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APOBEC3G Interacts with ssDNA by Two Modes: AFM Studies.

Luda S Shlyakhtenko1, Samrat Dutta1, Jaspreet Banga1

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APOBEC3G (A3G) protein binds single-stranded DNA (ssDNA) with higher affinity to specific sequences. This binding involves two distinct modes, indicating both A3G domains contribute to sequence-specific ssDNA interaction.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Virology

Background:

  • APOBEC3G (A3G) protein exhibits antiviral properties against HIV and other retroviruses.
  • A3G possesses distinct N-terminal (NTD) and C-terminal (CTD) domains, responsible for ssDNA binding and cytidine deamination, respectively.
  • The precise relationship between A3G's sequence-specific deaminase activity and its ssDNA binding remains incompletely understood.

Purpose of the Study:

  • To investigate the interaction between APOBEC3G (A3G) protein and single-stranded DNA (ssDNA) substrates.
  • To elucidate the role of sequence specificity in A3G-ssDNA binding using Atomic Force Spectroscopy (AFM).

Main Methods:

  • Utilized Atomic Force Spectroscopy (AFM) with topographic imaging and force spectroscopy modalities.
  • Characterized the binding of A3G protein to both deaminase-specific and non-specific ssDNA substrates.

Main Results:

  • AFM imaging revealed a higher affinity of A3G for deaminase-specific ssDNA compared to non-specific ssDNA.
  • AFM force spectroscopy identified two distinct binding modes for A3G interaction with ssDNA.
  • Sequence-specific binding resulted in stronger and more stable A3G-ssDNA complexes than non-specific binding.

Conclusions:

  • APOBEC3G (A3G) demonstrates a preference for binding deaminase-specific single-stranded DNA (ssDNA).
  • A3G interacts with ssDNA through at least two distinct binding mechanisms.
  • These findings support the model where both the NTD and CTD of A3G contribute to sequence-specific ssDNA binding.