Circular dichroism spectra demonstrate formation of the thrombin-binding DNA aptamer G-quadruplex under stabilizing-cation-deficient conditions

Nagatoishi, Satoru; Tanaka, Yoshikazu; Tsumoto, Kouhei

doi:10.1016/j.bbrc.2006.11.088

Cited by 145 publications

(93 citation statements)

References 42 publications

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“…After 20 min rotation, the pH was neutralized to pH 7.0 with 1 M Hepes buffer to a final concentration of 130 mM Hepes. To maximize the quantity of aptamer bound to the surface, the particles were salt aged by adding 20× SSC in 300-mM increments every 20 min to a final NaCl concentration of ∼1 M. Along with the first 300-mM SSC addition, we added 50 mM KPB to help the aptamers form G-quadruplex structures and minimize overpacking (15,22). The AuNPs were sonicated in a bath (Branson Ultrasonic Bath) as needed to prevent aggregation.…”

Section: Methodsmentioning

confidence: 99%

Dual-reporter SERS-based biomolecular assay with reduced false-positive signals

Chuong

Pallaoro

Chaves

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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We present a sensitive and quantitative protein detection assay that can efficiently distinguish between specific and nonspecific target binding. Our technique combines dual affinity reagents with surfaceenhanced Raman spectroscopy (SERS) and chemometric analysis. We link one Raman reporter-tagged affinity reagent to gold nanoparticles and another to a gold film, such that protein-binding events create a "hot spot" with strong SERS spectra from both Raman reporter molecules. Any signal generated in this context is indicative of recognition by both affinity labels, whereas signals generated by nonspecific binding lack one or the other label, enabling us to efficiently distinguish true from false positives. We show that the number of hot spots per unit area of our substrate offers a quantitative measure of analyte concentration and demonstrate that this duallabel, SERS-linked aptasensor assay can sensitively and selectively detect human α-thrombin in 1% human serum with a limit of detection of 86 pM.surface-enhanced Raman spectroscopy | SERS | protein detection | nanoparticle | ELISA

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Section: Methodsmentioning

confidence: 99%

Dual-reporter SERS-based biomolecular assay with reduced false-positive signals

Chuong

Pallaoro

Chaves

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…The substantial difference between these aptamers consists in replacement of T with A in a quadruplex loop. Earlier, circular dichroism (CD) and differential scanning calorimetry methods were shown to be sensitive tools for examining the stability of fibrinogen-specific binding site G-quadruplexes in the presence of potassium or other ions (see for example [15]) or thrombin [16]. Using CD, we showed that also the G-quadruplex forming binding motif at the heparin-binding site on thrombin is stable [14].…”

Section: Accepted M Manuscriptmentioning

confidence: 99%

“…2. [14][15][16]21] in the presence of potassium ions. Such CD pattern is observed when antiparallel G-quadruplex is formed.…”

Section: Spectral Studiesmentioning

confidence: 99%

The circular dichroism and differential scanning calorimetry study of the properties of DNA aptamer dimers

Poniková

Tlučková

Antalı́k

et al. 2011

Biophysical Chemistry

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We have applied circular dichroism (CD), temperature-gradient gel electrophoresis (TGGE) and differential scanning calorimetry (DSC) to study the properties of novel bioengineered DNA aptamer dimers sensitive to fibrinogen (F) and heparin (H) binding sites of thrombin and compared them with canonical single stranded aptamer sensitive to fibrinogen binding site of thrombin (Fibri). The homodimer (FF) and heterodimer (FH) aptamers were constructed based on hybridization of their supported parts. CD results showed that both FF and FH dimers form stable guanine quadruplexes in the presence of potassium ions like those in Fibri. The thermal stability of aptamer dimers was slightly lower compared to those of canonical aptamers, but sufficient for practical applications. Both FF and FH aptamer dimers exhibited a potassium-dependent inhibitory effect on thrombin-* Corresponding author: Tel: +421-2-60295683; fax: +421-2-65412305; e-mail: tibor.hianik@fmph.uniba.sk A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT2 mediated fibrin gel formation, which was on average two-fold higher than those of canonical single stranded Fibri aptamers.

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“…polyethylene glycol (PEG200) and ethanol (Renciuk et al 2009). A decrease in temperature also supports the formation of G-quadruplexes in the absence of cations (Nagatoishi et al 2007).…”

Section: Stability Of Guanine Quadruplexes In Dna Aptamers At Presencmentioning

confidence: 80%

“…Potassium is also required for the inhibition of thrombin-clotting Tsiang et al 1995). Aptamer quadruplex conformation is also stabilized in the presence of other cations (Wang et al 1995;Smirnov and Shafer 2000;Kankia and Marky 2001); the presence of Sr 2+ , Ba 2+ and Pb 2+ was found to have a powerful stabilizing effect on G-quadruplexes (Smirnov and Shafer 2000;Kankia and Marky 2001), while sodium ions were shown to form markedly weaker binds to the aptamer (Kankia and Marky 2001;Nagatoishi et al 2007). …”

Section: Stability Of Guanine Quadruplexes In Dna Aptamers At Presencmentioning

confidence: 99%

Potential uses of G-quadruplex-forming aptamers

Víglaský

Hianik

2013

gpb

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Abstract. Guanine quadruplex (G-quadruplex) structures are one of a number of structures which are capable of adopting aptamers. G-rich DNA or RNA has an increased propensity to form quadruplex structures which have unusual biophysical and biological properties. G-rich aptamers which form G-quadruplexes have several advantages over unstructured sequences: G-quadruplexes are non-immunogenic, thermodynamically and chemically stable and they have both higher resistance to various serum nucleases and an enhanced cellular uptake. These advantages have led to a number of synthetic oligonucleotides being studied for their potential use as therapeutic agents for cancer therapy and in the treatment of various other diseases. In addition to their suitability in the fields of medicine and biotechnology, these, highly specified, aptameric G-quadruplexes also have great potential in the further development of nano-devices; e.g. basic components in microarrays, microfluidics, sandwich assays and electrochemical biosensors. This review summarizes the biophysical properties of G-quadruplexes and highlights the importance of the stability and recognition properties of aptamers. Examples of the application of aptamers in medical therapy and in biosensors are also discussed.

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Circular dichroism spectra demonstrate formation of the thrombin-binding DNA aptamer G-quadruplex under stabilizing-cation-deficient conditions

Cited by 145 publications

References 42 publications

Dual-reporter SERS-based biomolecular assay with reduced false-positive signals

Dual-reporter SERS-based biomolecular assay with reduced false-positive signals

The circular dichroism and differential scanning calorimetry study of the properties of DNA aptamer dimers

Potential uses of G-quadruplex-forming aptamers

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