The inherent properties of DNA four-way junctions: comparing the crystal structures of holliday junctions

Interaction of dinuclear Co(III) cylinders with higher-order DNA structures

Alternative DNA structures play critical roles in fundamental biological processes linked to human diseases. Thus, targeting and stabilizing these structures by specific ligands could affect the progression of cancer and other diseases. Here, we describe, using methods of molecular biophysics, the interactions of two oxidatively locked [Co2L3]6+ cylinders, rac-2 and meso-1, with diverse alternative DNA structures, such as junctions, G quadruplexes, and bulges. This study was motivated by earlier results demonstrating that both Co(III) cylinders exhibit potent and selective activity against cancer cells, accumulate in the nucleus of cancer cells, and prove to be efficient DNA binders. The results show that the bigger cylinder rac-2 stabilizes all DNA structures, while the smaller cylinder meso-1 stabilizes just the Y-shaped three-way junctions. Collectively, the results of this study suggest that the stabilization of alternative DNA structures by Co(III) cylinders investigated in this work might contribute to the mechanism of their biological activity.

Prokaryotic DNA Crossroads: Holliday Junction Formation and Resolution

Cells are continually exposed to a multitude of internal and external stressors, which give rise to various types of DNA damage. To protect the integrity of their genetic material, cells are equipped with a repertoire of repair proteins that engage in various repair mechanisms, facilitated by intricate networks of protein-protein and protein-DNA interactions. Among these networks is the homologous recombination (HR) system, a molecular repair mechanism conserved in all three domains of life. On one hand, HR ensures high-fidelity, template-dependent DNA repair, while on the other hand, it results in the generation of combinatorial genetic variations through allelic exchange. Despite substantial progress in understanding this pathway in bacteria, yeast, and humans, several critical questions remain unanswered, including the molecular processes leading to the exchange of DNA segments, the coordination of protein binding, conformational switching during branch migration, and the resolution of Holliday Junctions (HJs). This Review delves into our current understanding of the HR pathway in bacteria, shedding light on the roles played by various proteins or their complexes at different stages of HR. In the first part of this Review, we provide a brief overview of the end resection processes and the strand-exchange reaction, offering a concise depiction of the mechanisms that culminate in the formation of HJs. In the latter half, we expound upon the alternative methods of branch migration and HJ resolution more comprehensively and holistically, considering the historical research timelines. Finally, when we consolidate our knowledge about HR within the broader context of genome replication and the emergence of resistant species, it becomes evident that the HR pathway is indispensable for the survival of bacteria in diverse ecological niches.

Metallohelices stabilize DNA three-way junctions and induce DNA damage in cancer cells

DNA three-way junctions (3WJ) represent one of the simplest supramolecular DNA structures arising as intermediates in homologous recombination in the absence of replication. They are also formed transiently during DNA replication. Here we examine the ability of Fe(II)-based metallohelices to act as DNA 3WJ binders and induce DNA damage in cells. We investigated the interaction of eight pairs of enantiomerically pure Fe(II) metallohelices with four different DNA junctions using biophysical and molecular biology methods. The results show that the metallohelices stabilize all types of tested DNA junctions, with the highest selectivity for the Y-shaped 3WJ and minimal selectivity for the 4WJ. The potential of the best stabilizer of DNA junctions and, at the same time, the most selective 3WJ binder investigated in this work to induce DNA damage was determined in human colon cancer HCT116 cells. These metallohelices proved to be efficient in killing cancer cells and triggering DNA damage that could yield therapeutic benefits.

30th Annual GP2A Medicinal Chemistry Conference

The Group for the Promotion of Pharmaceutical Chemistry in Academia (GP2A) held their 30th annual conference in August 2022 in Trinity College Dublin, Ireland. There were 9 keynote presentations, 10 early career researcher presentations and 41 poster presentations.

