nucleosides, d(m 5 C) and d(m 1 G), are site selectively incorporated. The modified nucleosides aided in signal assignments in lieu of isotope labeling. Signal assignments were accomplished for 80% of the exchangeable and non‐exchangeable protons. Titration of the DNA with Mn 2+ , monitored by 1 H NMR spectroscopy, indicated that the Mg 2+ binding site is located in the loop of the hairpin at the bottom of the stem. The binding of Mg 2+ contributed to loop stability. Loop dynamics were evidenced by line broadness on the methyl signal of d(m 1 G) and were compared with that of an identical tDNA stem and loop hairpin that lacked the d(m 1 G) modification but contained d(m 5 U). TDNA hairpin dynamics are discussed in the light of the Mg 2+ binding constants for the two tDNA Phe . A highly refined, Mg 2+ ‐bound structure of the tDNA AC Phe is presented along with computer‐simulated effects of Mg 2+ on the tDNA's net surface charge and surface of H 2 O.