Issue 11, 2016
From the journal:

Physical Chemistry Chemical Physics

Understanding the effect of the nature of the nucleobase in the loops on the stability of the i-motif structure†

Sanae Benabou,a   Miguel Garavís,b   Sébastien Lyonnais,c   Ramon Eritja,d   Carlos Gonzálezbe  and  Raimundo Gargallo*ae  

* Corresponding authors

a Department of Analytical Chemistry, University of Barcelona, Diagonal 645, E-08028 Barcelona, Spain
E-mail: raimon_gargallo@ub.edu

b Institute of Physical Chemistry “Rocasolano”, CSIC, Serrano 119, E-28006 Madrid, Spain

c Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri i Reixac 4-8, 08028 Barcelona, Spain

d Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain

e BIOESTRAN, associated unit UB-CSIC,

Abstract

The nature and the length of loops connecting cytosine tracts in i-motif structures may affect their stability. In this work, the influence of the nature of the nucleobases located in two of the loops of an intramolecular i-motif is studied using spectroscopy, separation techniques, and multivariate data analysis. The insertion of bases other than thymine induces an additional acid–base equilibrium with pKa ∼ 4.5. The presence of two guanine bases in the loops, placed opposite to each other, decreases the thermal stability of the structure. In contrast, thymine and cytosine bases in these positions stabilize the structure.

Graphical abstract: Understanding the effect of the nature of the nucleobase in the loops on the stability of the i-motif structure

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Article information

DOI
https://doi.org/10.1039/C5CP07428B
Article type
Paper
Submitted
02 Dec 2015
Accepted
09 Feb 2016
First published
09 Feb 2016

Phys. Chem. Chem. Phys., 2016,18, 7997-8004

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Understanding the effect of the nature of the nucleobase in the loops on the stability of the i-motif structure

S. Benabou, M. Garavís, S. Lyonnais, R. Eritja, C. González and R. Gargallo, Phys. Chem. Chem. Phys., 2016, 18, 7997 DOI: 10.1039/C5CP07428B

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