The i-motif structure (iM) has attracted much attention,
because
of its in vivo bioactivity and wide in vitro applications such as
DNA-based switches. Herein, the length-dependent folding of cytosine-rich
repeats of the human telomeric 5′-(CCCTAA)n‑1CCC-3′ (iM-n, where n =
2–8) was fully explored. We found that iM-4, iM-5, and iM-8
mainly form the intramolecular monomer iM structures, while a tetramolecular
structure populates only for iM-3. However, iM-6 and iM-7 have the
potential to fold as well into the dimeric iM structures besides the
monomer ones. The natural hypericin (Hyp) was used as the polymorphism-selective
probe to recognize the iM structures. Interestingly, only iM-3, iM-6,
and iM-7 can efficiently switch on the Hyp fluorescence by specifically
binding with the outmost C–C+ base pairs that are
exposed directly to solution. However, other iM structures that fold
in a way with a coverage of the outmost C–C+ pairs
by loop sequences are totally unavailable for the Hyp binding. Theoretical
modeling indicates that adaptive π–π and cation-π
interactions contribute to the Hyp recognition toward the exposed
C–C+ pairs. This specific iM recognition can be
boosted by a photocatalytic DNAzyme construct. Our work provides a
reliable fluorescence method to selectively explore the polymorphism
of iM structures.
Trihydroxyphenyl porphyrin (POH3) was designed to specifically bind with a triplex DNA by a resultant turn-on fluorescence response. This ensemble can be developed into a catalytic triplex DNAzyme towards porphyrin...
Switching of G-quadruplex (G4) structures between variant types of folding has been proved to be a versatile tool for regulation of genomic expression and development of nucleic acid-based constructs. Various specific ligands have been developed to target G4s in K+ solution with therapeutic prospects. Although G4 structures have been reported to be converted by sequence modification or a unimolecular ligand binding event in K+-deficient conditions, switching G4s towards non-G4 folding continues to be a great challenge due to the stability of G4 in physiological K+ conditions. Herein, we first observed the G4 switching towards parallel-stranded duplex (psDNA) by multimolecular ligand binding (namely ligand clustering) to overcome the switching barrier in K+. Purine-rich sequences (e.g. those from the KRAS promoter region) can be converted from G4 structures to dimeric psDNAs using molecular rotors (e.g. thioflavin T and thiazole orange) as initiators. The formed psDNAs provided multiple binding sites for molecular rotor clustering to favor subsequent structures with stability higher than the corresponding G4 folding. Our finding provides a clue to designing ligands with the competency of molecular rotor clustering to implement an efficient G4 switching.
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