O-GlcNAcylation of High Mobility Group Box 1 (HMGB1) Alters Its DNA Binding and DNA Damage Processing Activities

Protein O-GlcNAcylation is an essential and dynamic regulator of myriad cellular processes, including DNA replication and repair. Proteomic studies have identified the multifunctional nuclear protein HMGB1 as O-GlcNAcylated, providing a potential link between this modification and DNA damage responses. Here, we verify the protein's endogenous modification at S100 and S107 and found that the major modification site is S100, a residue that can potentially influence HMGB1-DNA interactions. Using synthetic protein chemistry, we generated site-specifically O-GlcNAc-modified HMGB1 at S100 and characterized biochemically the effect of the sugar modification on its DNA binding activity. We found that O-GlcNAc alters HMGB1 binding to linear, nucleosomal, supercoiled, cruciform, and interstrand cross-linked damaged DNA, generally resulting in enhanced oligomerization on these DNA structures. Using cell-free extracts, we also found that O-GlcNAc reduces the ability of HMGB1 to facilitate DNA repair, resulting in error-prone processing of damaged DNA. Our results expand our understanding of the molecular consequences of O-GlcNAc and how it affects protein-DNA interfaces. Importantly, our work may also support a link between upregulated O-GlcNAc levels and increased rates of mutations in certain cancer states.

A Biological Take on Halogen Bonding and Other Non-Classical Non-Covalent Interactions

Classical hydrogen bonds have, for many decades, been the dominant non-covalent interaction in the toolbox that chemists and chemical engineers have used to design and control the structures of compounds and molecular assemblies as novel materials. Recently, a set of non-classical non-covalent (NC-NC) interactions have emerged that exploit the properties of the Group IV, V, VI, and VII elements of the periodic table (the tetrel, pnictogen, chalcogen, and halogen bonds, respectively). Our research group has been characterizing the prevalence, geometric constraints, and structure-function relationship specifically of the halogen bond in biological systems. We have been particularly interested in exploiting the biological halogen bonds (or BXBs) to control the structures, stabilities, and activities of biomolecules, including the DNA Holliday junction and enzymes. In this review, we first provide a set of criteria for how to determine whether BXBs or any other NC-NC interactions would have biological relevance. We then navigate the trail of studies that had led us from an initial, very biological question to our current point in the journey to establish BXBs as a tool for biomolecular engineering. Finally, we close with a perspective on future directions for this line of research.

Protein-Assisted Room-Temperature Assembly of Rigid, Immobile Holliday Junctions and Hierarchical DNA Nanostructures

Immobile Holliday junctions represent not only the most fundamental building block of structural DNA nanotechnology but are also of tremendous importance for the in vitro investigation of genetic recombination and epigenetics. Here, we present a detailed study on the room-temperature assembly of immobile Holliday junctions with the help of the single-strand annealing protein Redβ. Individual DNA single strands are initially coated with protein monomers and subsequently hybridized to form a rigid blunt-ended four-arm junction. We investigate the efficiency of this approach for different DNA/protein ratios, as well as for different DNA sequence lengths. Furthermore, we also evaluate the potential of Redβ to anneal sticky-end modified Holliday junctions into hierarchical assemblies. We demonstrate the Redβ-mediated annealing of Holliday junction dimers, multimers, and extended networks several microns in size. While these hybrid DNA–protein nanostructures may find applications in the crystallization of DNA–protein complexes, our work shows the great potential of Redβ to aid in the synthesis of functional DNA nanostructures under mild reaction conditions.

Sulfur as an Acceptor to Bromine in Biomolecular Halogen Bonds

The halogen bond (X-bond) has become an important design element in chemistry, including medicinal chemistry and biomolecular engineering. Although oxygen is the most prevalent and best characterized X-bond acceptor in biomolecules, the interaction is seen with nitrogen, sulfur, and aromatic systems as well. In this study, we characterize the structure and thermodynamics of a Br···S X-bond between a 5-bromouracil base and a phosphorothioate in a model DNA junction. The single-crystal structure of the junction shows the geometry of the Br···S to be variable, while calorimetric studies show that the anionic S acceptor is comparable to or slightly more stable than the analogous O acceptor, with a -3.5 kcal/mol difference in ΔΔH^25°C and -0.4 kcal/mol ΔΔG^25°C (including an entropic penalty ΔΔS^25°C of -10 cal/(mol K)). Thus sulfur is shown to be a favorable acceptor for bromine X-bonds, extending the application of this interaction for the design of inhibitors and biological materials.

