+ Site Statistics
References:
52,654,530
Abstracts:
29,560,856
PMIDs:
28,072,755
+ Search Articles
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ PDF Full Text
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn

+ Translate
+ Recently Requested

Frequency and effect of the binding of Mg2+, Mn2+, and Co2+ ions on the guanine base in Watson-Crick and reverse Watson-Crick base pairs



Frequency and effect of the binding of Mg2+, Mn2+, and Co2+ ions on the guanine base in Watson-Crick and reverse Watson-Crick base pairs



Journal of Physical Chemistry. B 113(47): 15670-8



We performed MP2 calculations to elucidate the structure and energetics of the Mg(2+), Mn(2+), and Co(2+) hexahydrated aquaions, and the effect of the metal binding to the N7 atom of (i) a single guanine, (ii) a guanine involved in a Watson-Crick pair, and (iii) a guanine involved in a reverse Watson-Crick base pair. Our comparative analysis of the three aquaions indicates a clear inverse correlation between the radius of the cation and the binding energy, that indeed increases in the order Mn(2+) < Co(2+) < Mg(2+). The trend in the binding energies of the pentahydrated cations to the N7 atom of the guanine is instead Mg(2+) < Mn(2+) < Co(2+), suggesting a rather different bonding scheme that, for the two transition metals, involves back-donation from the aromatic ring of the guanine to their empty d orbitals. In the gas phase, the three hydrated metals significantly stabilize both G-C base pair geometries, Watson-Crick and reverse Watson-Crick, we investigated. Inclusion of a continuous solvent model, however, remarkably reduces this additional stabilization, which becomes almost negligible in the case of the Mg(2+) cation coordinated to the guanine in the standard Watson-Crick geometry. Conversely, all three metal ions sensibly stabilize the reverse Watson-Crick geometry, also in water. Our results are supported by a screening of the structures available in the Protein Data Bank, which clearly indicates that the two transition metals we investigated have a tendency greater than Mg(2+) to coordinate to the N7 atom of guanines, and that there is no clear correlation between the number of guanines in experimental structures with a metal bound to N7 atom and their involvement in Watson-Crick base pairs.

(PDF emailed within 0-6 h: $19.90)

Accession: 053301729

Download citation: RISBibTeXText

PMID: 19921955

DOI: 10.1021/jp906847p


Related references

Quantum chemical studies of structures and binding in noncanonical RNA base pairs: the trans Watson-Crick:Watson-Crick family. Journal of Biomolecular Structure & Dynamics 25(6): 709-732, 2008

Binding effects of Mn2+ and Zn2+ ions on the vibrational properties of guanine-cytosine base pairs in the Watson-Crick and Hoogsteen configurations. Journal of Molecular Modeling 18(11): 4781-4786, 2012

Binding effects of Mn²⁺ and Zn²⁺ ions on the vibrational properties of guanine-cytosine base pairs in the Watson-Crick and Hoogsteen configurations. Journal of Molecular Modeling 18(11): 4781-4786, 2013

Non-Watson-Crick base pairing in RNA. quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family. Journal of Physical Chemistry. A 109(10): 2292-2301, 2006

A highly fluorescent DNA base analogue that forms Watson-Crick base pairs with guanine. Journal of the American Chemical Society 123(10): 2434-2435, 2001

An innate twist between Crick's wobble and Watson-Crick base pairs. Rna 19(8): 1038-1053, 2013

Base pairing of cytosine analogues with adenine and guanine in oligonucleotide duplexes evidence for exchange between watson crick and wobble base pairs using proton nmr spectroscopy. Journal of the Chemical Society Chemical Communications (19): 1357-1359, 1991

The influence of Li+, Na+, Mg2+, Ca2+, and Zn2+ ions on the hydrogen bonds of the Watson-Crick base pairs. Biopolymers 29(4-5): 757-769, 1990

Under what conditions does G.C Watson-Crick DNA base pair acquire all four configurations characteristic for A.T Watson-Crick DNA base pair?. Ukrains'kyi Biokhimichnyi Zhurnal 85(4): 98-103, 2014

Silver(I)-mediated base pairs in DNA sequences containing 7-Deazaguanine/Cytosine Base Pairs: Towards DNA with entirely metallated Watson-Crick base pairs. Chemistry: -, 2017

88 Interplay of water molecules and Mg(2+) ions in stability of RNA containing non-Watson-Crick base pairs. Journal of Biomolecular Structure & Dynamics 33 Suppl 1: 57-58, 2015

The structures and relative stabilities of d(G x G) reverse Hoogsteen, d(G x T) reverse wobble, and d(G x C) reverse Watson-Crick base-pairs in DNA crystals. Journal of Molecular Biology 269(5): 796-810, 1997

The structures and relative stabilities of d reverse Hoogsteen, d reverse wobble, and d reverse Watson-Crick base-pairs in DNA crystals. Journal of Molecular Biology 269(5): 796-810, 1997

Numerical simulations of Raman spectra of guanine-cytosine Watson-Crick and protonated Hoogsteen base pairs. Biopolymers 72(5): 339-344, 2003

Prediction of interaction energies of substituted hydrogen-bonded Watson-Crick cytosine:guanine(8X) base pairs. Journal of Physical Chemistry. B 113(10): 3245-3250, 2009