Nucleic Acids in Chemistry and Biology

260 Chapter 7

assemble usually into a unique folded structure. However, this process is very sensitive to reaction condi-
tions, such as temperature changes, and requires cations to overcome electrostatic repulsion.
An early event in RNA folding is the formation of secondary structure. This is promoted by cations,
including monovalent ions, since duplex formation is stimulated by simple charge screening. Tertiary
structure formation involves the tight packing of RNA strands and the formation of cavities. Most RNA
molecules begin to form tertiary structure upon interaction with divalent cations, particularly Mg^2 . RNA
molecules tend to fold in a hierarchical manner in which one domain of the molecule precedes the forma-
tion of other domains. This is particularly easy to observe in cases where the folding intermediate is
stable (as in group I intron folding), but it can still occur in cases where the intermediate is transient. In some

a

b

N

N

O

N

O

O O

O

H

H

H

N

N

O N

N

N O

O O

O

H

H

H

N

N

N

N

O NH 2

O

O

O

H H

Figure 7.9 A-minor motifs and ribosomal RNA packing. (a) A class of A-minor motif, showing adenosine docked
into the minor groove of a G–C pair. (b) A-minor interactions (adenosine in red) in the 50S ribosomal
subunit
(Reprinted from Ref. 10. © (2001), with permission from the National Academy of Sciences, USA)

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