Structure of the Holliday junction: applications beyond recombination

The Holliday junction (HJ) is an essential element in recombination and related mechanisms. The structure of this four-stranded DNA assembly, which is now well-defined alone and in complex with proteins, has led to its applications in areas well outside of molecular recombination, including nanotechnology and biophysics. This minireview explores some interesting recent research on the HJ, as it has been adapted to design regular two- or three-dimensional lattices for crystal engineering, and more complex systems through DNA origami. In addition, the sequence dependence of the structure is discussed in terms how it can be applied to characterize the geometries and energies of various noncovalent interactions, including halogen bonds in oxidatively damaged (halogenated) bases and hydrogen bonds associated with the epigenetic 5-hydroxylmethylcytosine base.

Relationships between hydrogen bonds and halogen bonds in biological systems

The recent recognition that halogen bonding (XB) plays important roles in the recognition and assembly of biological molecules has led to new approaches in medicinal chemistry and biomolecular engineering. When designing XBs into strategies for rational drug design or into a biomolecule to affect its structure and function, we must consider the relationship between this interaction and the more ubiquitous hydrogen bond (HB). In this review, we explore these relationships by asking whether and how XBs can replace, compete against or behave independently of HBs in various biological systems. The complex relationships between the two interactions inform us of the challenges we face in fully utilizing XBs to control the affinity and recognition of inhibitors against their therapeutic targets, and to control the structure and function of proteins, nucleic acids and other biomolecular scaffolds.

Probing the Ion Binding Site in a DNA Holliday Junction Using Förster Resonance Energy Transfer (FRET)

Holliday Junctions are critical DNA intermediates central to double strand break repair and homologous recombination. The junctions can adopt two general forms: open and stacked-X, which are induced by protein or ion binding. In this work, fluorescence spectroscopy, metal ion luminescence and thermodynamic measurements are used to elucidate the ion binding site and the mechanism of junction conformational change. Förster resonance energy transfer measurements of end-labeled junctions monitored junction conformation and ion binding affinity, and reported higher affinities for multi-valent ions. Thermodynamic measurements provided evidence for two classes of binding sites. The higher affinity ion-binding interaction is an enthalpy driven process with an apparent stoichiometry of 2.1 ± 0.2. As revealed by Eu(3+) luminescence, this binding class is homogeneous, and results in slight dehydration of the ion with one direct coordination site to the junction. Luminescence resonance energy transfer experiments confirmed the presence of two ions and indicated they are 6-7 Å apart. These findings are in good agreement with previous molecular dynamics simulations, which identified two symmetrical regions of high ion density in the center of stacked junctions. These results support a model in which site-specific binding of two ions in close proximity is required for folding of DNA Holliday junctions into the stacked-X conformation.

2′-O-Methyl- and 2′-O-propargyl-5-methylisocytidine: synthesis, properties and impact on the isoCd–dG and the isoCd–isoGd base pairing in nucleic acids with parallel and antiparallel strand orientation

The impact of 2′-O-alkyl residues on the stability of iC_d–dG and iC_d–iG_d base pairs was studied in DNA with parallel and antiparallel chain orientation.

Identification and conformational analysis of putative microRNAs in Maruca vitrata (Lepidoptera: Pyralidae)

MicroRNAs (miRNAs) are a class of small RNAs, evolutionarily conserved endogenous non-coding RNAs that regulate their target mRNA expression by either inactivating or degrading mRNA genes; thus playing an important role in the growth and development of an organism. Maruca vitrata is an insect pest of leguminous plants like pigeon pea, cowpea and mung bean and is pantropical. In this study, we perform BLAST on all known miRNAs against the transcriptome data of M. vitrata and thirteen miRNAs were identified. These miRNAs were characterised and their target genes were identified using TargetScan and were functionally annotated using FlyBase. The importance of the structure of pre-miRNA in the Drosha activity led to study the backbone torsion angles of predicted pre-miRNAs (mvi-miR-9751, mvi-miR-649-3p, mvi-miR-4057 and mvi-miR-1271) to identify various nucleotide triplets that contribute to the variation of torsion angle values at various structural motifs of a pre-miRNA.

