6B1S

Hydrogen Bonding Complementary, not size complementarity is key in the formation of the double helix


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

"Skinny" and "Fat" DNA: Two New Double Helices.

Hoshika, S.Singh, I.Switzer, C.Molt Jr., R.W.Leal, N.A.Kim, M.J.Kim, M.S.Kim, H.J.Georgiadis, M.M.Benner, S.A.

(2018) J Am Chem Soc 140: 11655-11660

  • DOI: 10.1021/jacs.8b05042
  • Primary Citation of Related Structures:  
    6B1R, 6B1Q, 6B1S

  • PubMed Abstract: 
  • According to the iconic model, the Watson-Crick double helix exploits nucleobase pairs that are both size complementary (big purines pair with small pyrimidines) and hydrogen bond complementary (hydrogen bond donors pair with hydrogen bond acceptors) ...

    According to the iconic model, the Watson-Crick double helix exploits nucleobase pairs that are both size complementary (big purines pair with small pyrimidines) and hydrogen bond complementary (hydrogen bond donors pair with hydrogen bond acceptors). Using a synthetic biology strategy, we report here the discovery of two new DNA-like systems that appear to support molecular recognition with the same proficiency as standard Watson-Crick DNA. However, these both violate size complementarity (big pairs with small), retaining hydrogen bond complementarity (donors pair with acceptors) as their only specificity principle. They exclude mismatches as well as standard Watson-Crick DNA excludes mismatches. In crystal structures, these "skinny" and "fat" systems form the expected hydrogen bonds, while conferring novel minor groove properties to the resultant duplex regions of the DNA oligonucleotides. Further, computational tools, previously tested primarily on natural DNA, appear to work well for these two new molecular recognition systems, offering a validation of the power of modern computational biology. These new molecular recognition systems may have application in materials science and synthetic biology, and in developing our understanding of alternative ways that genetic information might be stored and transmitted.


    Organizational Affiliation

    Firebird Biomolecular Sciences LLC , 13709 Progress Boulevard, Box 17 , Alachua , Florida 32615 , United States.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Reverse transcriptaseAB259Moloney murine leukemia virusMutation(s): 0 
EC: 2.7.7.49 (PDB Primary Data), 3.4.23 (UniProt), 2.7.7.7 (UniProt), 3.1.26.4 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03355 (Moloney murine leukemia virus (isolate Shinnick))
Explore P03355 
Go to UniProtKB:  P03355
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*TP*TP*AP*TP*AP*(CGY)P*(CGY)P*TP*TP*TP*AP*TP*AP*AP*G)-3')E, F16Escherichia coli
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.00 Å
    • R-Value Free: 0.251 
    • R-Value Work: 0.217 
    • R-Value Observed: 0.218 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 53.119α = 90
    b = 95.797β = 90
    c = 144.488γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    Aimlessdata scaling
    PDB_EXTRACTdata extraction
    MOSFLMdata reduction
    MOLREPphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2018-09-19
      Type: Initial release
    • Version 1.1: 2018-09-26
      Changes: Data collection, Database references
    • Version 1.2: 2018-10-03
      Changes: Data collection, Database references
    • Version 1.3: 2019-12-25
      Changes: Author supporting evidence