A sequence specific threading tetra intercalator with an extremely slow dissociation rate constant
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A sequence-specific threading tetra-intercalator with an extremely slow dissociation rate constant. Article by: Garn F. Holman, Maha Zewail-Foote, Amy Rhoden Smith, Kenneth A. Johnson, and Brent L. Iverson Presentation by: Maggie Palmer and Joy Uyanwune.

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A sequence specific threading tetra intercalator with an extremely slow dissociation rate constant

A sequence-specific threading tetra-intercalator with an extremely slow dissociation rate constant

Article by: Garn F. Holman, Maha Zewail-Foote, Amy Rhoden Smith, Kenneth A. Johnson, and Brent L. Iverson

Presentation by: Maggie Palmer and Joy Uyanwune


“If you think of DNA as a spiral staircase imagine sliding something between the steps. That’s what our molecule does. It can be visualized as binding to DNA in the same way a snake might climb a ladder.” ~Brent L. Iverson

Photo/quote source: http://web5.cns.utexas.edu/news/2012/02/dna-wranglers/


What is a threading intercalator
What is a threading Intercalator? something between the steps. That’s what our molecule does. It can be visualized as binding to DNA in the same way a snake might climb a ladder.” ~Brent L. Iverson

  • A molecule that is capable of binding and inserting itself into a DNA sequence.

  • Sequence specific binding

    • 5’ – GATAAGTACTTATC – 3’

http://sketchfu.com/drawing/1919089-snake-and-ladder-


Why is this important
Why is this important? something between the steps. That’s what our molecule does. It can be visualized as binding to DNA in the same way a snake might climb a ladder.” ~Brent L. Iverson

Molecules that can bind to DNA can interfere and possibly control transcription, repair and replication.

Possible cure for chronic diseases

Photo source: http://www.nature.com/nchem/journal/v3/n11/full/nchem.1173.html


Tetra intercalator 3
Tetra-intercalator 3 something between the steps. That’s what our molecule does. It can be visualized as binding to DNA in the same way a snake might climb a ladder.” ~Brent L. Iverson

  • Designed with a minor-major-minor groove binding linkers

  • Tetra-intercalator 3 was designed using studies done previously on 1 and 2.

  • -βAla3-Lys- is the minor groove binding linker taken from bisintercalator 2.

  • Adipic acid with 2 L-Lysine residues are part of the major groove binding linker.

    • Causes C2 symmetry that simplifies the NMF

  • 14 Basepair binding site.

  • Pieced together by connecting together NDI units


How to make a tetra intercalator
How to make a tetra-intercalator something between the steps. That’s what our molecule does. It can be visualized as binding to DNA in the same way a snake might climb a ladder.” ~Brent L. Iverson

http://io9.com/5885072/dna+tangling-molecule-could-revolutionize-treatments-for-cancer-and-hiv

Naphthalenetetracarboxylic diimide (NDI) molecules are chained together with resin beads.

Reactions are ran directly on the resin beads until the molecule is large enough to cleave.

“The larger molecule is composed of little pieces that bind to short segments of DNA, kind of life the way Legos fit together” ~Amy Rhoden-Smith


Napthalenetetracarboxylic diimide
Napthalenetetracarboxylic diimide something between the steps. That’s what our molecule does. It can be visualized as binding to DNA in the same way a snake might climb a ladder.” ~Brent L. Iverson

  • NDI units can be pieced together in different ways

  • The different arrangements then must be scanned in order to find the sequences the new arrangements will select for

http://www.chemspider.com/Chemical-Structure.24771033.html


Picture source: Lee et.al something between the steps. That’s what our molecule does. It can be visualized as binding to DNA in the same way a snake might climb a ladder.” ~Brent L. Iverson


Slowed dissociation rate
Slowed Dissociation Rate something between the steps. That’s what our molecule does. It can be visualized as binding to DNA in the same way a snake might climb a ladder.” ~Brent L. Iverson

3 will have a slow dissociation from its preferred DNA binding site.