A unique HMG-box domain of mouse Maelstrom binds structured RNA but not double stranded DNA

Piwi-interacting piRNAs are a major and essential class of small RNAs in the animal germ cells with a prominent role in transposon control. Efficient piRNA biogenesis and function require a cohort of proteins conserved throughout the animal kingdom. Here we studied Maelstrom (MAEL), which is essential for piRNA biogenesis and germ cell differentiation in flies and mice. MAEL contains a high mobility group (HMG)-box domain and a Maelstrom-specific domain with a presumptive RNase H-fold. We employed a combination of sequence analyses, structural and biochemical approaches to evaluate and compare nucleic acid binding of mouse MAEL HMG-box to that of canonical HMG-box domain proteins (SRY and HMGB1a). MAEL HMG-box failed to bind double-stranded (ds)DNA but bound to structured RNA. We also identified important roles of a novel cluster of arginine residues in MAEL HMG-box in these interactions. Cumulatively, our results suggest that the MAEL HMG-box domain may contribute to MAEL function in selective processing of retrotransposon RNA into piRNAs. In this regard, a cellular role of MAEL HMG-box domain is reminiscent of that of HMGB1 as a sentinel of immunogenic nucleic acids in the innate immune response.

Structure of d(CCCCGGTACCGGGG)2 at 1.65 Å resolution

The crystal structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 has previously been reported as an A-type double helix at a resolution of 2.5 Å in space group P41. Here, the structure of this sequence was determined at a significantly higher resolution of 1.65 Å in space group P4₁2₁2. The differences in crystal packing between the former and latter are described. The crystallographic asymmetric unit consists of one tetradecanucleotide duplex that spans more than one full turn of the A-helix. This structure allowed the unambiguous identification of solvent interactions.

Structure of d(CCGGGACCGG)4 as a four-way junction at 1.6 Å resolution: new insights into solvent interactions

The crystal structure of the decamer sequence d(CCGGGACCGG)(4) has previously been reported at 2.16 Å resolution as a four-way junction. Here, the structure of this sequence is reported at the significantly higher resolution of 1.6 Å, which is the highest resolution reported for a four-way junction. This allowed the unambiguous identification of an extensive hydration network with distinct patterns and solvent-mediated interactions that shed new light on the role of water in the formation and stabilization of junction structures.

Structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 as an A-DNA duplex

The crystal structure of the tetradecanucleotide sequence d(CCCCGGTACCGGGG)(2) has been determined at 2.5 Å resolution in the tetragonal space group P4(1). This sequence was designed with the expectation of a four-way junction. However, the sequence crystallized as an A-DNA duplex and represents more than one full turn of the A-helix. The crystallographic asymmetric unit consists of one tetradecanucleotide duplex. The structural parameters of the A-type DNA duplex structure and the crystal-packing arrangement are described. One Mn(2+) ion was identified with direct coordination to the N7 position of G(13) and a water molecule at the major-groove side of the C(2)·G(13) base pair.

Structure of d(CGGGTACCCG)4 as a four-way Holliday junction

The crystal structure of the decamer sequence d(CGGGTACCCG)(4) as a four-way Holliday junction has been determined at 2.35 Å resolution. The sequence was designed in order to understand the principles that govern the relationship between sequence and branching structure. It crystallized as a four-way junction structure with an overall geometry similar to those of previously determined Holliday junction structures.

Local sensing of global DNA topology: from crossover geometry to type II topoisomerase processivity

Type II topoisomerases are ubiquitous enzymes that control the topology and higher order structures of DNA. Type IIA enzymes have the remarkable property to sense locally the global DNA topology. Although many theoretical models have been proposed, the molecular mechanism of chiral discrimination is still unclear. While experimental studies have established that topoisomerases IIA discriminate topology on the basis of crossover geometry, a recent single-molecule experiment has shown that the enzyme has a different processivity on supercoiled DNA of opposite sign. Understanding how cross-over geometry influences enzyme processivity is, therefore, the key to elucidate the mechanism of chiral discrimination. Analysing this question from the DNA side reveals first, that the different stability of chiral DNA cross-overs provides a way to locally sense the global DNA topology. Second, it shows that these enzymes have evolved to recognize the G- and T-segments stably assembled into a right-handed cross-over. Third, it demonstrates how binding right-handed cross-overs across their large angle imposes a different topological link between the topoIIA rings and the plectonemes of opposite sign thus directly affecting the enzyme freedom of motion and processivity. In bridging geometry and kinetic data, this study brings a simple solution for type IIA topoisomerase chiral discrimination.

