Cellular macromolecules-tethered DNA walking indexing to explore nanoenvironments of chromatin modifications

Abstract

Exploring spatial organization and relationship of diverse biomolecules within cellular nanoenvironments is important to elucidate the fundamental processes of life. However, it remains methodologically challenging. Herein, we report a molecular recognition mechanism cellular macromolecules-tethered DNA walking indexing (Cell-TALKING) to probe the nanoenvironments containing diverse chromatin modifications. As an example, we characterize the nanoenvironments of three DNA modifications around one histone posttranslational modification (PTM). These DNA modifications in fixed cells are labeled with respective DNA barcoding probes, and then the PTM site is tethered with a DNA walking probe. Cell-TALKING can continuously produce cleavage records of any barcoding probes nearby the walking probe. New 3’-OH ends are generated on the cleaved barcoding probes to induce DNA amplification for downstream detections. Combining fluorescence imaging, we identify various combinatorial chromatin modifications and investigate their dynamic changes during cell cycles. We also explore the nanoenvironments in different cancer cell lines and clinical specimens. In principle, using high-throughput sequencing instead of fluorescence imaging may allow the detection of complex cellular nanoenvironments containing tens of biomolecules such as transcription factors.

Bioorthogonal Chemical Signature Enabling Amplified Visualization of Cellular Oxidative Thymines

“…ATP and propargylamine were used to prepare ATP-γ-alkyne. ATP disodium salt (4.9 mM) and propargylamine (245 mM) were dissolved in water. − The solution pH was adjusted to 6.0 with dilute HCl. Also, then EDC-HCl (490 mM) was added to the above solution and the mixture was stirred for 24 h at room temperature.…”

Advances in Designer DNA Nanorobots Enabling Programmable Functions

“…[56a] Zhao et al reported a molecular recognition mechanism cellular macromoleculestethered DNA walking indexing (Cell-TALKING) to probe the nano environments containing diverse chromatin modifications. [64] Taking the exosome as 3D track and split aptamers as a recognition element, a self-serviced-track DNA walker (STDW) was designed for wash-free and highly sensitive detection of tumor exosomes by glycoprotein profiling. [65] To further explore the functionality of the continuously actuating DNA nanorobot in cell manipulation, our group recently developed an autonomous DNA nanorobot by extending the track of DNA nanorobots from fixed DNA origami to the floating receptors in the fluidic cell membrane (Figure 6d).…”

“…Zhao et al. reported a molecular recognition mechanism cellular macromolecules‐tethered DNA walking indexing (Cell‐TALKING) to probe the nano environments containing diverse chromatin modifications [64] . Taking the exosome as 3D track and split aptamers as a recognition element, a self‐serviced‐track DNA walker (STDW) was designed for wash‐free and highly sensitive detection of tumor exosomes by glycoprotein profiling [65] …”

Applications of DNA-Functionalized Proteins

“…Chen’s group introduced a structure of macromolecules-tethered DNA walking indexing to probe the biological environment around multi-DNA-modified histone post-translational modification (PTM). They indicated that this one-to-many nanoenvironments detection was expected to be used in clinical applications [ 106 ]. Furthermore, DNA can also be applied for structure inspection so as to better understand life activities.…”