Parallel Polyadenine Duplex Formation at Low pH Facilitates DNA Conjugation onto Gold Nanoparticles

Huang, Zhicheng; Liu, Biwu; Liu, Juewen

doi:10.1021/acs.langmuir.6b03253

Cited by 64 publications

(49 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…In the past years, significant effort has been devoted to finding ideal fluorescent ligands for binding and lighting up DNA structures used in a diversity of label-free biosensors and devices ( 1 – 3 ). Among them, thioflavin T (ThT) has recently attracted increasing interest.…”

Section: Introductionmentioning

confidence: 99%

Thioflavin T binds dimeric parallel-stranded GA-containing non-G-quadruplex DNAs: a general approach to lighting up double-stranded scaffolds

Liu

Peng

Shi

et al. 2017

Nucleic Acids Research

View full text Add to dashboard Cite

A molecular rotor thioflavin T (ThT) is usually used as a fluorescent ligand specific for G-quadruplexes. Here, we demonstrate that ThT can tightly bind non-G-quadruplex DNAs with several GA motifs and dimerize them in a parallel double-stranded mode, accompanied by over 100-fold enhancement in the fluorescence emission of ThT. The introduction of reverse Watson–Crick T-A base pairs into these dimeric parallel-stranded DNA systems remarkably favors the binding of ThT into the pocket between G•G and A•A base pairs, where ThT is encapsulated thereby restricting its two rotary aromatic rings in the excited state. A similar mechanism is also demonstrated in antiparallel DNA duplexes where several motifs of two consecutive G•G wobble base pairs are incorporated and serve as the active pockets for ThT binding. The insight into the interactions of ThT with non-G-quadruplex DNAs allows us to introduce a new concept for constructing DNA-based sensors and devices. As proof-of-concept experiments, we design a DNA triplex containing GA motifs in its Hoogsteen hydrogen-bonded two parallel strands as a pH-driven nanoswitch and two GA-containing parallel duplexes as novel metal sensing platforms where C–C and T–T mismatches are included. This work may find further applications in biological systems (e.g. disease gene detection) where parallel duplex or triplex stretches are involved.

show abstract

Section: Introductionmentioning

confidence: 99%

Thioflavin T binds dimeric parallel-stranded GA-containing non-G-quadruplex DNAs: a general approach to lighting up double-stranded scaffolds

Liu

Peng

Shi

et al. 2017

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…It is noted that the polyA-containing ssDNA used in the literature usually had a relatively short sequence (i.e., less than 30 bases). [20][21][22][23][24][25][26] Therefore, it is of great interest to test the effectiveness of the polyAmediated immobilization method for long aptamer probes. In this regard, the immobilization of a series aptamers of different lengths ranging from 37 to 88 bases on a planar gold substrate was studied in this project.…”

Section: Introductionmentioning

confidence: 99%

Polyadenine-mediated Immobilization of Aptamers on a Gold Substrate for the Direct Detection of Bacterial Pathogens

2019

View full text Add to dashboard Cite

Nucleic acid aptamers have been widely used as synthetic probes for bioanalytical applications. Herein, we carried out a detailed study on the immobilization of a series of aptamers ranging from 37 to 88 bases, which are specific to either Escherichia coli (E. coli) or Staphylococcus aureus (S. aureus), on a planar gold substrate via a polyadenine-mediated immobilization method. The resultant surfaces were characterized by both surface plasmon resonance spectroscopy (SPR) and X-ray photoelectron spectroscopy. The results clearly show that the aptamer solution at a lower ionic strength gives rise to a higher lateral density of the aptamer when compared to that at a higher ionic strength. The SPR aptasensors are then employed for detecting their corresponding bacteria (i.e., E. coli and S. aureus, respectively). The data indicate that the SPR aptasensor with a higher density of aptamer exhibits a better capture of target bacteria.

show abstract

“…This enhancement is reminiscent of poly-A parallel duplex formed at acidic pH, and asimilar structure might also form by freezing. [14] An interesting question is the length requirement for DNAalignment upon freezing, and TO staining can answer it. Thel ength of poly-A DNAw as varied (Figure 2c).…”

mentioning

confidence: 99%

Freezing‐directed Stretching and Alignment of DNA Oligonucleotides

Liu

Huang

et al. 2019

Angewandte Chemie

Self Cite

View full text Add to dashboard Cite

Most single-stranded DNAo ligonucleotides are random coils with ap ersistence length of below1nm. So far, no good methods are available to stretcho ligonucleotides. Herein, it is shown that freezing can stretchDNA,asconfirmed using fluorescence resonance energy transfer,t hiazole-orange staining,a nd surface-enhanced Raman spectroscopy. Lateral inter-strand interactions are critical, and the stretched DNA oligonucleotides are aligned. This work also provides as et of methods for studying frozen oligonucleotides.U pon freezing, DNAo ligonucleotides are readily adsorbed onto various nanomaterials,i ncluding gold nanoparticles,g raphene oxide, iron oxide,a nd WS 2 via the most thermodynamically stable conformation, leading to more stable conjugates. Cy3-30-Cy5 mixed with 200 mm sDNA in 5mm HEPES, pH 7.6 with 50 mm NaCl before and after freezing. Schemes for two possible reasons of enhanced FRET by freezing (c), and inhibited intermolecular FRET by adding excess non-labeled sDNA (f).

show abstract

Parallel Polyadenine Duplex Formation at Low pH Facilitates DNA Conjugation onto Gold Nanoparticles

Cited by 64 publications

References 49 publications

Thioflavin T binds dimeric parallel-stranded GA-containing non-G-quadruplex DNAs: a general approach to lighting up double-stranded scaffolds

Thioflavin T binds dimeric parallel-stranded GA-containing non-G-quadruplex DNAs: a general approach to lighting up double-stranded scaffolds

Polyadenine-mediated Immobilization of Aptamers on a Gold Substrate for the Direct Detection of Bacterial Pathogens

Freezing‐directed Stretching and Alignment of DNA Oligonucleotides

Contact Info

Product

Resources

About