Helical chirality: a link between local interactions and global topology in DNA

DNA supercoiling plays a major role in many cellular functions. The global DNA conformation is however intimately linked to local DNA-DNA interactions influencing both the physical properties and the biological functions of the supercoiled molecule. Juxtaposition of DNA double helices in ubiquitous crossover arrangements participates in multiple functions such as recombination, gene regulation and DNA packaging. However, little is currently known about how the structure and stability of direct DNA-DNA interactions influence the topological state of DNA. Here, a crystallographic analysis shows that due to the intrinsic helical chirality of DNA, crossovers of opposite handedness exhibit markedly different geometries. While right-handed crossovers are self-fitted by sequence-specific groove-backbone interaction and bridging Mg(2+) sites, left-handed crossovers are juxtaposed by groove-groove interaction. Our previous calculations have shown that the different geometries result in differential stabilisation in solution, in the presence of divalent cations. The present study reveals that the various topological states of the cell are associated with different inter-segmental interactions. While the unstable left-handed crossovers are exclusively formed in negatively supercoiled DNA, stable right-handed crossovers constitute the local signature of an unusual topological state in the cell, such as the positively supercoiled or relaxed DNA. These findings not only provide a simple mechanism for locally sensing the DNA topology but also lead to the prediction that, due to their different tertiary intra-molecular interactions, supercoiled molecules of opposite signs must display markedly different physical properties. Sticky inter-segmental interactions in positively supercoiled or relaxed DNA are expected to greatly slow down the slithering dynamics of DNA. We therefore suggest that the intrinsic helical chirality of DNA may have oriented the early evolutionary choices for DNA topology.

Does topoisomerase II specifically recognize and cleave hairpins, cruciforms and crossovers of DNA?

DNA topoisomerase II is an enzyme that specializes in DNA disentanglement. It catalyzes the interconversion of DNA between different topological states. This event requires the passage of one duplex through another one via a transient double-strand break. Topoisomerase II is able to process any type of DNA, including structures such as DNA juxtapositions (crossovers), DNA hairpins or cruciforms, which are recognized with high specificity. In this review, we focused our attention on topoisomerase II recognizing DNA substrates that possess particular geometries. A strong cleavage site, as we identified in pBR322 DNA in the presence of ellipticine (site 22), appears to be characterized by a cruciform structure formed from two stable hairpins. The same sequence could also constitute a four-way junction structure stabilized by interactions involving ATC sequences. The latter have been shown to be able to promote Holliday junctions. We reviewed the recent literature that deals with the preferential recognition of crossovers by various topoisomerases. The single molecule relaxation experiments have demonstrated the differential abilities of the topoisomerases to recognize crossovers. It appears that enzymes, which distinguish the chirality of the crossovers, possess specialized domains dedicated to this function. We also stress that the formation of crossovers is dependent on the presence of adequate stabilizing sequences. Investigation of the impact of such structures on enzyme activity is important in order to both improve our knowledge of the mechanism of action of the topoisomerase II and to develop new inhibitors of this enzyme.

A left-handed supramolecular assembly around a right-handed screw axis in the crystal structure of homo-DNA

Duplexes of homo-DNA, a hexose analogue of DNA and autonomous pairing system, exhibit unusual conformational features, and in the crystal structure create a unique double-helical supramolecular motif whose main characteristic is a handedness that is opposite to that of the underlying crystallographic symmetry.

