28  Coaxial Stacking

28.1 Introduction

Coaxial stacking is the stacking of two base pairs at the terminii of adjacent helices. This stacking aligns the two helices along a common axis. In unimolecular secondary structures, coaxial stacking occurs in multibranch and exterior loops.

This set of nearest neighbor parameters allows for two types of coaxial stacking, flush stacking of helices that are directly adjacent (no intervening unpaired nucleotides) and mismatch-mediated coaxial stacking in which a single mistmatch occurs between the stacked helices. Mismatch-mediated coaxial stacking of helices is only allowed when there is exactly one unpaired nucleotide between the helices that can form a non-canonical pair with a nucleotide on the other side of one of the two helices.

28.2 Flush Coaxial Stacking

In flush coaxial stacking, the free energy and enthalpy changes of the coaxial stack are approximated using the helical nearest neighbor parameters Watson-Crick-Franklin as though there is no break in the backbone.

28.3 Mismatch-Mediated Coaxial Stacking

In the case of mismatch-mediated coaxial stacking, there are two adjacent stacks. The stack of the mismatch on the adjacent helix, where there is no break in the backbone, is approximated using the terminal mismatch parameters. The second stack is the stack of the mismatch on the second helix, where the backbone is not continuous.

28.4 Examples

Flush coaxial stacking

ΔG°37 coaxial stack = ΔG°37(Watson-Crick-Franklin stack)

ΔG°37 coaxial stack = ΔG°37(AT pair followed by CG pair)

ΔG°37 coaxial stack = -1.4 kcal/mol

ΔH°coaxial stack = ΔH°(Watson-Crick-Franklin stack)

ΔH°coaxial stack = ΔH°(AT pair followed by CG pair)

ΔH°coaxial stack = -0.8 kcal/mol

Note that at this interface, the terminal AT pair penalty would still apply when calculating the helix stability.

Mismatch-mediated coaxial stacking

ΔG°37 coaxial stack = ΔG°37(continuous backbone stack) + ΔG°37(discontinuous backbone stack)

ΔG°37 coaxial stack = ΔG°37(AT pair followed by GG mismatch) + ΔG°37(discontinuous backbone stack)

ΔG°37 coaxial stack = -0.4 kcal/mol -2.1 kcal/mol

ΔG°37 coaxial stack = -2.5 kcal/mol

ΔH°coaxial stack = ΔH°(continuous backbone stack) + ΔH°(discontinuous backbone stack)

ΔH°coaxial stack = ΔH°(AT pair followed by GG mismatch) + ΔH°(discontinuous backbone stack)

ΔH°coaxial stack = 1.5 kcal/mol - 8.4 kcal/mol

ΔH°coaxial stack = -6.9 kcal/mol

Note that at this interface, the terminal AT pair penalty would still apply when calculating the helix stability.

28.5 Parameter Tables

A table summarizing the parameters is available in html format.