title: Understanding the effect of the nature of the nucleobase in the loops on the stability of the i-motif structure.
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.
authors.affiliation: Department of Analytical Chemistry, University of Barcelona, Diagonal 645, E-08028 Barcelona, Spain. raimon_gargallo@ub.edu.
authors.forename: Sanae
authors.initials: S
authors.lastname: Benabou
authors.affiliation: Institute of Physical Chemistry "Rocasolano", CSIC, Serrano 119, E-28006 Madrid, Spain.
authors.forename: Miguel
authors.initials: M
authors.lastname: Garavís
authors.affiliation: Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri i Reixac 4-8, 08028 Barcelona, Spain.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Lyonnais
authors.affiliation: Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain.
authors.forename: Ramon
authors.initials: R
authors.lastname: Eritja
authors.affiliation: Institute of Physical Chemistry "Rocasolano", CSIC, Serrano 119, E-28006 Madrid, Spain and BIOESTRAN, associated unit UB-CSIC.
authors.forename: Carlos
authors.initials: C
authors.lastname: González
authors.affiliation: Department of Analytical Chemistry, University of Barcelona, Diagonal 645, E-08028 Barcelona, Spain. raimon_gargallo@ub.edu and BIOESTRAN, associated unit UB-CSIC.
authors.forename: Raimundo
authors.initials: R
authors.lastname: Gargallo
mesh_terms: D020029:Base Pairing; D002850:Chromatography, Gel; D002942:Circular Dichroism; D004591:Electrophoresis, Polyacrylamide Gel; D009682:Magnetic Resonance Spectroscopy; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*
chemical_list: D009696:Nucleic Acids