A universal mode of helix packing in RNA.
RNA molecules fold into specific three-dimensional shapes to perform structural and catalytic functions. Large RNAs can form compact globular structures, but the chemical basis for close helical packing within these molecules has been unclear. Analysis of transfer, catalysis, in vitro-selected and ribosomal RNAs reveal that helical packing predominantly involves the interaction of single-stranded adenosines with a helix minor groove. Using the Tetrahymena thermophila group I ribozyme, we show here that the near-perfect shape complementarity between the adenine base and the minor groove allows for optimal van der Waals contacts, extensive hydrogen bonding and hydrophobic surface burial, creating a highly energetically favorable interaction. Adenosine is recognized in a chemically similar fashion by a combination of protein and RNA components in the ribonucleoprotein core of the signal recognition particle. These results provide a thermodynamic explanation for the noted abundance of conserved adenosines within the unpaired regions of RNA secondary structures.
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.
E A
EA
Doherty
R T
RT
Batey
B
B
Masquida
J A
JA
Doudna
D000241:Adenosine / Q000235:genetics / Q000378:metabolism; D000818:Animals; D017124:Conserved Sequence / Q000235:genetics; D003698:Hepatitis Delta Virus / Q000201:enzymology / Q000235:genetics; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D011485:Protein Binding; D015347:RNA Probes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016337:RNA, Catalytic / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012338:RNA, Ribosomal, 23S / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012261:Ribonucleoproteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012269:Ribosomal Proteins / Q000378:metabolism; D018271:Signal Recognition Particle / Q000737:chemistry / Q000235:genetics; D013379:Substrate Specificity; D016808:Tetrahymena thermophila / Q000201:enzymology / Q000235:genetics*; D013816:Thermodynamics
D015347:RNA Probes; D016337:RNA, Catalytic; D012338:RNA, Ribosomal, 23S; D012261:Ribonucleoproteins; D012269:Ribosomal Proteins; D018271:Signal Recognition Particle; C027624:ribosomal protein L11; D000241:Adenosine