A study published in Nature (2009) reveals the architecture and secondary structure of the entire HIV-1 RNA genome at single nucleotide resolution using SHAPE technology. The genome encodes 15 proteins and contains multiple RNA structures that regulate viral functions, including transcription, reverse transcription, and protein folding. The study identifies structured and unstructured regions of the genome, with structured regions correlating with protein domains and sequences that encode inter-domain loops. Unstructured regions, such as hypervariable domains, are sequestered by stable RNA helices. The research highlights that RNA structure may constitute an additional level of the genetic code, influencing protein folding and function. The study also shows that RNA structures can modulate ribosome elongation, facilitating native protein folding. The findings emphasize the importance of RNA structure in HIV-1 replication and suggest that many coding RNAs may have similar regulatory features. The study provides a detailed RNA secondary structure model for the HIV-1 genome, revealing how RNA structure encodes protein structure at two levels: primary sequence and higher-order structure. The results suggest that RNA structure plays a critical role in viral replication and host defense evasion. The study also identifies regulatory motifs in the HIV-1 genome, including the gag-pol frameshift signal, which is part of a three-helix junction structure. The research underscores the significance of RNA structure in viral biology and highlights the need for further investigation into the role of RNA structure in genetic regulation.A study published in Nature (2009) reveals the architecture and secondary structure of the entire HIV-1 RNA genome at single nucleotide resolution using SHAPE technology. The genome encodes 15 proteins and contains multiple RNA structures that regulate viral functions, including transcription, reverse transcription, and protein folding. The study identifies structured and unstructured regions of the genome, with structured regions correlating with protein domains and sequences that encode inter-domain loops. Unstructured regions, such as hypervariable domains, are sequestered by stable RNA helices. The research highlights that RNA structure may constitute an additional level of the genetic code, influencing protein folding and function. The study also shows that RNA structures can modulate ribosome elongation, facilitating native protein folding. The findings emphasize the importance of RNA structure in HIV-1 replication and suggest that many coding RNAs may have similar regulatory features. The study provides a detailed RNA secondary structure model for the HIV-1 genome, revealing how RNA structure encodes protein structure at two levels: primary sequence and higher-order structure. The results suggest that RNA structure plays a critical role in viral replication and host defense evasion. The study also identifies regulatory motifs in the HIV-1 genome, including the gag-pol frameshift signal, which is part of a three-helix junction structure. The research underscores the significance of RNA structure in viral biology and highlights the need for further investigation into the role of RNA structure in genetic regulation.