Base‐Pairing Directed Folding of a Bimolecular G‐Quadruplex: New Insights into G‐Quadruplex‐Based DNAzymes

Li, Tao; Wang, Erkang; Dong, Shaojun

doi:10.1002/chem.200801825

Cited by 23 publications

(28 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The results reveal that, in our experimental conditions, the aptamer I binds hemin with a submicromolar affinity ( K d = 194±10 n m ), which is higher than that of the aptamer 1 ( K d = 258±7 n m ). That is, the DNA duplex flanking the G-quadruplex contributes to high-affinity binding, consistent with previous observations [9], [41].…”

Section: Resultssupporting

confidence: 92%

“…The hemin-binding affinities of aptamers 1 and I are determined as described previously [41]. The results reveal that, in our experimental conditions, the aptamer I binds hemin with a submicromolar affinity ( K d = 194±10 n m ), which is higher than that of the aptamer 1 ( K d = 258±7 n m ).…”

Section: Resultsmentioning

confidence: 54%

“…This indicates the formation of hemin−G-quadruplex DNAzyme. In general, the DNAzyme functions of G-quadruplex aptamers are quantitatively evaluated by the initial catalytic rates (denoted by ν) [29], [30], [41]. The ν values of 1 and I can be obtained from the corresponding kinetic curves of enzymatic reactions (Figure 3B).…”

Section: Resultsmentioning

confidence: 99%

“…These studies indicate appropriate base-pairing duplexes that flank the G-quadruplex structures of thrombin-binding aptamers contribute to high-affinity binding. Base pairing has also proven a magic hand that controls the folding of G-quadruplex DNAs and regulates their intrinsic properties [41]. An appropriate base-pairing duplex flanking the G-quadruplex is found to confer higher hemin-binding affinity and more excellent DNAzyme function.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

A Grafting Strategy for the Design of Improved G-Quadruplex Aptamers and High-Activity DNAzymes

Wang

Dong

2009

PLoS ONE

Self Cite

View full text Add to dashboard Cite

Nucleic acid aptamers are generally obtained by in vitro selection. Some have G-rich consensus sequences with ability to fold into the four-stranded structures known as G-quadruplexes. A few G-quadruplex aptamers have proven to bind hemin to form a new class of DNAzyme with the peroxidase-like activity, which can be significantly promoted by appending an appropriate base-pairing duplex onto the G-quadruplex structures of aptamers. Knowing the structural role of base pairing, here we introduce a novel grafting strategy for the design of improved G-quadruplex aptamers and high-activity DNAzymes. To demonstrate this strategy, three existing G-quadruplex aptamers are chosen as the first generation. A base-pairing DNA duplex is grafted onto the G-quadruplex motif of the first generation aptamers. Consequently, three new aptamers with the quadruplex/duplex DNA structures are produced as the second generation. The hemin-binding affinities and DNAzyme functions of the second generation aptamers are characterized and compared with the first generation. The results indicate three G-quadruplex aptamers obtained by the grafting strategy have more excellent properties than the corresponding original aptamers. Our findings suggest that, if the structures and functions of existing aptamers are thoroughly known, the grafting strategy can be facilely utilized to improve the aptamer properties and thereby producing better next-generation aptamers. This provides a simple but effective approach to the design of nucleic acid aptamers and DNAzymes.

show abstract

Section: Resultssupporting

confidence: 92%

Section: Resultsmentioning

confidence: 54%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

A Grafting Strategy for the Design of Improved G-Quadruplex Aptamers and High-Activity DNAzymes

Wang

Dong

2009

PLoS ONE

Self Cite

View full text Add to dashboard Cite

show abstract

“…294 A similar system provides a colourimetric assay for Hg(II) ions involving phosphorothioated strands involving a T-T mismatch 296 as well as in a quadruplex with a native backbone structure. 295 The effect of base pairing in the stem of another bimolecular G-quadruplex has been investigated in an ABTS-activated peroxidase DNAzyme, 375 and a human telomeric G-quadruplex has been shown to exhibit peroxidase activity. 376 Split G-quadruplex structures have been used as peroxidase sensors for stem-loop nucleic acid structures such that the stem loop interacts with the reconstructed aptamer.…”

Section: Aptamers and (Deoxy)ribozymesmentioning

confidence: 99%

Nucleotides and nucleic acids; oligo- and polynucleotides

Loakes¹

Organophosphorus Chemistry

View full text Add to dashboard Cite

G‐Quadruplex Aptamers with Peroxidase‐Like DNAzyme Functions: Which Is the Best and How Does it Work?

Dong

Wang

2009

Chemistry An Asian Journal

Self Cite

133

View full text Add to dashboard Cite

Select the best: Five G‐quadruplex hemin‐binding aptamers are compared to determine the best candidate for DNAzyme‐based sensing application. The structural model and catalytic mechanism of the hemin–G‐quadruplex complex are proposed to indicate how it works in a manner similar to the peroxidase. Some G‐quadruplex DNA aptamers have been found to strongly bind hemin to form DNAzymes with peroxidase‐like activity. To help determine the most suitable DNAzymes and to understand how they work, five previously reported G‐quadruplex aptamers were compared for their binding affinity and then the potential catalytic mechanism of their corresponding hemin‐G‐quadruplex DNAzymes was explored. Among these aptamers, a G‐quadruplex named AGRO100 was shown to possess the highest hemin‐binding affinity and the best DNAzyme function. This means that AGRO100 is the most ideal candidate for DNAzyme‐based analysis. Furthermore, we found the peroxidase‐like activity of DNAzyme to be primarily dependent on the concentration of H2O2 and independent of that of the peroxidase substrate (that is, 2,2′‐azino‐bis(3‐ethylbenzothiazoline‐6‐sulfonic acid)diammonium salt). Accordingly, a reaction mechanism for DNAzyme‐catalyzed peroxidation is proposed. This study provides new insights into the G‐quadruplex‐based DNAzymes and will help us to further extend their applications in the analytical field.

show abstract

Base‐Pairing Directed Folding of a Bimolecular G‐Quadruplex: New Insights into G‐Quadruplex‐Based DNAzymes

Cited by 23 publications

References 26 publications

A Grafting Strategy for the Design of Improved G-Quadruplex Aptamers and High-Activity DNAzymes

A Grafting Strategy for the Design of Improved G-Quadruplex Aptamers and High-Activity DNAzymes

Nucleotides and nucleic acids; oligo- and polynucleotides

G‐Quadruplex Aptamers with Peroxidase‐Like DNAzyme Functions: Which Is the Best and How Does it Work?

Contact Info

Product

Resources

About