Soft Materials Seminar - "Using Optical Tweezers to Observe DDX11 Helicase Protein Unwinding Dynamics"

DDX11/ChlR1 (DEAD/H-box helicase 11) is a 5’-3’ superfamily 2 helicase within the XPD-like family that contains other Fe-S cluster helicases (XPD, RTEL1, and FANCJ). It plays a role in genomic maintenance via resolution of alternative secondary structures. DDX11 mutations are associated with a rare genetic disorder named Warsaw breakage syndrome, characterized by sister chromatid cohesion defects. To-date, the exact mechanism by which DDX11 interacts with DNA and processes alternative structures remains unclear due to a lack of biochemical and high-resolution structural data. While comparative analyses of homologous helicases (especially XPD) have been used to speculate on its mechanisms, an insertion in the HD1-domain present in DDX11 but absent in XPD may be critical to its function in DNA-recognition.

Here, we use a single-molecule optical trapping assay with near base-pair resolution to measure the unwinding dynamics of DDX11 on a DNA hairpin under force. We investigate how DDX11 negotiates obstacles in the form of different types of DNA modifications (abasic site, bulky lesion, etc.).

Our findings reveal that, compared to XPD, DDX11 is more processive but typically dissociates after a single unwinding attempt. DNA unwinding is often interrupted by pauses at various points along the hairpin, particularly at modifications. When encountering these sites, DDX11’s ability to bypass them varies: DDX11 is unable to bypass CPD, but it can bypass both fluorescein and abasic sites. Our work provides insights into how DDX11 responds to DNA modifications, paving the way to understanding how it will interact to other obstacles, such as alternative DNA structures.