Assessment of nucleotide excision repair protein binding forces by atomic force microscopy and optical trapping

Inhaltsverzeichnis (Table of Contents)

• Introduction
• Specific Aims
  • DNA-Protein Binding
  • DNA Strength during UvrABC Binding
  • Optical Tweezers
• Background and Significance
  • Dimerization
• Preliminary Studies
  • Force Spectroscopy
  • Dynamic Force Spectroscopy
  • DNA Stretching
  • Groove Binding
• Research Design and Methods
  • Sample Preparation
    • DNA Damage
    • DNA Damage Quantification
    • Binding DNA to AFM Tip
    • Binding DNA to Polystyrene Bead
    • Protein Sample Preparation
    • Binding Protein to Slide
  • AFM Setup
  • Optical Trapping Setup
  • Expected Sources of Error
  • Experimental Analysis
    • DNA-Protein Rupture Forces
    • Force Spectroscopy
• Alternative Methods
  • Scanning Probe
  • Mutations
  • Species of Protein

Zielsetzung und Themenschwerpunkte (Objectives and Key Themes)

This research program aims to investigate DNA repair proteins, specifically the UvrABC complex, by examining the binding force between the protein and damaged DNA molecules. The research utilizes atomic force microscopy (AFM) and optical trapping techniques to determine the strength of DNA-protein interactions. It also investigates how the DNA molecule's strength is affected during the repair process.

• DNA-protein binding forces
• DNA tensile properties during repair
• UvrABC complex structure and function
• Mechanisms of nucleotide excision repair
• Applications in genetic engineering and cancer treatment

Zusammenfassung der Kapitel (Chapter Summaries)

• Introduction: This chapter provides an overview of DNA repair mechanisms, emphasizing the importance of the UvrABC complex in repairing UV-induced damage. It highlights the significance of understanding these processes for various fields, including cancer treatment and genetic engineering.
• Specific Aims: This chapter outlines the three primary aims of the research project. These include determining the binding force of the UvrA and UvrB proteins to damaged DNA, measuring the tensile properties of DNA during repair by the UvrABC complex, and verifying results using optical tweezers.
• Background and Significance: This chapter focuses on the types of DNA damage, particularly UV-induced dimerization. It explains how this damage disrupts the DNA structure and hinders cellular processes.
• Preliminary Studies: This chapter provides a summary of previous studies related to force spectroscopy, dynamic force spectroscopy, DNA stretching, and groove binding.
• Research Design and Methods: This chapter details the experimental procedures, including sample preparation, AFM and optical trapping setups, and data analysis methods. It describes how different factors will be modulated in the experiments, such as the concentration of UvrABC complex and the rate of stage movement.

Schlüsselwörter (Keywords)

Key terms and concepts covered in this study include DNA repair, nucleotide excision repair, UvrABC complex, atomic force microscopy, optical trapping, DNA-protein interactions, binding forces, DNA tensile strength, UV damage, dimerization, genetic engineering, and cancer treatment.