Why do all lariat RNA introns have adenosine as the branch-point nucleotide? Conformational study of naturally-occurring branched trinucleotides and its eleven analogues by 1H-, 31P-NMR and CD spectroscopy.
1H-NMR conformational studies of six branched triribonucleotides where the branch-point nucleotide was either U, C or G (4-9) have been carried out by assigning 1H resonances through 2D NMR and then observing the temperature-dependent (i) chemical shifts of the aromatic and the anomeric protons, and (ii) shifts of the equilibrium of N and S pseudorotamer populations of each sugar moiety. The data have been compared with those of 2'----5' dimers (1-3) and other branched trimers (10-16). It emerged that all the branched trimers (4-16) adopt a conformational state closer to the corresponding 2'----5' dimers than the corresponding 3'----5' dimers. A temperature-dependent 31P chemical shift study confirmed that the conformational constraint is mainly associated with the 2'----5' phosphate linkage. Although, it appeared with the CD data that when C or especially when U is at the branch-point the overall constraint is weak. This suggests that even if these trimers adopt a 2'----5' dimer geometry, there is a lack of stabilization by strong stackings within the molecule. This is in sharp contrast with the results found for A (10-16) and to a smaller extent for G (8, 9) at the branch-point.
Remaud
G
G
Department of Bioorganic Chemistry, University of Uppsala, Sweden.
Balgobin
N
N
Sandström
A
A
Vial
J M
JM
Koole
L H
LH
Buck
H M
HM
Drake
A F
AF
Zhou
X X
XX
Chattopadhyaya
J
J
D000241:Adenosine; D002942:Circular Dichroism; D006859:Hydrogen; D007438:Introns; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides; D010758:Phosphorus; D012313:RNA / Q000235:genetics; D013816:Thermodynamics
D009843:Oligoribonucleotides; D010758:Phosphorus; D012313:RNA; D006859:Hydrogen; D000241:Adenosine