Recognization Of Nucleic Acid Structure Ploymorphism By Fluorescent Probes And Applications

In recent years,with the continuous deepening of nucleic acid research,people have found that nucleic acids with non-classical structures are closely related to human diseases.For example,the human telomere terminal DNA region is rich in G sequences,which can form G-quadruplex(G4)structures.The stable G4 can inhibit the activity of telomerase,thereby controlling the growth of cancer cells.In addition,studies have found that trinucleotide repeat sequences are closely related to more than30 neurodegenerative diseases.Therefore,the structures of nucleic acids are very important in exerting normal function of nucleic acids.However,the structures of nucleic acids have complex polymorphism.Factors such as small molecule ligands,cations,p H,nucleic acid sequences can affect the formation of different conformations of nucleic acids,and nucleic acids of different conformations may also exist in solution at the same time.Therefore,despite the long-standing focus on nucleic acids,the structures of nucleic acids are far from being fully understood.The selective recognition of nucleic acid structures by ligands has always been a research hotspot.In this thesis,probe recognition studies were carried out on DNAs containing three G-tracts to form G-quadruplexes and trinucleotide repeats to form E-motif structures:1.DNA containing three G-tracts forms an intermolecular G-quadruplex structureG-triplex(G3)has been recognized as a popular intermediate during the folding of G-quadruplex(G4).This has raised interest to anticipate the ultimate formation of G3 by shortening the G4-forming oligonucleotides with the remaining three G-tracts.Some G3 structures have been validated and their stability has been found to be affected by the loop sequences similar to G4s.In this work,however,we first found that an intermolecular parallel G4 structure was preferred in K~+for the oligonucleotide 5'-TGGGTAGGGCGGG-3'(DZ3)containing only three G-tracts.We screened auramine O(AO)as the appropriate fluorophore with a molecular rotor feature to target this G4 structure.AO bound with DZ3 in a 1:4 ratio,as confirmed by isothermal titration calorimetry experiments,suggesting the formation of a tetramolecular G4 structure(4er G4).The excimer emission from the labelled pyrene and the DNA melting behavior at various p H in the presence of Ag~+proved the formation of the 4er G4 structure rather than the prevalent intramolecular G3 folding.This work demonstrates that one should be cautious while putatively predicting a G3structure from an oligonucleotide containing three G-tracts.2.Targeting the strand polarity-determined DNA E-motif structureTrinucleotide repeats(TRs)with abnormal lengthenings and atypical foldings implicate many neurodegenerative diseases including fragile X syndrome and Huntington's disease.The least stable cytosine-cytosine(C-C)mismatches in5'-GCC-3'(or 5'-CCG-3')DNA TRs towards structuring into homoduplexes/hairpins have more chance in certain sequence context to adopt an extrahelical(E-motif)conformation than those in the polarity-inverted counterparts.However,Using ligands to distinguish polarity-dependent e-motif patterns has always been a challenge in TRS recognition because of the same sequence context,and both of them form global B-like DNA structures.Herein,we synthesized a porphyrin derivative(POH3)containing one p-hydroxyl group and two m-hydroxyl groups on each phenyl substituent to meet the challenge during recognizing the E-motif conformation.POH3exhibited a specific 2:1 binding with DNAs containing the E-motif cytosines,independent of the TRs length.The three hydroxyl groups in POH3 are important for selective recognition of E-motif structures and POH3 bonded to cytosine with E-motif configuration via the complementary hydrogen bonding in minor groove.Our work first elucidates the rationale in designing ligands to selectively target the E-motif nucleotides within TRs.