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Related Experiment Videos

Inosine.adenine base pairs in a B-DNA duplex.

P W Corfield1, W N Hunter, T Brown

  • 1University Chemical Laboratory, Cambridge, UK.

Nucleic Acids Research
|October 12, 1987
PubMed
Summary

This study determined the B-DNA helix structure of a synthetic deoxydodecamer containing inosine.adenine pairs, revealing their stable incorporation and hydrogen bonding, offering insights into RNA interactions.

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • The structure and stability of DNA helices are fundamental to genetic processes.
  • Understanding non-canonical base pairing, such as inosine-adenine (I.A) pairs, is crucial for deciphering genetic code variations and stability.
  • Oligonucleotides containing modified bases like inosine are relevant to various biological interactions, including RNA codon-anticodon pairing.

Purpose of the Study:

  • To determine the three-dimensional structure of the synthetic deoxydodecamer d(C-G-C-I-A-A-T-T-A-G-C-G) using X-ray crystallography.
  • To elucidate the specific base-pairing interactions and conformational characteristics of inosine-adenine (I.A) pairs within a B-DNA helix.
  • To provide a structural model for I.A base-pairs relevant to RNA codon-anticodon interactions and explain the thermodynamic stability of inosine-containing base pairs.

Main Methods:

  • Single crystal X-ray diffraction at 2.5A resolution.
  • Crystallographic refinement to R=0.19, including identification of 64 solvent molecules.
  • Analysis of conformational parameters and base stacking interactions.

Main Results:

  • The synthetic deoxydodecamer crystallized as a B-DNA helix containing 10 Watson-Crick base pairs and 2 inosine-adenine (I.A) pairs.
  • In the I.A purine.purine base pairs, adenine adopts a syn orientation, while inosine is in the anti orientation.
  • Two hydrogen bonds (N-1(I)-N-7(A) and O-6(I)-N-6(A)) stabilize the I.A pair, which is incorporated with minimal distortion to the DNA helix.

Conclusions:

  • The determined structure provides a precise model for I.A base-pair formation in DNA.
  • This structural insight supports the role of I.A pairs in RNA codon-anticodon interactions and contributes to understanding the thermodynamic stability of inosine-containing nucleic acid structures.
  • The findings highlight the adaptability of the DNA double helix to accommodate non-canonical purine.purine base pairs without significant conformational disruption.

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