6B1R

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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

    Foundation for Applied Molecular Evolution (FfAME) , 13709 Progress Boulevard, Box 7 , Alachua , Florida 32615 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase
A
259Moloney murine leukemia virusMutation(s): 0 
Gene Names: gag-pol
Find proteins for P03355 (Moloney murine leukemia virus)
Go to UniProtKB:  P03355
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*TP*AP*TP*(1WA)P*(1WA)P*(1WA))-3')B8synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*(IGU)P*(IGU)P*(IGU)P*AP*TP*AP*AP*G)-3')G8synthetic construct
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
1WA
Query on 1WA
B
DNA LINKINGC10 H16 N5 O7 P

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IGU
Query on IGU
G
DNA LINKINGC10 H14 N5 O7 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 55.214α = 90.00
b = 146.194β = 90.00
c = 47.073γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United States--

Revision History 

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-09-26
    Type: Data collection, Database references
  • Version 1.2: 2018-10-03
    Type: Data collection, Database references