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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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Schematic depictions of quadruplex folding patterns. The patterns are labeled P for parallel, A for anti-parallel and M for mixed which is also known as 3+1. The quartets are shown in blue and the loops in red. Only two quartets are shown for illustration purposes.
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Figure 1: Schematic depictions of quadruplex folding patterns. The patterns are labeled P for parallel, A for anti-parallel and M for mixed which is also known as 3+1. The quartets are shown in blue and the loops in red. Only two quartets are shown for illustration purposes.

Mentions: Some of the quadruplex folding patterns that have been observed are depicted in Figure 1. The details of the experimental conditions, in particular the concentration of potassium, can play a significant role in determining which, if any, quadruplex structure is formed (12–18). At present it is not possible to predict which quadruplex structural type will be adopted by a particular sequence under a given set of conditions. It is known that modest changes such as the substitution of dU for dT, the addition of one or two nucleotides as a dangling end or even the addition of a terminal 5′ P can alter the quadruplex structural type (9,19,20). Thus, there are many regions of the genome that can adopt quadruplex structures and there are many types of quadruplex structure. This diversity of structures and sequences suggests that selective targeting is possible though it may be challenging to attain.Figure 1.


Mix and measure fluorescence screening for selective quadruplex binders.

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

Schematic depictions of quadruplex folding patterns. The patterns are labeled P for parallel, A for anti-parallel and M for mixed which is also known as 3+1. The quartets are shown in blue and the loops in red. Only two quartets are shown for illustration purposes.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 1: Schematic depictions of quadruplex folding patterns. The patterns are labeled P for parallel, A for anti-parallel and M for mixed which is also known as 3+1. The quartets are shown in blue and the loops in red. Only two quartets are shown for illustration purposes.
Mentions: Some of the quadruplex folding patterns that have been observed are depicted in Figure 1. The details of the experimental conditions, in particular the concentration of potassium, can play a significant role in determining which, if any, quadruplex structure is formed (12–18). At present it is not possible to predict which quadruplex structural type will be adopted by a particular sequence under a given set of conditions. It is known that modest changes such as the substitution of dU for dT, the addition of one or two nucleotides as a dangling end or even the addition of a terminal 5′ P can alter the quadruplex structural type (9,19,20). Thus, there are many regions of the genome that can adopt quadruplex structures and there are many types of quadruplex structure. This diversity of structures and sequences suggests that selective targeting is possible though it may be challenging to attain.Figure 1.

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