In order for 3 to fully dissociate from DNA it the individual units will have to dissociate in an ordered fashion before rebinding occurs.

Photo source: http://mysam.net/wiki/index.php/%ED%8A%B9%EC%88%98%EA%B8%B0%EB%8A%A5:NatureNews?reply=4&page=1


Experiment section
Experiment Section something between the steps. That’s what our molecule does. It can be visualized as binding to DNA in the same way a snake might climb a ladder.” ~Brent L. Iverson


Threading bisintercalators 1 2
Threading bisintercalators 1&2 something between the steps. That’s what our molecule does. It can be visualized as binding to DNA in the same way a snake might climb a ladder.” ~Brent L. Iverson

  • figure 1a picture here

  • figure 1b picture here.


Tetra intercalator 31
Tetra-Intercalator 3 something between the steps. That’s what our molecule does. It can be visualized as binding to DNA in the same way a snake might climb a ladder.” ~Brent L. Iverson

Figure 1c


Threading polyintercalator of 3
Threading Polyintercalator of 3 something between the steps. That’s what our molecule does. It can be visualized as binding to DNA in the same way a snake might climb a ladder.” ~Brent L. Iverson

Show extremely slow dissociation from its preferred DNA sequence.

Association is suspected to be rapid result of electrostatic interactions.


Dnase footprinting
DNase/Footprinting something between the steps. That’s what our molecule does. It can be visualized as binding to DNA in the same way a snake might climb a ladder.” ~Brent L. Iverson

Figure 2


Dissociation kinetics
Dissociation Kinetics something between the steps. That’s what our molecule does. It can be visualized as binding to DNA in the same way a snake might climb a ladder.” ~Brent L. Iverson


Nonspecific dissociation kinetic
Nonspecific Dissociation Kinetic something between the steps. That’s what our molecule does. It can be visualized as binding to DNA in the same way a snake might climb a ladder.” ~Brent L. Iverson

Stopped Flow Method


Association rate measurements
Association rate measurements something between the steps. That’s what our molecule does. It can be visualized as binding to DNA in the same way a snake might climb a ladder.” ~Brent L. Iverson

1H NMR spectroscopy,

Gel mobility shift assay and

stopped-flow ultraviolet–visible spectroscopy.


Stopped flow ultraviolet visible spectroscopy
Stopped Flow Ultraviolet-visible Spectroscopy something between the steps. That’s what our molecule does. It can be visualized as binding to DNA in the same way a snake might climb a ladder.” ~Brent L. Iverson

Figure 5


Conclusion
Conclusion something between the steps. That’s what our molecule does. It can be visualized as binding to DNA in the same way a snake might climb a ladder.” ~Brent L. Iverson

Tetra-intercalator 3 has a slow dissociation rate.

The half life of tetra-intercalator 3 was found to be16 days.

Tetra-intercalator 3 also shows a rapid association rate to its target specific sequence driven by electrostatic attraction.

Suspected to have the same threading topology on long pieces of DNA.


Work cited
Work Cited something between the steps. That’s what our molecule does. It can be visualized as binding to DNA in the same way a snake might climb a ladder.” ~Brent L. Iverson

Holman, Garen G., Zewail-Foote, Maha; Smith, Amy Rhoden; Johnson, Kenneth A.; & Iverson, Brent L. 2001. A Sequence-specific threading teta-intercalator with an extremely slow dissociation rate constant. Nature Chemistry. 3; 875-881

Lee, J.; Guelev, V.; Sorey, S.;Hoffman, D.W. &Iverson, B.L.2004 NMR Structural analysis of a modular threading tetraintercalator bound to DNA. J. Am. Chem. Soc, 126; 14036-14042


Work cited cont
Work Cited Cont. something between the steps. That’s what our molecule does. It can be visualized as binding to DNA in the same way a snake might climb a ladder.” ~Brent L. Iverson

Oppenheimer, Daniel. 2012 DNA- Targeting Molecule has Potential to Help Treat Genetic Disease and HIV. Online at. http://web5.cns.utexas.edu/news/2012/02/dna-wranglers


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