Assignment of hydrogen-bond structure in a ligand-nucleobase complex inside duplex DNA: combined use of quantum chemical calculations and 15N NMR experiments.

10Citations
Citations of this article
5Readers
Mendeley users who have this article in their library.

This article is free to access.

Abstract

We present a combined experimental and theoretical approach, whereby a comparison of calculated and experimental 15N NMR chemical shifts allows the elucidation of hydrogen-bond structure in a ligand-nucleobase complex inside duplex DNA. In this work, we focus on the highly selective interaction of 2-amino-7-methyl-1,8-naphthyridine (AMND) to cytosine (C) base opposite the abasic site in DNA duplexes, despite the hydrogen-bond array of neutral AMND being fully complementary to guanine (G). Examination of the salt dependence of the binding constants reveals that the effective number of charges on the ligand is +1.0, indicating protonated AMND does bind to C. This is clearly supported by 15N NMR measurements, where the drastic changes in chemical shift are observed for the aromatic nitrogens on the ligand when binding to C. Furthermore, from the complexation-induced changes in chemical shift at 15N1 (83.1 ppm upfield), 15N8 (14.1 ppm upfield), and 15NH2 (18.3 ppm downfield) on AMND, the ligand is found to bind to C via three point hydrogen-bonds. The chemical shifts of the AMND-C complex, calculated by gauge-independent atomic orbital-DFT method, are in fair agreement with the experimental values. These results clearly explain the selective binding of AMND to C over G in abasic site-containing duplex DNA.

Cite

CITATION STYLE

APA

Yoshimoto, K., Nishizawa, S., Koshino, H., Sato, Y., Teramae, N., & Maeda, M. (2005). Assignment of hydrogen-bond structure in a ligand-nucleobase complex inside duplex DNA: combined use of quantum chemical calculations and 15N NMR experiments. Nucleic Acids Symposium Series (2004), (49), 255–256. https://doi.org/10.1093/nass/49.1.255

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Save time finding and organizing research with Mendeley

Sign up for free