DNA topology and geometry in Flp and Cre recombination

The Flp recombinase of yeast and the Cre recombinase of bacteriophage P1 both belong to the lambda-integrase (Int) family of site-specific recombinases. These recombination systems recognize recombination-target sequences that consist of two 13bp inverted repeats flanking a 6 or 8bp spacer sequence. Recombination reactions involve particular geometric and topological relationships between DNA target sites at synapsis, which we investigate using nicked-circular DNA molecules. Examination of the tertiary structure of synaptic complexes formed on nicked plasmid DNAs by atomic-force microscopy, in conjunction with detailed topological analysis using the mathematics of tangles, shows that only a limited number of recombination-site topologies are consistent with the global structures of plasmids bearing directly and inversely repeated sites. The tangle solutions imply that there is significant distortion of the Holliday-junction intermediate relative to the planar structure of the four-way DNA junction present in the Flp and Cre co-crystal structures. Based on simulations of nucleoprotein structures that connect the two-dimensional tangle solutions with three-dimensional models of the complexes, we propose a recombination mechanism in which the synaptic intermediate is characterized by a non-planar, possibly near-tetrahedral, Holliday-junction intermediate. Only modest conformational changes within this structure are needed to form the symmetric, planar DNA junction, which may be characteristic of shorter-lived intermediates along the recombination pathway.

Holliday junction dynamics and branch migration: single-molecule analysis

The Holliday junction (HJ) is a central intermediate in various genetic processes including homologous and site-specific recombination and DNA replication. Branch migration allows the exchange between homologous DNA regions, but the detailed mechanism for this key step of DNA recombination is unidentified. Here, we report direct real-time detection of branch migration in individual molecules. Using appropriately designed HJ constructs we were able to follow junction branch migration at the single-molecule level. Branch migration is detected as a stepwise random process with the overall kinetics dependent on Mg2+ concentration. We developed a theoretical approach to analyze the mechanism of HJ branch migration. The data show steps in which the junction flips between conformations favorable to branch migration and conformations unfavorable to it. In the favorable conformation (the extended HJ geometry), the branch can migrate over several base pairs detected, usually as a single large step. Mg2+ cations stabilize folded conformations and stall branch migration for a period considerably longer than the hopping step. The conformational flip and the variable base pair hopping step provide insights into the regulatory mechanism of genetic processes involving HJs.

How sequence defines structure: a crystallographic map of DNA structure and conformation

The fundamental question of how sequence defines conformation is explicitly answered if the structures of all possible sequences of a macromolecule are determined. We present here a crystallographic screen of all permutations of the inverted repeat DNA sequence d(CCnnnN6N7N8GG), where N6, N7, and N8 are any of the four naturally occurring nucleotides. At this point, 63 of the 64 possible permutations have been crystallized from a defined set of solutions. When combined with previous work, we have assembled a data set of 37 single-crystal structures from 29 of the sequences in this motif, representing three structural classes of DNA (B-DNA, A-DNA, and four-stranded Holliday junctions). This data set includes a unique set of amphimorphic sequence, those that crystallize in two different conformations and serve to bridge the three structural phases. We have thus constructed a map of DNA structures that can be walked through in single nucleotide steps. Finally, the resulting data set allows us to dissect in detail the stabilization of and conformational variations within structural classes and identify significant conformational deviations within a particular structural class that result from sequence rather than crystal or crystallization effects.

Nucleic acid crystallography: current progress

Fifty years after the publication of the DNA double helix model by Watson and Crick, new nucleic acid structures keep emerging at an ever-increasing rate. The past three years have brought a flurry of new oligonucleotide structures, including those of a Hoogsteen-paired DNA duplex, Holliday junctions, DNA-drug complexes, quadruplexes, a host of RNA motifs and various nucleic acid analogues. Major advances were also made in terms of the structure and function of catalytic RNAs. These range from improved models of the phosphodiester cleavage reactions catalyzed by the hairpin and hepatitis delta virus ribozymes to the visualization of a complete active site of a group I self-splicing intron with bound 5'- and 3'-exons. These triumphs are complemented by a refined understanding of cation-nucleic-acid interactions and new routes to the generation of derivatives for phasing of DNA and RNA structures.

