Structures of helical junctions in nucleic acids
Authors: Lilley David M. J. 
Published: July 2002

1. Introduction 110

2. The occurrence of helical junctions in nucleic acids 111

2.1 The four-way DNA junction and genetic recombination 111

2.2 Helical junctions in RNA 112

2.3 Homology and branch migration of four-way junctions 112

2.4 Forms of helical junctions available for study 113

3. The structure of the four-way DNA junction 114

3.1 The global structure of the junction 114

3.2 The stacked X-structure 114

3.3 The junction has antiparallel character 115

3.4 The stereochemistry of the four-way DNA junction 116

3.4.1 Molecular modelling 116

3.4.2 NMR studies 116

3.4.3 Crystallography 116

4. Role of metal ions in the folding of the four-way DNA junction 122

4.1 An extended structure of the four-way junction at low salt concentrations 122

4.2 Structural interconversion between the extended and stacked X-structures 122

4.3 Location of structural metal ions in the four-way junction 124

5. Conformational variation in the four-way junction 125

5.1 Formation of alternative stacking conformers and sequence-dependent bias 125

5.1.1 Demonstration of alternative stacking conformers 125

5.1.2 Simultaneous presence of both stacking conformers 126

5.1.3 Exchange between stacking conformers 128

5.1.4 Longer-range sequence dependence 129

5.2 Variability in the interhelical angle 129

5.2.1 The interhelical angle 129

5.2.2 Variation, flexibility and malleability of the interhelical angle 130

5.3 Perturbation of the junction structure 130

6. Branch migration 131

6.1 Strand exchange between homologous sequences, and branch migration 131

6.2 The rate of branch migration 131

6.3 The effect of magnesium ions on branch migration rates 132

6.4 Branch migration and the structure of the DNA junction 132

7. Three-way DNA junctions 133

7.1 The perfectly basepaired three-way junction 133

7.2 The effect of unpaired bases; the bulged three-way junction 134

7.3 Two inequivalent stacking conformers 134

7.4 The stereochemistry of the bulged three-way junction 136

8. Helical junctions in RNA 136

8.1 The four-way junction in RNA 136

8.2 Some important four-way junctions in functional RNA species 137

8.2.1 The U1 snRNA junction 137

8.2.2 The four-way junction of the hairpin ribozyme 138

8.3 Three-way helical junctions in RNA 138

9. Recognition and distortion of four-way DNA junctions by proteins 139

9.1 Junction-resolving enzymes 139

9.1.1 Occurrence of junction-resolving enzymes 140

9.1.2 Cleavage of DNA junctions by resolving enzymes 140

9.1.3 Structure-selective binding of resolving enzymes to four-way junctions 143

9.1.4 Distortion of the structure of junctions by resolving enzymes 143

9.1.5 Relationship between distortion and cleavage of DNA junctions 144

9.2 Branch migration proteins 145

9.3 Site-specific recombinases 146

9.4 Other proteins 149

10. Summary and conclusions 149

11. Acknowledgements 151

12. References 151

Helical junctions in nucleic acids are important in biology. In DNA, their main significance
is as intermediates in both homologous and site-specific recombination events. In RNA they
are important architectural elements.

Helical junctions may be defined as branchpoints where double-helical segments intersect
with axial discontinuities, such that strands are exchanged between the different helical
sections. Thus the integrity of junctions is maintained by the covalent continuity of the
component strands. Junctions can be perfectly basepaired, such that every base is paired with
its Watson–Crick complement, or they can contain mismatches or unpaired bases; the latter
can have significant effects on the folding of the structures. A systematic nomenclature exists
for the unambiguous description of different junctions (Lilley et al. 1995) and some examples
are illustrated in Fig. 1.

The purpose of the present article is to review what is known about the structures of helical
junctions, and their recognition by proteins. The recent presentation of crystal structures of
four-way junctions (Nowakowski et al. 1999; Ortiz-Lombardía et al. 1999; Eichman et al.
2000) provides a good opportunity to examine the current state of knowledge. We can also
ask whether there are general principles behind the folding of branched nucleic acid species.
Two possible principles emerge.