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Investigation on the Secondary Structures Formed in Full-length Telomere Overhang and Rational Design of Ligands for Targeting Telomere G-quadruplexes

Abraham Punnoose, Jibin
http://orcid.org/0000-0003-2367-6874
http://rave.ohiolink.edu/etdc/view?acc_num=kent1516742818621033

Abstract Details

2018, PHD, Kent State University, College of Arts and Sciences / Department of Chemistry.
The 3′ human telomeric overhang provides ample opportunities for the formation and interaction of G-quadruplexes, which have shown impacts on many biological functions including telomerase activities in the telomere region. However, in the few investigations on DNA sequences that approach to the full length of the human telomeric overhang, the presence of higher order quadruplex-quadruplex interactions is still a subject of debate. As a part of this dissertation, an enzymatic dynamic splint ligation (DSL) strategy was developed to prepare a DNA construct of 24G-tracts and longer, which has the length comparable to the full stretch of 3′ human telomeric overhang. Using mechanical unfolding assays in laser tweezers, we observed a minor population (~5%) of higher order interactions between G-quadruplexes while the majority of the quadruplexes follow the beads-on-a-string model. Analyses on the non-interacting G-quadruplexes in the 24G construct showed features similar to those of the stand-alone G-quadruplexes in the 5′-(TTAGGG)4 (4G) construct. As each 24G construct contains as many as six G-quadruplexes, this method offers increased throughput for the time-consuming mechanical unfolding experiments of non-B DNA structures. Targeting DNA G-quadruplexes using small-molecule ligands has shown to modulate biological functions mediated by G-quadruplexes inside cells. Given >716,000 G-quadruplex hosting sites in the human genome, the specific binding of ligands to quadruplex becomes problematic. Here, a polyvalency based mechanism was innovated to target multiple telomeric G-quadruplexes specifically. A tetrameric telomestatin derivative was evaluated for its complex polyvalent binding with multiple G-quadruplexes by single-molecule mechanical unfolding in laser tweezers. We found a derivative of telomestatin (L2H2-6OTD) tetramer binds to multimeric telomeric G-quadruplexes 40 times stronger than monomeric quadruplexes, which can be ascribed to the polyvalency induced unstacking of binding units (or PIU binding) for G-quadruplexes. While stacking of telomestatin units in the tetramer imparts steric hindrance for the ligand to access standalone G-quadruplexes, the stacking disassembles to accommodate the potent polyvalent binding between the tetramer ligand and multimeric G-quadruplexes. This adaptive PIU binding offers a generic mechanism to target polymeric biomolecules prevalent inside cells selectively.
Hanbin Mao, Ph.D. (Committee Chair)
Mietek Jaroniec, Ph.D. (Committee Member)
Robert Twieg, Ph.D. (Committee Member)
Quan Li, Ph.D. (Committee Member)
Edgar Kooijman, Ph.D. (Committee Member)
121 p.
Biochemistry; Chemistry; Molecular Biology
G-quadruplex, Telomere, G-triplex, Higher-order structure, Telomere targeting, L2H2-6OTD, G-quadruplex ligands

Recommended Citations

Citations

  • Abraham Punnoose, J. (2018). Investigation on the Secondary Structures Formed in Full-length Telomere Overhang and Rational Design of Ligands for Targeting Telomere G-quadruplexes [Doctoral dissertation, Kent State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=kent1516742818621033

    APA Style (7th edition)

  • Abraham Punnoose, Jibin. Investigation on the Secondary Structures Formed in Full-length Telomere Overhang and Rational Design of Ligands for Targeting Telomere G-quadruplexes. 2018. Kent State University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=kent1516742818621033.

    MLA Style (8th edition)

  • Abraham Punnoose, Jibin. "Investigation on the Secondary Structures Formed in Full-length Telomere Overhang and Rational Design of Ligands for Targeting Telomere G-quadruplexes." Doctoral dissertation, Kent State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=kent1516742818621033

    Chicago Manual of Style (17th edition)

kent1516742818621033
398
© 2018, all rights reserved.
This open access ETD is published by Kent State University and OhioLINK.