7KZL

Cyclopentane peptide nucleic acid in complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Conformational constraints of cyclopentane peptide nucleic acids facilitate tunable binding to DNA.

Zheng, H.Botos, I.Clausse, V.Nikolayevskiy, H.Rastede, E.E.Fouz, M.F.Mazur, S.J.Appella, D.H.

(2021) Nucleic Acids Res 

  • DOI: 10.1093/nar/gkaa1249
  • Primary Citation of Related Structures:  
    7KZL

  • PubMed Abstract: 
  • We report a series of synthetic, nucleic acid mimics with highly customizable thermodynamic binding to DNA. Incorporation of helix-promoting cyclopentanes into peptide nucleic acids (PNAs) increases the melting temperatures (Tm) of PNA+DNA duplexes b ...

    We report a series of synthetic, nucleic acid mimics with highly customizable thermodynamic binding to DNA. Incorporation of helix-promoting cyclopentanes into peptide nucleic acids (PNAs) increases the melting temperatures (Tm) of PNA+DNA duplexes by approximately +5°C per cyclopentane. Sequential addition of cyclopentanes allows the Tm of PNA + DNA duplexes to be systematically fine-tuned from +5 to +50°C compared with the unmodified PNA. Containing only nine nucleobases and an equal number of cyclopentanes, cpPNA-9 binds to complementary DNA with a Tm around 90°C. Additional experiments reveal that the cpPNA-9 sequence specifically binds to DNA duplexes containing its complementary sequence and functions as a PCR clamp. An X-ray crystal structure of the cpPNA-9-DNA duplex revealed that cyclopentanes likely induce a right-handed helix in the PNA with conformations that promote DNA binding.


    Organizational Affiliation

    Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Drive, Room 404, Bethesda, MD 20892, USA.



Macromolecules

  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
XDJ-XDD-XDY-XDJ-XDY-XDJ-XDD-XDY-XDD-XDVB10synthetic constructMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*AP*TP*CP*AP*CP*AP*TP*C)-3')A9synthetic construct
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.30 Å
    • R-Value Free: 0.189 
    • R-Value Work: 0.172 
    • R-Value Observed: 0.173 
    • Space Group: P 43 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 54.704α = 90
    b = 54.704β = 90
    c = 39.633γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-2000data reduction
    HKL-2000data scaling
    PHENIXphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesZIA-DK031143

    Revision History 

    • Version 1.0: 2020-12-23
      Type: Initial release
    • Version 1.1: 2021-01-20
      Changes: Database references