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Mix and measure fluorescence screening for selective quadruplex binders.

Paramasivan S, Bolton PH - Nucleic Acids Res. (2008)

Bottom Line: The successful targeting of a particular quadruplex structure requires distinguishing that structure from all of the other quadruplex structures that may be present.The screening is based on observing the increase or decrease in the fluorescence of the reporter molecules.The selectivity of a set of test molecules has been determined by this approach.

View Article: PubMed Central - PubMed

Affiliation: Chemistry Department, Wesleyan University, Middletown, CT 06459, USA.

ABSTRACT
The human genome contains thousands of regions, including that of the telomere, that have the potential to form quadruplex structures. Many of these regions are potential targets for therapeutic intervention. There are many different folding patterns for quadruplex DNAs and the loops exhibit much more variation than do the quartets. The successful targeting of a particular quadruplex structure requires distinguishing that structure from all of the other quadruplex structures that may be present. A mix and measure fluorescent screening method has been developed, that utilizes multiple reporter molecules that bind to different features of quadruplex DNA. The reporter molecules are used in combination with DNAs that have a variety of quadruplex structures. The screening is based on observing the increase or decrease in the fluorescence of the reporter molecules. The selectivity of a set of test molecules has been determined by this approach.

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The CD spectra of quadruplex DNAs are shown in the presence and in the absence of DODC and DTDC. The spectra show that the CD bands of the DNAs are essentially the same in the presence and in the absence of the reporter molecules. The CD bands of the reporter molecules depend on DNA that is present. The CD spectra have been normalized to the maximum of the DNA for comparison.
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Figure 3: The CD spectra of quadruplex DNAs are shown in the presence and in the absence of DODC and DTDC. The spectra show that the CD bands of the DNAs are essentially the same in the presence and in the absence of the reporter molecules. The CD bands of the reporter molecules depend on DNA that is present. The CD spectra have been normalized to the maximum of the DNA for comparison.

Mentions: If a reporter dye alters the structure of the quadruplex DNA then it will have limited usefulness in screening. Therefore, CD was used to examine the effects of the reporter dyes on the structures of the quadruplex DNAs. The CD of each of the DNAs was monitored as a function of reporter dye concentration. The results in Figure 3 show that the presence of the reporter dyes do not alter the CD spectra of the DNAs. Since the CD spectrum is a sensitive monitor of structural change these results indicate that the reporter dyes do not change the structures of the DNAs under these conditions as was previously shown for NMM under similar conditions (38).Figure 3.


Mix and measure fluorescence screening for selective quadruplex binders.

Paramasivan S, Bolton PH - Nucleic Acids Res. (2008)

The CD spectra of quadruplex DNAs are shown in the presence and in the absence of DODC and DTDC. The spectra show that the CD bands of the DNAs are essentially the same in the presence and in the absence of the reporter molecules. The CD bands of the reporter molecules depend on DNA that is present. The CD spectra have been normalized to the maximum of the DNA for comparison.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2553591&req=5

Figure 3: The CD spectra of quadruplex DNAs are shown in the presence and in the absence of DODC and DTDC. The spectra show that the CD bands of the DNAs are essentially the same in the presence and in the absence of the reporter molecules. The CD bands of the reporter molecules depend on DNA that is present. The CD spectra have been normalized to the maximum of the DNA for comparison.
Mentions: If a reporter dye alters the structure of the quadruplex DNA then it will have limited usefulness in screening. Therefore, CD was used to examine the effects of the reporter dyes on the structures of the quadruplex DNAs. The CD of each of the DNAs was monitored as a function of reporter dye concentration. The results in Figure 3 show that the presence of the reporter dyes do not alter the CD spectra of the DNAs. Since the CD spectrum is a sensitive monitor of structural change these results indicate that the reporter dyes do not change the structures of the DNAs under these conditions as was previously shown for NMM under similar conditions (38).Figure 3.

Bottom Line: The successful targeting of a particular quadruplex structure requires distinguishing that structure from all of the other quadruplex structures that may be present.The screening is based on observing the increase or decrease in the fluorescence of the reporter molecules.The selectivity of a set of test molecules has been determined by this approach.

View Article: PubMed Central - PubMed

Affiliation: Chemistry Department, Wesleyan University, Middletown, CT 06459, USA.

ABSTRACT
The human genome contains thousands of regions, including that of the telomere, that have the potential to form quadruplex structures. Many of these regions are potential targets for therapeutic intervention. There are many different folding patterns for quadruplex DNAs and the loops exhibit much more variation than do the quartets. The successful targeting of a particular quadruplex structure requires distinguishing that structure from all of the other quadruplex structures that may be present. A mix and measure fluorescent screening method has been developed, that utilizes multiple reporter molecules that bind to different features of quadruplex DNA. The reporter molecules are used in combination with DNAs that have a variety of quadruplex structures. The screening is based on observing the increase or decrease in the fluorescence of the reporter molecules. The selectivity of a set of test molecules has been determined by this approach.

Show MeSH
Related in: MedlinePlus