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Thymine-methyl/pi interaction implicated in the sequence-dependent deformability of DNA.

Yoji Umezawa1, Motohiro Nishio

  • 1Institute of Microbial Chemistry, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan. umezaway@bikaken.or.jp

Nucleic Acids Research
|May 10, 2002
PubMed
Summary

The thymidine 5-methyl group stabilizes DNA structures through favorable interactions with adenine. These methyl groups play a key role in DNA sequence stability and deformability.

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Area of Science:

  • * Structural Biology
  • * Nucleic Acid Chemistry
  • * Bioinformatics

Background:

  • * Deoxy-oligonucleotides exhibit diverse structural features influencing their function.
  • * The role of specific chemical modifications, like methyl groups, in DNA structure is an area of ongoing research.

Purpose of the Study:

  • * To analyze the structural impact of the thymidine 5-methyl group in deoxy-oligonucleotides.
  • * To investigate the interaction between thymidine methyl groups and adenine bases in DNA sequences.
  • * To explore the contribution of these interactions to DNA stability and deformability.

Main Methods:

  • * Retrieval of deoxy-oligonucleotide crystal structures from the Nucleic Acid Database.
  • * Analysis of DNA structures using a custom program (CHPI).

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  • * Examination of A-T rich sequences and DNA duplexes incorporating A-tracts.

    • Main Results:

    • * The thymidine 5-methyl group favorably interacts with preceding adenine pi-rings, stabilizing structures like 5'-ApTpApT-3'.
    • * A 'twin A/T-Me interaction' is formed in duplexes due to complementary strand interactions.
    • * Thymidine methyl groups consistently interact with adenine in A-T rich sequences and A-tracts, contributing to their robustness.

    Conclusions:

    • * The thymidine 5-methyl group is a significant stabilizing element in DNA, particularly in A-T rich regions.
    • * The identified N/T-Me and twin A/T-Me motifs may influence DNA deformability.
    • * Methyl groups in modified DNA play a crucial role in structural integrity and potentially function.