Analyzing Telomeric Protein-DNA Interactions Using Single-Molecule Magnetic Tweezers
Summary
This protocol demonstrates using single-molecule magnetic tweezers to study interactions between telomeric DNA-binding proteins (Telomere Repeat-binding Factor 1 [TRF1] and TRF2) and long telomeres extracted from human cells. It describes the preparatory steps for telomeres and telomeric repeat-binding factors, the execution of single-molecule experiments, and the data collection and analysis methods.
Abstract
Telomeres, the protective structures at the ends of chromosomes, are crucial for maintaining cellular longevity and genome stability. Their proper function depends on tightly regulated processes of replication, elongation, and damage response. The shelterin complex, especially Telomere Repeat-binding Factor 1 (TRF1) and TRF2, plays a pivotal role in telomere protection and has emerged as a potential anti-cancer target for drug discovery. These proteins bind to the repetitive telomeric DNA motif TTAGGG, facilitating the formation of protective structures and recruitment of other telomeric proteins. Structural methods and advanced imaging techniques have provided insights into telomeric protein-DNA interactions, but probing the dynamic processes requires single-molecule approaches. Tools like magnetic tweezers, optical tweezers, and atomic force microscopy (AFM) have been employed to study telomeric protein-DNA interactions, revealing important details such as TRF2-dependent DNA distortion and telomerase catalysis. However, the preparation of single-molecule constructs with telomeric repetitive motifs continues to be a challenging task, potentially limiting the breadth of studies utilizing single-molecule mechanical methods. To address this, we developed a method to study interactions using full-length human telomeric DNA with magnetic tweezers. This protocol describes how to express and purify TRF2, prepare telomeric DNA, set up single-molecule mechanical assays, and analyze data. This detailed guide will benefit researchers in telomere biology and telomere-targeted drug discovery.
Introduction
Telomeres are protective structures at the ends of chromosomes1,2,3. Telomere erosion during cell division leads to cell senescence and aging, while abnormal elongation of telomeres contributes to cancer4,5. For telomeres to function properly, their replication, elongation, and damage responses must be highly regulated6,7,8. Shelterin, composed of six subunits, plays a central role in telomere protection9,10,11. A deeper understanding of telomeres will provide valuable insights into telomere biology.
TRF1 and TRF2, core subunits of shelterin, are telomeric binding proteins12,13. Both TRF1 and TRF2 bind to the repetitive DNA motif TTAGGG in telomeres via their Myb domains14. They form dimers through their shared TRFH domains, which allow them to encircle telomeric double-stranded DNA and to recruit telomeric proteins15,16,17,18,19. TRF2 is particularly important for the formation of telomeric D-loops and T-loops20,21. Due to their crucial roles in telomere protection, TRF1 and TRF2 have emerged as potential anti-cancer drug targets22,23,24,25.
Significant efforts have been made to investigate the protein-DNA interactions at telomeres. Biochemical methods such as Electrophoretic Mobility Shift Assay (EMSA) and Surface Plasmon Resonance (SPR) have been used to examine binding affinities20,26. Numerous structures of telomeric binding proteins complexed with DNA have been elucidated using cryo-electron microscopy (cryo-EM), X-ray crystallography, and nuclear magnetic resonance (NMR)27,28,29. Super-resolution imaging techniques like stochastic optical reconstruction microscopy (STORM) have revealed TRF2-dependent T-loop formation21. Recently, nanopore sequencing has been developed to profile telomeric sequences4,30,31. These structural insights have greatly enhanced our understanding of telomeric protein-DNA interactions. To further explore the dynamics of telomeric protein-DNA interactions, the development of new technologies is essential.
Single-molecule tools are powerful techniques for exploring protein-DNA interactions at telomere32,33,34. Single-molecule mechanical methods, such as magnetic tweezers, optical tweezers and AFM, have been employed to investigate TRF2-dependent DNA distortion, reveal TRF2-mediated columnar stacking of human telomeric chromatin and observe processive telomerase catalysis, among other applications35,36,37,38,39,40. These methods are particularly useful for probing topological conformations and the kinetics of protein-DNA association and dissociation.
