title: Effect of loop length variation on quadruplex-Watson Crick duplex competition.
abstract: The effect of loop length on quadruplex stability has been studied when the G-rich strand is present along with its complementary C-rich strand, thereby resulting in competition between quadruplex and duplex structures. Using model sequences with loop lengths varying from T to T5, we carried out extensive FRET to discover the influence of loop length on the quadruplex-Watson Crick duplex competition. The binding data show an increase in the binding affinity of quadruplexes towards their complementary strands upon increasing the loop length. Our kinetic data reveal that unfolding of the quadruplex in presence of a complementary strand involves a contribution from a predominant slow and a small population of fast opening conformer. The contribution from the fast opening conformer increases upon increasing the loop length leading to faster duplex formation. FCS data show an increase in the interconversion between the quadruplex conformers in presence of the complementary strand, which shifts the equilibrium towards the fast opening conformer with an increase in loop length. The relative free-energy difference (Delta DeltaG(o)) between the duplex and quadruplex indicates that an increase in loop length favors duplex formation and out competes the quadruplex.
authors.affiliation: Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India.
authors.forename: Niti
authors.initials: N
authors.lastname: Kumar
authors.forename: Bankanidhi
authors.initials: B
authors.lastname: Sahoo
authors.forename: K A S
authors.initials: KA
authors.lastname: Varun
authors.forename: Sudipta
authors.initials: S
authors.lastname: Maiti
authors.forename: Souvik
authors.initials: S
authors.lastname: Maiti
mesh_terms: D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D031541:Fluorescence Resonance Energy Transfer; D054856:G-Quadruplexes; D007700:Kinetics; D013050:Spectrometry, Fluorescence; D013816:Thermodynamics
chemical_list: D004247:DNA