Click chemistry assisted single-molecule fingerprinting reveals a 3D biomolecular folding funnel.
A 3D folding funnel was proposed in the 1990s to explain the fast kinetics exhibited by a biomacromolecule in presence of seemingly unlimited folding pathways. Over the years, numerous simulations have been performed with this concept; however, experimental verification is yet to be attained even for the simplest proteins. Here, we have used a click chemistry based strategy to introduce six pairs of handles in a human telomeric DNA sequence. A laser-tweezers-based, single-molecule structural fingerprinting on the six inter-handle distances reveals the formation of a hybrid-1 G-quadruplex in the sequence. Kinetic and thermodynamic fingerprinting on the six trajectories defined by each handle-pair depict a 3D folding funnel and a kinetic topology in which the kinetics pertaining to each handle residue is annotated for this G-quadruplex. We anticipate the methods and the concepts developed here are well applicable to other biomacromolecules, including RNA and proteins.
Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States.
Zhongbo
Z
Yu
Deepak
D
Koirala
Yunxi
Y
Cui
Leah F
LF
Easterling
Yuan
Y
Zhao
Hanbin
H
Mao
D057930:Click Chemistry; D004247:DNA / Q000737:chemistry*; D054856:G-Quadruplexes; D006801:Humans; D007700:Kinetics; D008958:Models, Molecular; D052898:Optical Tweezers; D013816:Thermodynamics
D004247:DNA