Electrostatic Interactions and the Folding of the Four-way DNA Junction: Analysis by Selective Methyl Phosphonate Substitution

The structure and dynamics of the four-way (Holliday) junction are strongly dependent on the presence of metal ions. In this study, the importance of phosphate charge in and around the point of strand exchange has been explored by selective replacement with electrically neutral methyl phosphonate groups, guided by crystal structures of the junction in the folded, stacked X conformation. Junction conformation has been analysed by comparative gel electrophoresis and fluorescence resonance energy transfer (FRET). Three of sets of phosphate groups on the exchanging strands have been analysed; those at the point of strand exchange and those to their 3' and 5' sides. The exchanging and 3' phosphate groups form a box of negatively charged groups on the minor groove face of the junction, while the 5' phosphate groups face each other on the major groove side, with their proR oxygen atoms directed at one another. The largest effects are observed on substitution of the exchanging phosphate groups; replacement of both groups leads to the loss of the requirement for addition of metal ions to allow junction folding. When the equivalent phosphate groups on the continuous strands were substituted, a proportion of the junction folded into the alternative conformer so as to bring these phosphate groups onto the exchanging strands. These species did not interconvert, and thus this is likely to result from the alternative diasteromeric forms of the methyl phosphonate group. This shows that some of the conformational effects result from more than purely electrostatic interactions. Smaller but significant effects were observed on substitution of the flanking phosphate groups. All methyl phosphonate substitutions at these positions allowed folding to proceed at a reduced concentration of magnesium ions, with double substitutions more effective than single substitutions. Substitution of 5' phosphates resulted in a greater degree of folding at a given ionic concentration compared to the corresponding 3' phosphate substitutions. These results show that the phosphate groups at the point of strand exchange exert the largest electrostatic effect on junction folding, but a number of phosphate groups in the vicinity of the exchange region contribute to the overall effects.

Influence of minor groove substituents on the structure of DNA Holliday junctions

The inosine-containing sequence d(CCIGTACm(5)CGG) is shown to crystallize as a four-stranded DNA junction. This structure is nearly identical to the antiparallel junction formed by the parent d(CCGGTACm(5)()CGG) sequence [Vargason, J. M., and Ho, P. S. (2002) J. Biol. Chem. 277, 21041-21049] in terms of its conformational geometry, and inter- and intramolecular interactions within the DNA and between the DNA and solvent, even though the 2-amino group in the minor groove of the important G(3).m(5)C(8) base pair of the junction core trinucleotide (italicized) has been removed. In contrast, the analogous 2,6-diaminopurine sequence d(CCDGTACTGG) crystallizes as resolved duplex DNAs, just like its parent sequence d(CCAGTACTGG) [Hays, F. A., Vargason, J. M., and Ho, P. S. (2003) Biochemistry 42, 9586-9597]. These results demonstrate that it is not the presence or absence of the 2-amino group in the minor groove of the R(3).Y(8) base pair that specifies whether a sequence forms a junction, but the positions of the extracyclic amino and keto groups in the major groove. Finally, the study shows that the arms of the junction can accommodate perturbations to the B-DNA conformation of the stacked duplex arms associated with the loss of the 2-amino substituent, and that two hydrogen bonding interactions from the C(7) and Y(8) pyrimidine nucleotides to phosphate oxygens of the junction crossover specify the geometry of the Holliday junction.

“Deoxyribo Nanonucleic Acid”

The crystal structure of a single-stranded DNA oligonucleotide has revealed formation of a unique three-dimensional array by continuous antiparallel and parallel pairing between monomers. The array is based on tertiary interactions and represents a second-generation nanotechnological system.

Definitions and analysis of DNA Holliday junction geometry

A number of single-crystal structures have now been solved of the four-stranded antiparallel stacked-X form of the Holliday junction. These structures demonstrate how base sequence, substituents, and drug and ion interactions affect the general conformation of this recombination intermediate. The geometry of junctions had previously been described in terms of a specific set of parameters that include: (i) the angle relating the ends of DNA duplexes arms of the junction (interduplex angle); (ii) the relative rotation of the duplexes about the helix axes of the stacked duplex arms (J(roll)); and (iii) the translation of the duplexes along these helix axes (J(slide)). Here, we present a consistent set of definitions and methods to accurately calculate each of these parameters based on the helical features of the stacked duplex arms in the single-crystal structures of the stacked-X junction, and demonstrate how each of these parameters contributes to an overall conformational feature of the structure. We show that the values for these parameters derived from global rather than local helical axes through the stacked bases of the duplex arms are the most representative of the stacked-X junction conformation. In addition, a very specific parameter (J(twist)) is introduced which relates the relative orientation of the stacked duplex arms across the junction which, unlike the interduplex angle, is length independent. The results from this study provide a general means to relate the geometric features seen in the crystal structures to those determined in solution.

