Studies On Ligand Binding Properties And Molecular Recognition Induced By Nucleic Acid Modification

As the main carrier of genetic information,nucleic acid plays an important role in the genetic variation of organisms and the biosynthesis of proteins,but its structure and function are deeply subject to molecular ligands(including small biomolecules or proteins)that can interact with them.Therefore,it is of great biological significance to study the ligand binding properties and molecular recognition induced by nucleic acid modification.In this thesis,polarity-inverted G-quadruplex and abasic site-containing DNA(AP-DNA)are used as the objects of study.Based on studies of interactions between biological ligands and nucleic acid molecules of different structures.We developed a DNA-based topology selector for planar natural isoquinoline alkaloids(IAs)and a cucurbituril-based supramolecular and multicolor DNA recognition rationale via indicator competition assay(ICA).The main research contents are as follows:1.Structuring Polarity-Inverted TBA to G-quadruplex for Selective Recognition of Planarity of Natural Isoquinoline Alkaloids.Efficient structuring of DNA by small molecules is very crucial in developing DNA-based novel switches with an ideal performance.In this work,we found that inverting only the polarity of the 3'terminal guanine of the thrombin-binding aptamer(3iTBA)totally eradicates the original TBA G-quadruplex(G4)structure in K~+.The unstructured 3iTBA can be further refolded upon specifically interacting with small molecules of natural isoquinoline alkaloids(IAs)due to their fruitful binding patterns with variant nucleic acid structures.We identified that 3iTBA can serve as a topology selector for planar IAs.Nitidine(NIT),owing to the planar aromatic ring and coplanar substituents,is the most efficient to restructure the 3iTBA random coil toward the anti-parallel G4 conformation.However,common metal ions can't realize this structuring.The topology selector competency of 3iTBA toward IAs'planarity can be visualized using gold nanoparticles(AuNPs)as the chromogenic readout.Our work expands the G4 repertoire by exploring the polarity inversion regulation and provides a new approach to switch nucleic acid structures toward a small molecule structure-sensitive sensor.2.Supramolecularly Multicolor DNA Decoding Using an Indicator Competition Assay.Relative to the individual intensity-dependent strategy,the multicolor fluorescence sensor has promise to achieve a high signaling contrast.In this work,we develop a cucurbituril-based supramolecular and multicolor DNA recognition rationale via indicator competition assay(ICA).Alkaloids of coptisine(COP)and palmatine(PAL)are identified as the proof-of-principle indicators with a lighting up fluorescence upon supramolecular complexation to cucurbit[7]uril(CB[7]).With an introduced abasic site(AP site)as the contestant,DNAs having pyrimidines opposite this site can compete for COP with CB[7]to bring an emission color change from green to yellow brown,while those having purines opposite the AP site do not compete for COP and still have the green emission,indicative of a high selectivity for the multicolor nucleotide transversion recognition.However,because of the relatively weaker binding of PAL with CB[7],the AP site-containing DNA can take away PAL from its CB[7]complex and resultantly bring a blue-to-green emission color change independent of the AP site-opposite nucleotide identity,dissimilar to the remaining blue color for the fully matched DNA without the AP site,suggesting a preferable strategy for the AP site biomarker detection.Our method demonstrates a new way to develop an ICA-based multicolor DNA sensor with the supramolecular cucurbituril complexation to ensure a highly selective performance...