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Single Molecule Studies of Telomere DNA

  • Author(s): Long, Xi
  • Advisor(s): Stone, Michael D
  • et al.
Abstract

Since the discovery by Blackburn in 1978, telomere has been the subject of intense research focus due to its close relationship with aging and cancer. Despite extensive research efforts more than three decades, the structural properties of telomere remain elusive. In this dissertation, I used single molecule techniques to examine the physical properties of telomere. These studies have identified the kinetically favorable telomere G-quadruplex (GQ) structure, revealed the mechanical unfolding pathway of telomere GQ, and characterized the mechanical properties of duplex telomere DNA and the formation of the telomere D-loop.

Since the discovery by Blackburn in 1978, the telomere has been the subject of intense research focus due to its close relationship with aging and cancer. Despite extensive research efforts for more than three decades, the structural properties of telomere remain elusive. In this dissertation, I used single molecule techniques to examine the physical properties of telomere. These studies have identified the kinetically favorable telomere G- quadruplex (GQ) structure, revealed the mechanical unfolding pathway of telomere GQ, and characterized the mechanical properties of duplex telomere DNA and the formation of the telomere D-loop. Telomeres are specialize DNA sequence that prevent degradation and aberrant fusion of chromosome ends. The foundation of human telomeres consists of 5-10 kb of duplex TTAGGG repeats follow by a 50 to 200 nucleotides of 3' single stranded overhang. The G-rich single stranded telomere has a propensity to fold into a secondary structure known as GQ. In Chapter 2, single-molecule Förster resonance energy transfer (smFRET) was used for constructing the distribution of telomere DNA GQ conformations under physiological salt conditions. With circular dichroism, the kinetic trapped GQ conformation was discovered. In Chapter 3, smFRET and magnetic tweezers (MT) was used to dissect the folding property telomere GQ. Under stretching force, the unfolding pathway of telomere GQ was characterized by a distance less than 1nm. In Chapter 4, the magnetic tweezers assay revealed that telomere is more resistant to torque-induced denaturation. The direct observation of telomere strand invasion suggested that the stretching force can influence the rate of the invasion and the formation of the telomere displacement loop. The subsequent chapters detail the setup and experimental protocol for the MT-FRET, and describe how to use MT to manipulate DNA. These single molecule assays setup a foundation for investigating the interaction between the telomere and its associated proteins and serve as an experimental platform for telomere drug assessment. Ultimately, with these single molecule assays we will enhance our knowledge on how telomere regulates telomerase activity.

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