DNA recombination: holliday junctions dynamics and branch migration

Holliday junctions are critical intermediates for homologous, site-specific recombination, DNA repair, and replication. A wealth of structural information is available for immobile four-way junctions, but the controversy on the mechanism of branch migration of Holliday junctions remains unsolved. Two models for the mechanism of branch migration were suggested. According to the early model of Alberts-Meselson-Sigal (Sigal, N., and Alberts, B. (1972) J. Mol. Biol. 71, 789-793 and Meselson, M. (1972) J. Mol. Biol. 71, 795-798), exchanging DNA strands around the junction remain parallel during branch migration. Kinetic studies of branch migration (Panyutin, I. G., and Hsieh, P. (1994) Proc. Natl. Acad. Sci. U. S. A. 91, 2021-2025) suggest an alternative model in which the junction adopts an extended conformation. We tested these models using a Holliday junction undergoing branch migration and time-lapse atomic force microscopy, an imaging technique capable of imaging DNA dynamics. The single molecule atomic force microscopy experiments performed in the presence and in the absence of divalent cations show that mobile Holliday junctions adopt an unfolded conformation during branch migration that is retained despite a broad range of motion in the arms of the junction. This conformation of the junction remains unchanged until strand separation. The data obtained support the model for branch migration having the extended conformation of the Holliday junction.

Rad52-independent accumulation of joint circular minichromosomes during S phase in Saccharomyces cerevisiae

We investigated the formation of X-shaped molecules consisting of joint circular minichromosomes (joint molecules) in Saccharomyces cerevisiae by two-dimensional neutral/neutral gel electrophoresis of psoralen-cross-linked DNA. The appearance of joint molecules was found to be replication dependent. The joint molecules had physical properties reminiscent of Holliday junctions or hemicatenanes, as monitored by strand displacement, branch migration, and nuclease digestion. Physical linkage of the joint molecules was detected along the entire length of the minichromosome and most likely involved newly replicated sister chromatids. Surprisingly, the formation of joint molecules was found to be independent of Rad52p as well as of other factors associated with a function in homologous recombination or in the resolution of stalled replication intermediates. These findings thus imply the existence of a nonrecombinational pathway(s) for the formation of joint molecules during the process of DNA replication or minichromosome segregation.

Conformational and hydration effects of site-selective sodium, calcium and strontium ion binding to the DNA Holliday junction structure d(TCGGTACCGA)(4)

The role of metal ions in determining the solution conformation of the Holliday junction is well established, but to date the picture of metal ion binding from structural studies of the four-way DNA junction is very incomplete. Here we present two refined structures of the Holliday junction formed by the sequence d(TCGGTACCGA) in the presence of Na(+) and Ca(2+), and separately with Sr(2+) to resolutions of 1.85A and 1.65A, respectively. This sequence includes the ACC core found to promote spontaneous junction formation, but its structure has not previously been reported. Almost complete hydration spheres can be defined for each metal cation. The Na(+) sites, the most convincing observation of such sites in junctions to date, are one on either face of the junction crossover region, and stabilise the ordered hydration inside the junction arms. The four Ca(2+) sites in the same structure are at the CG/CG steps in the minor groove. The Sr(2+) ions occupy the TC/AG, GG/CC, and TA/TA sites in the minor groove, giving ten positions forming two spines of ions, spiralling through the minor grooves within each arm of the stacked-X structure. The two structures were solved in the two different C2 lattices previously observed, with the Sr(2+) derivative crystallising in the more highly symmetrical form with two-fold symmetry at its centre. Both structures show an opening of the minor groove face of the junction of 8.4 degrees in the Ca(2+) and Na(+) containing structure, and 13.4 degrees in the Sr(2+) containing structure. The crossover angles at the junction are 39.3 degrees and 43.3 degrees, respectively. In addition to this, a relative shift in the base pair stack alignment of the arms of 2.3A is observed for the Sr(2+) containing structure only. Overall these results provide an insight into the so-far elusive stabilising ion structure for the DNA Holliday junction.