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Structural basis for double-stranded RNA recognition by SID1.

Runhao Wang1, Ye Cong2, Dandan Qian1

  • 1State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, China.

Nucleic Acids Research
|May 14, 2024
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Summary
This summary is machine-generated.

Researchers elucidated the structure of the systemic RNAi-defective (SID) 1 protein bound to double-stranded RNA (dsRNA). This reveals how SID1 recognizes and binds dsRNA, crucial for RNA-based therapeutics.

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Area of Science:

  • Structural Biology
  • Molecular Biology
  • Biochemistry

Background:

  • The systemic RNAi-defective (SID) 1 family facilitates nucleic acid transport, making them targets for RNA therapeutics.
  • The precise molecular mechanism of double-stranded RNA (dsRNA) recognition by SID1 proteins is not well understood.

Purpose of the Study:

  • To determine the structural basis of dsRNA recognition and binding by the SID1 protein.
  • To provide insights into the sequence-independent binding of dsRNA by SID1.

Main Methods:

  • Cryo-electron microscopy (cryo-EM) was used to resolve the structures of Caenorhabditis elegans (c) SID1 alone and in complex with dsRNA.
  • Structural analysis focused on interactions between cSID1 and dsRNA, including ionic and hydrogen bonds, and electrostatic potential mapping.

Main Results:

  • The cryo-EM structure revealed dimeric cSID1 simultaneously binding two dsRNA molecules.
  • dsRNA binds at the interface of β-strand rich domains (BRD1 and BRD2), with interactions involving basic residues, phosphate backbone, and 2'-hydroxyl groups.
  • Three basic regions on cSID1 fit into the major grooves of dsRNA, enabling sequence-independent binding and discrimination between DNA and RNA.

Conclusions:

  • The study provides high-resolution structures of cSID1-dsRNA complexes, elucidating the molecular mechanism of dsRNA recognition.
  • These findings are critical for understanding SID1 function in dsRNA uptake and for the development of RNA-based therapeutics.