4RHD

DNA Duplex with Novel ZP Base Pair


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Evolution of functional six-nucleotide DNA.

Zhang, L.Yang, Z.Sefah, K.Bradley, K.M.Hoshika, S.Kim, M.J.Kim, H.J.Zhu, G.Jimenez, E.Cansiz, S.Teng, I.T.Champanhac, C.McLendon, C.Liu, C.Zhang, W.Gerloff, D.L.Huang, Z.Tan, W.Benner, S.A.

(2015) J Am Chem Soc 137: 6734-6737

  • DOI: https://doi.org/10.1021/jacs.5b02251
  • Primary Citation of Related Structures:  
    4RHD

  • PubMed Abstract: 

    Axiomatically, the density of information stored in DNA, with just four nucleotides (GACT), is higher than in a binary code, but less than it might be if synthetic biologists succeed in adding independently replicating nucleotides to genetic systems. Such addition could also add functional groups not found in natural DNA, but useful for molecular performance. Here, we consider two new nucleotides (Z and P, 6-amino-5-nitro-3-(1'-β-D-2'-deoxyribo-furanosyl)-2(1H)-pyridone and 2-amino-8-(1'-β-D-2'-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one). These are designed to pair via complete Watson-Crick geometry. These were added to a library of oligonucleotides used in a laboratory in vitro evolution (LIVE) experiment; the GACTZP library was challenged to deliver molecules that bind selectively to liver cancer cells, but not to untransformed liver cells. Unlike in classical in vitro selection, low levels of mutation allow this system to evolve to create binding molecules not necessarily present in the original library. Over a dozen binding species were recovered. The best had Z and/or P in their sequences. Several had multiple, nearby, and adjacent Zs and Ps. Only the weaker binders contained no Z or P at all. This suggests that this system explored much of the sequence space available to this genetic system and that GACTZP libraries are richer reservoirs of functionality than standard libraries.


  • Organizational Affiliation

    †Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA 9mer novel Z nucleobase
A, C, E, G
9synthetic construct
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA 9mer novel P nucleobase
B, D, F, H
9synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.429α = 90
b = 59.429β = 90
c = 87.048γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-08
    Type: Initial release
  • Version 1.1: 2015-07-15
    Changes: Structure summary
  • Version 1.2: 2016-05-18
    Changes: Other
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations