Sequence dependence and direct measurement of crossover isomer distribution in model Holliday junctions using NMR spectroscopy

Exciton Chirality Inversion in Dye Dimers Templated by DNA Holliday Junction

While only one enantiomer of chiral biomolecules performs a biological function, access to both enantiomers (or enantiomorphs) proved to be advantageous for technology. Using dye covalent attachment to a DNA Holliday junction (HJ), we created two pairs of dimers of bis(chloroindolenine)squaraine dye that enabled strongly coupled molecular excitons of opposite chirality in solution. The exciton chirality inversion was achieved by interchanging single covalent linkers of unequal length tethering the dyes of each dimer to the HJ core. Dimers in each pair exhibited profound exciton-coupled circular dichroism (CD) couplets of opposite signs. Dimer geometries, modeled by simultaneous fitting absorption and CD spectra, were related in each pair as nonsuperimposable and nearly exact mirror images. The origin of observed exciton chirality inversion was explained in the view of isomerization of the stacked Holliday junction. This study will open new opportunities for creating excitonic DNA-based materials that rely on programmable system chirality.

Computational investigation of the impact of core sequence on immobile DNA four-way junction structure and dynamics

Immobile four-way junctions (4WJs) are core structural motifs employed in the design of programmed DNA assemblies. Understanding the impact of sequence on their equilibrium structure and flexibility is important to informing the design of complex DNA architectures. While core junction sequence is known to impact the preferences for the two possible isomeric states that junctions reside in, previous investigations have not quantified these preferences based on molecular-level interactions. Here, we use all-atom molecular dynamics simulations to investigate base-pair level structure and dynamics of four-way junctions, using the canonical Seeman J1 junction as a reference. Comparison of J1 with equivalent single-crossover topologies and isolated nicked duplexes reveal conformational impact of the double-crossover motif. We additionally contrast J1 with a second junction core sequence termed J24, with equal thermodynamic preference for each isomeric configuration. Analyses of the base-pair degrees of freedom for each system, free energy calculations, and reduced-coordinate sampling of the 4WJ isomers reveal the significant impact base sequence has on local structure, isomer bias, and global junction dynamics.

Holliday junction resolvases

Four-way DNA intermediates, called Holliday junctions (HJs), can form during meiotic and mitotic recombination, and their removal is crucial for chromosome segregation. A group of ubiquitous and highly specialized structure-selective endonucleases catalyze the cleavage of HJs into two disconnected DNA duplexes in a reaction called HJ resolution. These enzymes, called HJ resolvases, have been identified in bacteria and their bacteriophages, archaea, and eukaryotes. In this review, we discuss fundamental aspects of the HJ structure and their interaction with junction-resolving enzymes. This is followed by a brief discussion of the eubacterial RuvABC enzymes, which provide the paradigm for HJ resolvases in other organisms. Finally, we review the biochemical and structural properties of some well-characterized resolvases from archaea, bacteriophage, and eukaryotes.

Observing spontaneous branch migration of Holliday junctions one step at a time

Genetic recombination occurs between homologous DNA molecules via a four-way (Holliday) junction intermediate. This ancient and ubiquitous process is important for the repair of double-stranded breaks, the restart of stalled replication forks, and the creation of genetic diversity. Once formed, the four-way junction alone can undergo the stepwise exchange of base pairs known as spontaneous branch migration. Conventional ensemble assays, useful for finding average migration rates over long sequences, have been unable to examine the affect of sequence and structure on the migration process. Here, we present a single-molecule spontaneous branch migration assay with single-base pair resolution in a study of individual DNA junctions that can undergo one step of migration. Junctions exhibit markedly different dynamics of exchange between stacking conformers depending on the point of strand exchange, allowing the moment at which branch migration occurs to be detected. The free energy landscape of spontaneous branch migration is found to be highly nonuniform and governed by two types of sequence-dependent barriers, with unmediated local migration being up to 10 times more rapid than the previously deduced average rate.

Conformational model of the Holliday junction transition deduced from molecular dynamics simulations

Homologous recombination plays a key role in the restart of stalled replication forks and in the generation of genetic diversity. During this process, two homologous DNA molecules undergo strand exchange to form a four-way DNA (Holliday) junction. In the presence of metal ions, the Holliday junction folds into the stacked-X structure that has two alternative conformers. Experiments have revealed the spontaneous transitions between these conformers, but their detailed pathways are not known. Here, we report a series of molecular dynamics simulations of the Holliday junction at physiological and elevated (400 K) temperatures. The simulations reveal new tetrahedral intermediates and suggest a schematic framework for conformer transitions. The tetrahedral intermediates bear resemblance to the junction conformation in complex with a junction-resolving enzyme, T7 endonuclease I, and indeed, one intermediate forms a stable complex with the enzyme as demonstrated in one simulation. We also describe free energy minima for various states of the Holliday junction system, which arise during conformer transitions. The results show that magnesium ions stabilize the stacked-X form and destabilize the open and tetrahedral intermediates. Overall, our study provides a detailed dynamic model of the Holliday junction undergoing a conformer transition.

