At the beginning of this review I suggested two simple folding principles for branched nucleic acids... these were the tendency for pairwise coaxial stacking of helical arms, and the importance of metal ion interactions in the induction of folding.
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metal ion-induced folding of branched nucleic acids
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Folding principles learned from branched DNA can guide analysis of corresponding RNA junctions, but extrapolation requires caution because RNA and DNA differ in stability and electrostatic behavior.
Quoted textsource-backed
In general the folding of branched DNA provides some good indications on the likely folding of the corresponding RNA species, but caution is required in making the extrapolation because the two polymers are significantly different.
Perfect three-way (3H) DNA junctions are described as an exception to the general folding principles because they resist coaxial stacking and show little conformational change upon metal ion addition, whereas added central base pairs can restore stacking-compatible behavior.
Quoted textsource-backed
Perfect three-way (3H) DNA junctions seem to defy these principles in that they appear reluctant to undergo coaxial stacking of arms, and exhibit little change in conformation with addition of metal ions... upon inclusion of a few additional base pairs at the centre (to create a 3HS2 junction for example) the additional stereochemical flexibility allows two arms to undergo coaxial stacking.
Two broad folding principles for branched nucleic acids emphasized by the review are pairwise coaxial stacking of helical arms and metal ion interactions that induce folding.
Quoted textsource-backed
At the beginning of this review I suggested two simple folding principles for branched nucleic acids... these were the tendency for pairwise coaxial stacking of helical arms, and the importance of metal ion interactions in the induction of folding. We see that both are important in a wide range of systems, both in DNA and RNA.
Four-way DNA junctions undergo metal ion-induced folding into a stacked X-structure based on coaxial stacking of arms, and alternative stacked conformers can exist in dynamic equilibrium with sequence-dependent relative stability.
Quoted textsource-backed
The premier example is the four-way DNA junction, which undergoes metal ion-induced folding into the stacked X-structure that is based on coaxial stacking of arms. As in many systems, there are two alternative ways to achieve this depending on the choice of stacking partners. Recent data reveal that both forms often exist in a dynamic equilibrium, and that the relative stability of the two conformers depends upon base sequence extending a significant distance from the junction.