9WHV | pdb_00009whv

Cross-Stacking-Stabilized Intra-Locked RNA G-Quadruplex

PDB DOI: https://doi.org/10.2210/pdb9WHV/pdb
NAKB: 9WHV

Classification: RNA
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2025-08-27 Released: 2025-10-15
Deposition Author(s): Xiao, C.D., Wang, L.W., Wang, S.Y., Xu, Y.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 10
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

An intra-locked RNA G-quadruplex topology confers enhanced nuclease resistance and cancer cell targeting.

Song, S.S., Yang, L., Wang, L.W., Tian, R.Q., Wang, S.Y., Jia, M.H., Xu, Y., Zhong, M.Q., Liang, X.G., Hu, K.L., Luo, H., Chen, Y., Hu, X.X., Shen, X.C., Xiao, C.D.

(2026) Int J Biol Macromol 367: 152564-152564

PubMed: 42142778 Search on PubMed
DOI: https://doi.org/10.1016/j.ijbiomac.2026.152564
Primary Citation Related Structures:
9WHV

PubMed Abstract:
Nucleic acid aptamers often suffer from poor serum nuclease resistance, which limits their translational applications. Here, we present Apt-10-2, a natural 10-nt RNA aptamer that forms a highly stable G-quadruplex (Tm > 90 °C) with prolonged serum persistence (>96 h), while maintaining nanomolar affinity for nucleolin (NCL). Functionally, Apt-10-2 distinguishes cancer cells from normal cells in vitro and demonstrates specific tumor accumulation (>8 h) in vivo. To investigate the molecular basis of its stability, we performed NMR-based structural analysis and proposed a restraint-supported structural model of Apt-10-2, suggesting a unique interlocked topology in which two subunits co-assemble into a 16-layered framework composed of G-, U-, and A-tetrad-like interactions.. The proposed structural model features an intra-locked domain stabilized by cross-stacking interactions between the G1-U2-U3 tetrads, which are critical for maintaining the aptamer's stability. Disruption of this domain significantly impairs the overall structure. Our findings provide a structural framework for understanding the prolonged stability of RNA G-quadruplexes, and highlight the potential of Apt-10-2 as a naturally stable, high-affinity aptamer scaffold for cancer-targeting applications, without the need for extensive chemical modifications.

Organizational Affiliation

The High Efficacy Application of Natural Medicinal Resources Engineering Center of Guizhou Province and The High Educational Key Laboratory of Guizhou Province for Natural Medicinal Pharmacology and Druggability, School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 561113, PR China; The State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 561113, PR China.

Department of Oncology, Affiliated Hospital of Guizhou Medical University, Guiyang 550001, PR China.

Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan.

College of Food Science and Engineering, Ocean University of China, Qingdao, 266404, PR China.

Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang 550025, Guizhou Province, PR China.

The High Efficacy Application of Natural Medicinal Resources Engineering Center of Guizhou Province and The High Educational Key Laboratory of Guizhou Province for Natural Medicinal Pharmacology and Druggability, School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 561113, PR China; Key Laboratory of Novel Anti-Cancer Drug Targets Discovery and Application, School of Pharmaceutical Sciences, Guizhou Medical University, No. 6 Ankang Avenue, Guian New District, Guizhou, 561113, PR China.

The High Efficacy Application of Natural Medicinal Resources Engineering Center of Guizhou Province and The High Educational Key Laboratory of Guizhou Province for Natural Medicinal Pharmacology and Druggability, School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 561113, PR China; The State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 561113, PR China. Electronic address: sxc@gmc.edu.cn.

The High Efficacy Application of Natural Medicinal Resources Engineering Center of Guizhou Province and The High Educational Key Laboratory of Guizhou Province for Natural Medicinal Pharmacology and Druggability, School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 561113, PR China; The State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 561113, PR China. Electronic address: xcd@gmc.edu.cn.

Macromolecule Content

Total Structure Weight: 25.75 kDa
Atom Count: 1,704
Modeled Residue Count: 80
Deposited Residue Count: 80
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
RNA (5'-R(GPUPUPAPGPGPGPUPUPA)-3')	A, B, C, D, E A, B, C, D, E, F, G, H	10	Homo sapiens
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Reference Sequence