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Related Concept Videos

RNA Structure01:19

RNA Structure

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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
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Nucleic Acid Structure01:25

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
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Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
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Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
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Structural basis for specific single-stranded RNA recognition by designer pentatricopeptide repeat proteins.

Cuicui Shen1, Delin Zhang1, Zeyuan Guan1

  • 1National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.

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Designer pentatricopeptide repeat (PPR) proteins bind single-stranded RNAs (ssRNAs) specifically. Crystal structures reveal how PPR protein modules recognize RNA bases, enabling synthetic RNA-binding protein design.

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • Pentatricopeptide repeat (PPR) proteins are crucial RNA-binding proteins involved in eukaryotic RNA metabolism.
  • PPR proteins recognize single-stranded RNAs (ssRNAs) in a modular and base-specific manner, offering potential for gene manipulation.
  • The precise structural mechanisms underlying nucleotide recognition by designer PPR (dPPR) proteins are not fully understood.

Purpose of the Study:

  • To elucidate the structural basis of nucleotide-specific recognition by designer PPR (dPPR) proteins.
  • To provide atomic-level insights into how dPPR proteins interact with their target ssRNAs.
  • To lay the groundwork for designing novel synthetic RNA-binding proteins.

Main Methods:

  • X-ray crystallography was employed to determine the structures of four dPPR proteins.
  • dPPR proteins were crystallized in complex with their respective ssRNA targets.
  • Structural analysis focused on the interactions between dPPR repeats and RNA bases.

Main Results:

  • Four crystal structures of dPPR-ssRNA complexes were determined.
  • dPPR repeats form a right-handed superhelical spiral shell that encapsulates the ssRNA.
  • Atomic-level interactions reveal the molecular basis for specific recognition of RNA bases (U, C, A, G) by different PPR codes.

Conclusions:

  • The study provides unprecedented structural insights into the sequence-specific RNA recognition mechanism of dPPR proteins.
  • These findings advance the understanding of natural PPR protein function in RNA metabolism.
  • The reported structures pave the way for the rational design of artificial sequence-specific RNA-binding proteins.