8Y0F

Solution NMR structure of the PTK7-binding DNA aptamer sgc8c

PDB DOI: https://doi.org/10.2210/pdb8Y0F/pdb
NAKB: 8Y0F

Classification: DNA
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2024-01-22 Released: 2024-06-26
Deposition Author(s): He, A., Wan, L., Guo, P., Han, D.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 10
Selection Criteria: structures with the lowest energy

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure-based investigation of a DNA aptamer targeting PTK7 reveals an intricate 3D fold guiding functional optimization.

He, A., Wan, L., Zhang, Y., Yan, Z., Guo, P., Han, D., Tan, W.

(2024) Proc Natl Acad Sci U S A 121: e2404060121-e2404060121

PubMed: 38985770 Search on PubMed
DOI: https://doi.org/10.1073/pnas.2404060121
Primary Citation of Related Structures:
8Y0F

PubMed Abstract:
DNA aptamers have emerged as novel molecular tools in disease theranostics owing to their high binding affinity and specificity for protein targets, which rely on their ability to fold into distinctive three-dimensional (3D) structures. However, delicate atomic interactions that shape the 3D structures are often ignored when designing and modeling aptamers, leading to inefficient functional optimization. Challenges persist in determining high-resolution aptamer-protein complex structures. Moreover, the experimentally determined 3D structures of DNA molecules with exquisite functions remain scarce. These factors impede our comprehension and optimization of some important DNA aptamers. Here, we performed a streamlined solution NMR-based structural investigation on the 41-nt sgc8c, a prominent DNA aptamer used to target membrane protein tyrosine kinase 7, for cancer theranostics. We show that sgc8c prefolds into an intricate three-way junction (3WJ) structure stabilized by long-range tertiary interactions and extensive base-base stackings. Delineated by NMR chemical shift perturbations, site-directed mutagenesis, and 3D structural information, we identified essential nucleotides constituting the key functional elements of sgc8c that are centralized at the core of 3WJ. Leveraging the well-established structure-function relationship, we efficiently engineered two sgc8c variants by modifying the apical loop and introducing _L-DNA base pairs to simultaneously enhance thermostability, biostability, and binding affinity for both protein and cell targets, a feat not previously attained despite extensive efforts. This work showcases a simplified NMR-based approach to comprehend and optimize sgc8c without acquiring the complex structure, and offers principles for the sophisticated structure-function organization of DNA molecules.