However, the preparation of single-molecule constructs with telomeric repetitive motifs still presents challenges, which limits studies using single-molecule mechanical methods. To address this limitation, we have developed a single-molecule mechanical method to study global protein-DNA interactions on full-length human telomeres41. This method directly extracts telomeric DNA from human cells, circumventing the laborious preparation of artificial telomeric DNA. It facilitates the investigation of kinetic processes on long native telomeres spanning several kilobases.
In this protocol, we provide a detailed description of the steps for probing telomeric protein-DNA interactions using magnetic tweezers, a popular single-molecule mechanical tool42,43,44. We demonstrate how to express and purify telomeric proteins, using TRF2 as an example, and how to prepare telomeric DNA from human cells. Additionally, we show how to set up a single-molecule assay on magnetic tweezers to study telomeric protein-DNA interactions, and we cover the subsequent data analysis of single-molecule experiments. This protocol will benefit researchers in the field of telomere biology and telomere-targeted drug discovery.
Protocol
Representative Results
Discussion
This protocol employs magnetic tweezers for the manipulation of TRFs at the single-molecule level57,58,59. We utilize magnetic beads to separate TRFs from genomic DNA fragments. Following restriction digestion, TRFs bind to the magnetic beads, enabling their easy separation from genomic DNA fragments. This approach allows for manipulation using magnetic tweezers, which can effectively trap magnetic beads, unlike optical tweezers…
Disclosures
The authors have nothing to disclose.
Acknowledgements
This work was supported by the National Natural Science Foundation of China [Grant 32071227 to Z.Y.], Tianjin Municipal Natural Science Foundation of China (22JCYBJC01070 to Z.Y.), and State Key Laboratory of Precision Measuring Technology and Instruments (Tianjin University) [Grant pilab2210 to Z.Y.].
Materials
| Anti-Digoxigenin | Roche | 11214667001 | |
| BfaI | New England Biolab (NEB) | R0568S | |
| BSA | Sigma-Aldrich | V900933 | |
| CMOS camera | Mikrotron | MC1362 | |
| CviAII | New England Biolab (NEB) | R0640S | |
| DIG-11-dUTP | Jena Bioscience | NU-803-DIGXL | |
| DNA extraction solution | G-CLONE | EX0108 | |
| Dnase I, Rnase-Free, Hc Ea | Thermo Fisher Scientific | EN0523 | |
| dNTP mixture | Nanjing Vazyme Biotech Co., Ltd (Vazyme) | P032-02 | |
| DTT | Solarbio | D1070 | |
| Dynabeads M-270 beads | Thermo Fisher Scientific | 65305 | Streptavidin beads |
| Dynabeads MyOne beads | Thermo Fisher Scientific | 65001 | Streptavidin beads |
| Ethanol | Tianjin No.6 Chemical Reagent Factory | 1083 | |
| Glycerol | Beijing Hwrkchemical Co,. Ltd | SMG66258-1 | |
| Imidazole | Solarbio | II0070 | |
| IPTG | Solarbio | I8070 | |
| Isopropanol | Tianjin No.6 Chemical Reagent Factory | A1079 | |
| Kanamycin | Thermo Fisher Scientific | EN0523 | |
| Klenow fragment (3′-5′ exo-) | New England Biolab (NEB) | M0212S | |
| LabView | National Instruments | https://www.ni.com/en-us/shop/product/labview.html | Graphical programming software |
| LiCl | Bide Pharmatech Co., Ltd (bidepharm) | BD136449 | |
| Lysozyme | Solarbio | L8120-5 | |
| MseI | New England Biolab (NEB) | R0525S | |
| NaCl | Shanghai Aladdin | C111533 | |
| NanoDrop | Thermo Fisher Scientific | Spectrophotometer | |
| NdeI | New England Biolab (NEB) | R0111S | |
| Ni NTA Beads 6FF | Changzhou Smart-Lifesciences Biotechnology Co.,Ltd | SA005025 | |
| Nitrocellulose membrane | ABclonal | RM02801 | |
| PMSF | Solarbio | P8340 | |
| Proteinase K | Beyotime Biotech Inc (beyotime) | ST535-500mg | |
| rCutSmart Buffer | New England Biolab (NEB) | B6004S | |
| Rnase A | Sigma-Aldrich | R4875 | |
| Sodium acetate | SERVA Electrophoresis GmbH | 2124902 | |
| Sumo protease | Beyotime Biotech Inc (beyotime) | P2312M |
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