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.

The charge conduction properties of DNA holliday junctions depend critically on the identity of the tethered photooxidant

The mechanism for electrical charge conduction in DNA has been the subject of much recent interest and debate. Many of the measurements of DNA conductivity have been made in aqueous solution, with an aromatic photooxidant moiety such as anthraquinone or a rhodium(III) complex covalently tethered to the DNA. Such studies, however, have given discrepant results, for instance, regarding the relative ability of AT- and GC-rich sequences to conduct charge and the possibility of thymine cyclobutane dimer repair through the DNA from a distance. A recent paper on conduction in DNA immobile four-way junctions using the rhodium photooxidant reported conduction in all four helical arms, contrary to what is known about the three-dimensional structure and stacking of 4-way junctions. We have reexamined conduction in such junctions using rhodium [Rh(phi)(2)(byp)Cl(3)] as well as the anthraquinone photooxidants, and find that although our rhodium data agree with the previously published work, the anthraquinone data reveal conduction in only two of the four helical arms, consistent with the known tertiary structure of four-way junctions. An electrophoretic investigation revealed the formation of intermolecular aggregates in the rhodium-derivatized junctions, but not in the anthraquinone-labeled junctions. Rhodium-specific aggregation was also observed with simple DNA duplexes under the same experimental conditions. A characteristic property of aggregation was that all participating DNA molecules required the rhodium derivatization, and underivatized molecules did not aggregate with the derivatized ones. It is conceivable that the results reported here will help reconcile the various discrepancies that have been reported from charge conduction experiments carried out on DNA utilizing different photooxidants.

Solid-phase synthesis of selectively labeled DNA: applications for multidimensional nuclear magnetic resonance spectroscopy

The solid-phase chemical synthesis method has a strong advantage over the enzymatic method for preparing selectively labeled DNA oligomers. Atom-specific and fully labeled 2'-deoxynucleosides are economically prepared with routinely available isotope precursors using this synthetic route. Special DNA oligomers prepared by advanced labeling techniques are needed for advanced NMR applications, and chemical synthesis is the method of choice to respond to such demands. As a summary of this chapter, two tables are given. Table I lists the labeled nucleosides reported to be available by chemical syntheses. Table II lists the NMR studies using labeled DNA oligomers that were prepared by chemical syntheses.

The crystal structures of DNA Holliday junctions

Nearly 40 years ago, Holliday proposed a four-stranded complex or junction as the central intermediate in the general mechanism of genetic recombination. During the past two years, six single-crystal structures of such DNA junctions have been determined by three different research groups. These structures all essentially adopt the antiparallel stacked-X conformation, but can be classified into three distinct categories: RNA-DNA junctions; ACC trinucleotide junctions; and drug-induced junctions. Together, these structures provide insight into how local and distant interactions help to define the detailed and general physical features of Holliday junctions at the atomic level.

Folding of branched RNA species

The global structures of branched RNA species are important to their function. Branched RNA species are defined as molecules in which double-helical segments are interrupted by abrupt discontinuities. These include helical junctions of different orders, and base bulges and loops. Common helical junctions are three- and four-way junctions, often interrupted by mispairs or additional nucleotides. There are many interesting examples of functional RNA junctions, including the hammerhead and hairpin ribozymes, and junctions that serve as binding sites for proteins. The junctions display some common structural properties. These include a tendency to undergo pairwise helical stacking and ion-induced conformational transitions. Helical branchpoints can act as key architectural components and as important sites for interactions with proteins. Copyright 1999 John Wiley & Sons, Inc.

