Circular dichroism of quadruplex DNAs: Applications to structure, cation effects and ligand binding

Paramasivan, Sattanathan; Rujan, Iulian; Bolton, Philip H.

doi:10.1016/j.ymeth.2007.02.009

Cited by 479 publications

(371 citation statements)

References 63 publications

Supporting

Mentioning

346

Contrasting

Order By: Relevance

“…Using the G-quadruplex secondary prediction algorithm Quadfinder (49), we now identified a potential G-quadruplex motif between nucleotides 66 and 94 of the human ADAM10 5Ј-UTR consistent with the transcriptome-wide prediction analysis of G-quadruplex structures reported previously (30,40). It was reported that RNA nucleosides prefer the anti-conformation of the glycosidic bond due to the C 3Ј -endo puckering of sugar, and hence RNA G-quadruplex structures adopt a parallel topology with a characteristic CD spectrum (34,51). Consistent with this finding and previously reported RNA-G-quadruplexes, our CD spectroscopy analyses provide evidence that the G-quadruplex sequence of the ADAM10 5Ј-UTR forms a parallel, intramolecular G-quadruplex secondary structure that is further stabilized by potassium ions.…”

Section: Discussionsupporting

confidence: 80%

“…In the presence of 1 mM LiCl, the CD spectrum was not altered as expected because lithium ions do not support the formation of G-quadruplexes (35, 37, 52). In our experiments, addition of 1 mM NaCl also had no effect on G-quadruplex formation, possibly due to the lower propensity of sodium ions compared with potassium ions to stabilize G-quadruplex structures (32,34,35,37,42,52).…”

Section: The 5ј-utr Of Adam10 Contains a G-rich Region Whichmentioning

confidence: 54%

“…To prove that this sequence indeed forms a stable G-quadruplex secondary structure, we performed CD spectroscopy, a standard technique to investigate the formation of G-quadruplex structures by oligonucleotides (34,50). We analyzed the CD spectrum of ADAM10GQ-WT RNA-oligonucleotide (Fig.…”

Section: The 5ј-utr Of Adam10 Contains a G-rich Region Whichmentioning

confidence: 99%

See 2 more Smart Citations

Translational Repression of the Disintegrin and Metalloprotease ADAM10 by a Stable G-quadruplex Secondary Structure in Its 5′-Untranslated Region

Lammich

Kamp

Wagner

et al. 2011

Journal of Biological Chemistry

View full text Add to dashboard Cite

Background: Translation of the ␣-secretase ADAM10 is repressed by its 5Ј-untranslated region (5Ј-UTR). Results: A G-rich region in the ADAM10 5Ј-UTR forms a highly stable G-quadruplex secondary structure, which inhibits translation of a luciferase reporter and ADAM10. Conclusion: The G-quadruplex secondary structure is one inhibitory element for ADAM10 translation. Significance: Our findings provide new insights in the translational regulation of ADAM10.

show abstract

Section: Discussionsupporting

confidence: 80%

Section: The 5ј-utr Of Adam10 Contains a G-rich Region Whichmentioning

confidence: 54%

See 1 more Smart Citation

Translational Repression of the Disintegrin and Metalloprotease ADAM10 by a Stable G-quadruplex Secondary Structure in Its 5′-Untranslated Region

Lammich

Kamp

Wagner

et al. 2011

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…Obviously, unlike CD spectrum (spectrum 1 in Fig. 1a) has a positive peak near 260 nm and a negative peak near 240 nm indicating a parallel stranded G-quadruplex [18][19][20]. As shown in Fig.…”

Section: Resultsmentioning

confidence: 85%

A spectroscopic investigation of the interaction between c-MYC DNA and tetrapyridinoporphyrazinatozinc(II)

et al. 2014

View full text Add to dashboard Cite

The c-MYC gene plays an important role in the regulation of cell proliferation and growth and it is overexpressed in a wide variety of human cancers. Around 90% of c-MYC transcription is controlled by the nuclease-hypersensitive element III1 (NHE III1), whose 27-nt purine-rich strand has the ability to form a G-quadruplex structure under physiological conditions. Therefore, c-MYC DNA is an attractive target for drug design, especially for cancer chemotherapy. Here, the interaction of water-soluble tetrapyridinoporphyrazinatozinc(II) with 27-nt G-rich strand (G/c-MYC), its equimolar mixture with the complementary sequence (GC/c-MYC) and related C-rich oligonucleotide (C/c-MYC) is investigated. Circular dichroism (CD) measurements of the G-rich 27-mer oligonucleotide in 150 mM KCl, pH 7 demonstrate a spectral signature consistent with parallel G-quadruplex DNA. Furthermore, the CD spectrum of the GC rich oligonucleotide shows characteristics of both duplex and quadruplex structures. Absorption spectroscopy implies that the complex binding of G/c-MYC and GC/c-MYC is a two-step process; in the first step, a very small red shift and hypochromicity and in the second step, a large red shift and hyperchromicity are observed in the Q band. Emission spectra of zinc porphyrazine are quenched upon addition of three types of DNA. According to the results of spectroscopy, it can be concluded the dominant binding mode is probably, outside binding and end stacking.

show abstract

“…Identification of G-quadruplex formation CD is a sensitive technology able to study the configuration inversion of DNA, which could report the structural variations intrinsically and kinetically [48]. To further confirm the formation of G-quadruplex, CD measurement is utilized to monitor the conformation change of DNA probe in the different cases.…”

Section: +mentioning

confidence: 99%

Colorimetric assay of lead using unmodified gold nanorods

et al. 2012

View full text Add to dashboard Cite

Lead poisoning in adults can affect the peripheral and central nervous systems, the kidneys, and blood pressure. Thus, the development of environment-friendly and simple methods for Pb 2+ detection is of great importance. Herein, a label-free colorimetric method has been developed for the detection of Pb 2+ based on the conformational switch from single-stranded DNA to G-quadruplex. The electrostatic interactions between DNA probe and gold nanorods (GNRs) induce GNRs to space closely. However, the electrostatic interaction is not strong enough to change the suspension state of GNRs. In the presence of Pb 2+ , the formation of G-quadruplexes increases the surface charge density around DNA, which is expected to strengthen the electrostatic interaction between the GNRs and the DNA. Therefore, the longitudinal absorption of GNRs decreased because the stronger interaction induced aggregation of GNRs. Importantly, the decrease in longitudinal absorption is proportional to concentration of Pb 2+ . By monitoring the change of absorbance, Pb 2+ can be detected at a level of 3 nM with a linear range from 5 nM to 1 μM. The overall test only takes a few minutes and very little interference is observed from other metal ions. The major advantages of this method are its low cost, convenience, simplicity, sensitivity, and specificity.

show abstract

Circular dichroism of quadruplex DNAs: Applications to structure, cation effects and ligand binding

Cited by 479 publications

References 63 publications

Translational Repression of the Disintegrin and Metalloprotease ADAM10 by a Stable G-quadruplex Secondary Structure in Its 5′-Untranslated Region

Translational Repression of the Disintegrin and Metalloprotease ADAM10 by a Stable G-quadruplex Secondary Structure in Its 5′-Untranslated Region

A spectroscopic investigation of the interaction between c-MYC DNA and tetrapyridinoporphyrazinatozinc(II)

Colorimetric assay of lead using unmodified gold nanorods

Contact Info

Product

Resources

About