2PIS

Efforts toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


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Literature

Efforts toward expansion of the genetic alphabet: structure and replication of unnatural base pairs.

Matsuda, S.Fillo, J.D.Henry, A.A.Rai, P.Wilkens, S.J.Dwyer, T.J.Geierstanger, B.H.Wemmer, D.E.Schultz, P.G.Spraggon, G.Romesberg, F.E.

(2007) J.Am.Chem.Soc. 129: 10466-10473

  • DOI: 10.1021/ja072276d

  • PubMed Abstract: 
  • Expansion of the genetic alphabet has been a long-time goal of chemical biology. A third DNA base pair that is stable and replicable would have a great number of practical applications and would also lay the foundation for a semisynthetic organism. W ...

    Expansion of the genetic alphabet has been a long-time goal of chemical biology. A third DNA base pair that is stable and replicable would have a great number of practical applications and would also lay the foundation for a semisynthetic organism. We have reported that DNA base pairs formed between deoxyribonucleotides with large aromatic, predominantly hydrophobic nucleobase analogues, such as propynylisocarbostyril (dPICS), are stable and efficiently synthesized by DNA polymerases. However, once incorporated into the primer, these analogues inhibit continued primer elongation. More recently, we have found that DNA base pairs formed between nucleobase analogues that have minimal aromatic surface area in addition to little or no hydrogen-bonding potential, such as 3-fluorobenzene (d3FB), are synthesized and extended by DNA polymerases with greatly increased efficiency. Here we show that the rate of synthesis and extension of the self-pair formed between two d3FB analogues is sufficient for in vitro DNA replication. To better understand the origins of efficient replication, we examined the structure of DNA duplexes containing either the d3FB or dPICS self-pairs. We find that the large aromatic rings of dPICS pair in an intercalative manner within duplex DNA, while the d3FB nucleobases interact in an edge-on manner, much closer in structure to natural base pairs. We also synthesized duplexes containing the 5-methyl-substituted derivatives of d3FB (d5Me3FB) paired opposite d3FB or the unsubstituted analogue (dBEN). In all, the data suggest that the structure, electrostatics, and dynamics can all contribute to the extension of unnatural primer termini. The results also help explain the replication properties of many previously examined unnatural base pairs and should help design unnatural base pairs that are better replicated.


    Organizational Affiliation

    Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*(CBR)P*GP*AP*AP*(FFD)P*TP*TP*CP*GP*CP*G)-3')A,B,C,D,E,F,G,H,I,J,K,L13N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
D, E, F, G
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CBR
Query on CBR
A, B, C, D, E, F, G, H, I, J, K, L
DNA LINKINGC9 H13 Br N3 O7 PDC
FFD
Query on FFD
A, B, C, D, E, F, G, H, I, J, K, L
DNA LINKINGC11 H14 F O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.224 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 146.025α = 90.00
b = 146.025β = 90.00
c = 93.140γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
HKL-2000data scaling
SOLVEphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance