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Binding mode of a cationic porphyrin to parallel and antiparallel thrombin binding aptamer G-quadruplex.
- Source :
-
Journal of biomolecular structure & dynamics [J Biomol Struct Dyn] 2020 Jun; Vol. 38 (9), pp. 2686-2692. Date of Electronic Publication: 2019 Aug 08. - Publication Year :
- 2020
-
Abstract
- The spectral properties of meso -tetrakis ( N -methylpyridinium-4-yl)porphyrin (TMPyP) in the presence of parallel and antiparallel G-quadruplexes formed from a thrombin-binding aptamer G-quadruplex (5'-G <subscript>3</subscript> T <subscript>2</subscript> G <subscript>3</subscript> TGTG <subscript>3</subscript> T <subscript>2</subscript> G <subscript>3</subscript> ) were investigated in this study. Red shift and hypochromism in the Soret absorption band of TMPyP were observed after binding to both parallel and antiparallel G-quadruplexes. The extent of changes in the absorption spectra were similar for both conformers. No circular dichroism spectrum was induced in the Soret region for both parallel and antiparallel G-quadruplexes. This is suggest that there is no or very weak interaction between electric transitions of nucleobases and porphyrin molecule. The accessibility of the neutral quencher I <subscript>2</subscript> to the G-quadruplex-bound TMPyP was similar for both parallel and antiparallel G-quadruplexes. All these observations suggest that TMPyP was bound at the outside of the quadruplexes, and conceivably interacted with the phosphate group via a weak electrostatic interaction.Communicated by Ramaswamy H. Sarma.
- Subjects :
- Circular Dichroism
Thrombin
Aptamers, Nucleotide
G-Quadruplexes
Porphyrins
Subjects
Details
- Language :
- English
- ISSN :
- 1538-0254
- Volume :
- 38
- Issue :
- 9
- Database :
- MEDLINE
- Journal :
- Journal of biomolecular structure & dynamics
- Publication Type :
- Academic Journal
- Accession number :
- 31307279
- Full Text :
- https://doi.org/10.1080/07391102.2019.1642241