7UID | pdb_00007uid

Thyclotides peptide nucleic acid in complex with DNA

• PDB DOI: https://doi.org/10.2210/pdb7UID/pdb
• NAKB: 7UID

• Classification: DNA/PEPTIDE NUCLEIC ACID
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2022-03-29 Released: 2023-04-05 
• Deposition Author(s): Botos, I., Appella, D.H.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.265 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Literature

Variation of Tetrahydrofurans in Thyclotides Enhances Oligonucleotide Binding and Cellular Uptake of Peptide Nucleic Acids.

Zheng, H., Clausse, V., Amarasekara, H., Mazur, S.J., Botos, I., Appella, D.H.

(2023) JACS Au 3: 1952-1964

• PubMed: 37502163 
• DOI: https://doi.org/10.1021/jacsau.3c00198
• Primary Citation Related Structures: 
  7UID


• PubMed Abstract: 
  

  Selective incorporation of conformational constraints into thyclotides can be used to modulate their binding to complementary oligonucleotides, increase polarity, and optimize uptake into HCT116 cells without assistance from moieties known to promote cell uptake. The X-ray structure and biophysical studies of a thyclotide-DNA duplex reveal that incorporation of tetrahydrofurans into an aeg PNA backbone promotes a helical conformation that enhances binding to complementary DNA and RNA. Selective incorporation of tetrahydrofurans into the aeg PNA backbone allows polarity to be increased incrementally so that uptake into HCT116 cells can be optimized. The enhanced binding, polarity, and cellular uptake properties of thyclotides were used to demonstrate effective inhibition of microRNA-21 in HCT116 cells.

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Organizational Affiliation: 
• Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, 8 Center Drive, Room 404, Bethesda, Maryland 20892, United States.
Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, United States.
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, United States.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.11 kDa 
• Atom Count: 954 
• Modeled Residue Count: 38 
• Deposited Residue Count: 38 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*TP*GP*TP*GP*AP*TP*A)-3')	A, B [auth C]	9	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Thyclotide	C [auth B], D	10	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], G [auth A], H [auth C], I [auth C], J [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	K [auth B], L [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.265 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.286	α = 90
b = 64.098	β = 90
c = 71.244	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
AutoSol	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-05 
Deposition Author(s): Botos, I., Appella, D.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	ZIA-DK031143

Revision History  

• Version 1.0: 2023-04-05
  Type: Initial release
  
• Version 1.1: 2023-08-09
  Changes: Database references
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-10-23
  Changes: Structure summary
• Version 3.0: 2025-07-02
  Changes: Polymer sequence