Thermodynamic properties of an intramolecular DNA four-way junction

We have investigated the thermodynamic properties of two homologous DNA four-way junctions, J4 and J4M, based on 46-mer linear DNA molecules. J4 and J4M have the same base sequence with the only difference that the latter contains an uncharged methylene-acetal linkage, -O3'-CH2-O5', instead of the phosphodiester linkage, -O3'-PO2-O5'-, between the residues T18 and C19. The comparison of the thermal unfolding of the J4 junction and J4M junction serves to investigate the effect of the uncharged methylene-acetal linkage on the stability of the junction. Our analysis is based on CD, UV absorbance spectroscopy, DSC, and chemical footprinting. The aim is to characterize in detail the structure and stability of the junctions. As demonstrated before by NMR, in the presence of 5 mM MgCl2 +/- 50 mM NaCl, both J4 and J4M form a complete four-way junction. This is now evidenced by protection from OsO4 cleavage (chemical footprinting). We can assume that full base pairing occurs throughout the arms even at the center of the junction. CD spectra suggest that the helices within the junctions adopt the regular B-DNA conformation. Almost identical melting temperatures and unfolding enthalpies are obtained for J4 and J4M both by UV and DSC. Furthermore, the Van't Hoff enthalpy (DeltaHVH) derived from UV melting equals the calorimetric enthalpy (DeltaHcal), which means that the melting process of the structures proceeds in a two-state manner. All results taken together support the conclusion that there are no major conformational and energetic differences between J4 and J4M. The inclusion of the uncharged methylene-acetal group into the junction has no effect on its stability.

Excess counterion binding and ionic stability of kinked and branched DNA

We compute the excess number of counterions associated with kinked and branched DNA, and the ionic stabilities of these structures as a function of chain length and both sodium and magnesium salt concentration, using numerical counterion condensation theory. The DNA structures are modeled as two or more finite lines of phosphate charges radiating from the kink or junction center. The number of excess counterions around the (40-90 degrees) kinked duplex is very small (at most four). The geometries of large three- and four-way DNA junctions (with > 50 base pairs per arm) in solutions containing low to moderate NaCl concentrations, by contrast, accumulate a substantial number of excess sodium ions (> 20) but no more than 15 magnesium counterions. The excess number of counterions surrounding the kinked linear chain and the branched DNA structures either remains invariant or increases with chain length, tending to reach a plateau value. Open configurations, such as the planar Y-shaped three-way junction (with three 120 degrees inter-arm angles) and the 90 degrees cross-shaped four-way junction, are ionically more stable than compact geometries, such as pyramidal three-way junctions and X-shaped four-way junctions, over the entire range of salt concentration considered (10(-5)-10(-1) M NaCl or MgCl2). The ionic stabilities of the compact forms increase with increasing salt concentration and become comparable to those of the extended geometries at high salt (especially when magnesium is the supporting salt).

NMR study of the exchange rate between two stacked conformers of a model Holliday junction

Our investigations into the folding behavior of a series of small model Holliday junctions in the presence of magnesium ions revealed a sequence (junction J9a) displaying a 71/29 population ratio between the two differently folded stacked X-conformers in slow exchange on the NMR chemical shift time scale. For the first time we report the rates of interconversion between two stacked X-conformers and their lifetimes as measured by chemical exchange (EXSY) NMR spectroscopy: k1 5.6 (+/-0.5) s-1, k-1 2.3 (+/-0.2) s-1. The corresponding lifetimes (tau=1/k) are: tau1 430 ms, tau2 180 ms and the conformational transition barrier amounts to DeltaGdouble dagger294 68 kJ/mol (16.2 kcal/mol). It is argued that this free-energy barrier reflects the maximum barrier that separates stacked X-conformers in junction 9a from the unfolded structure.

Design and NMR study of an immobile DNA four-way junction containing 38 nucleotides

The DNA Holliday junction is a central intermediate in genetic recombination. We have designed and synthesized a DNA oligomer, J1a, as a model compound for the Holliday junction suitable to be studied by NMR spectroscopy and future molecular modelling. The design was based on a 46-base oligomer, J4, previously studied by Pikkemaat, J. A., van den Elst, H., van Boom, J. H. & Altona, C. [Biochemistry 33, 14896-14907 (1994)], including the propensity to undergo a self-folding process to give a four-way junction in which three of the four arms are capped with a hairpin loop. J1a, however, is considerably shortened by eight bases and thus contains only 38 residues which significantly facilitates the proton resonance assignments. The base sequence at the branch point is identical to that in J4. 1H-NMR data clearly point to the presence of three hairpin loops in J1a and show that the double-helical arms adopt the B-DNA form. Quasicontinuous pairwise stacking between helical arms to give a single preferred stacked X-conformation is evident. The extent of folding into this stacked conformation is strongly dependent upon the magnesium concentration. Full Watson-Crick base pairing at the branch point is completely preserved. The A/D-stacking preference of the small junction is the same as that exhibited by J4.

Nucleic acid structure and recognition

We review the global structures adopted by branched nucleic acids, including three- and four-way helical junctions in DNA and RNA. We find that some general folding principles emerge. First, all the structures exhibit a tendency to undergo pairwise coaxial helical stacking when permitted by the local stereochemistry of strand exchange. Second, metal ions generally play an important role in facilitating folding of branched nucleic acids. These principles can be applied to functionally important branched nucleic acids, such as the Holliday DNA junction of genetic recombination, and the hammerhead ribozyme in RNA.

Crossover isomer bias is the primary sequence-dependent property of immobilized Holliday junctions

Recombination of genes is essential to the evolution of genetic diversity, the segregation of chromosomes during cell division, and certain DNA repair processes. The Holliday junction, a four-arm, four-strand branched DNA crossover structure, is formed as a transient intermediate during genetic recombination and repair processes in the cell. The recognition and subsequent resolution of Holliday junctions into parental or recombined products appear to be critically dependent on their three-dimensional structure. Complementary NMR and time-resolved fluorescence resonance energy transfer experiments on immobilized four-arm DNA junctions reported here indicate that the Holliday junction cannot be viewed as a static structure but rather as an equilibrium mixture of two conformational isomers. Furthermore, the distribution between the two possible crossover isomers was found to depend on the sequence in a manner that was not anticipated on the basis of previous low-resolution experiments.

Recognition and manipulation of branched DNA structure by junction-resolving enzymes

The junction-resolving enzymes are a class of nucleases that introduce paired cleavages into four-way DNA junctions. They are important in DNA recombination and repair, and are found throughout nature, from eubacteria and their bacteriophages through to higher eukaryotes and their viruses. These enzymes exhibit structure-selective binding to DNA junctions; although cleavage may be more or less sequence-dependent, binding affinity is purely related to the branched structure of the DNA. Binding and cleavage events can be separated for a number of the enzymes by mutagenesis, and mutant proteins that are defective in cleavage while retaining normal junction-selective binding have been isolated. Critical acidic residues have been identified in several resolving enzymes, suggesting a role in the coordination of metal ions that probably deliver the hydrolytic water molecule. The resolving enzymes all bind to junctions in dimeric form, and the subunits introduce independent cleavages within the lifetime of the enzyme-junction complex to ensure resolution of the four-way junction. In addition to recognising the structure of the junction, recent data from four different junction-resolving enzymes indicate that they also manipulate the global structure. In some cases this results in severe distortion of the folded structure of the junction. Understanding the recognition and manipulation of DNA structure by these enzymes is a fascinating challenge in molecular recognition.

Sequence-dependent crossed helix packing in the crystal structure of a B-DNA decamer yields a detailed model for the Holliday junction

The structure of the B-DNA decamer d(CGCAATTGCG)2 has been determined by X-ray diffraction analysis to a resolution of 2.3 A and an R-factor of 17.7%. The decamer crystallises in the monoclinic space group C2 and packs with a crossed arrangement of helices and a unique crossing contact distinct from all other decamer structures. This is believed to be a direct result of the sequence-dependent minor groove width of the duplex. Crossed helix structures of DNA are valuable starting points for modelling studies of the Holliday junction. Two unique sites are observed at the cross-over junction where strand exchange may occur. A Holliday junction model has been constructed for each case and modelled using molecular mechanics and dynamics techniques. One of these models was found to be fully consistent with the available physical data.

The resolving enzyme CCE1 of yeast opens the structure of the four-way DNA junction

Junction-resolving enzymes exhibit structure-selective binding to DNA, but may also manipulate the DNA structure. CCE1 is a junction-resolving enzyme found in the yeast mitochondrion. To facilitate the analysis of the CCE1-junction interaction, we have exploited the sequence dependence of the cleavage reaction to devise a junction that is refractory to cleavage by this enzyme, even in the presence of magnesium ions. On binding to four-way DNA junctions, pure recombinant CCE1 opens the global structure into a 4-fold symmetrical configuration of arms with an open, chemically reactive centre. The structure of the CCE1-junction complex is independent of the sequence of the junction, and of the presence or absence of magnesium or other ions. This and other functional properties of CCE1 are strikingly similar to those of RuvC resolving enzyme of Escherichia coli.

Three-way and four-way junctions in DNA: a conformational viewpoint

DNA junctions are potential intermediates in various important genetic processes, including mutagenesis and recombination. The quantity of research carried out in this area is rapidly increasing. Examples of three-way and four-way junctions are now relatively well characterized and a few common properties have been recognized, of which the most important is the tendency of junctions to fold into one or more coaxially stacked helical conformations or cross-over structures.