Interaction of linear homologous DNA duplexes via Holliday junction formation

Yakubovskaya, Marianna G.; Neschastnova, Anna A.; Humphrey, Karen E.; Babon, Jeffrey J.; Попенко, В. И.; Smith, Margaret J.; Lambrinakos, Andrianna; Lipatova, Zhanna V.; Dobrovolskaia, Marina A.; Cappai, Roberto; Masters, Colin L.; Belitsky, Gennady A.; Cotton, Richard G.H.

doi:10.1046/j.1432-1327.2001.01861.x

Cited by 17 publications

(8 citation statements)

References 49 publications

(89 reference statements)

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“…S2). This is in agreement with the well known slow migration of cruciform species (38). Second, the monoclinic DIS kissing complex crystal structure (20), obtained with a mutant sequence where the first G-C base pair of the stem was replaced by a destabilizing U-U mismatch (DIS-UU, Fig.…”

Section: ͑1͒supporting

confidence: 87%

Mechanism of Hairpin-Duplex Conversion for the HIV-1 Dimerization Initiation Site

Bernacchi

Ennifar

Tóth

et al. 2005

Journal of Biological Chemistry

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We have used the dimerization initiation site of HIV-1 genomic RNA as a model to investigate hairpin-duplex interconversion with a combination of fluorescence, UV melting, gel electrophoresis, and x-ray crystallographic techniques. Fluorescence studies with molecular beacons and crystallization experiments with 23-nucleotide dimerization initiation site fragments showed that the ratio of hairpin to duplex formed after annealing in water essentially depends on RNA concentration and not on cooling kinetics. With natural sequences allowing to form the most stable duplex, and thus also the loop-loop complex (or "kissing complex"), concentrations as low as 3 M in strands are necessary to obtain a majority of the hairpin form. With a mutated sequence preventing kissing complex formation, a majority of hairpins was even obtained at 80 M in strands. However, this did not prevent an efficient conversion from hairpin to duplex in the presence of salts. Kinetic considerations are in favor of duplex formation from intermediates involving hairpins engaged in cruciform dimers rather than from free strands. The very first step of formation of such a cruciform intermediate could be trapped in a crystal structure. This mechanism might be significant for the dynamics of small RNAs beyond the strict field of HIV-1.Stem-loops and bulged loops are common motifs found in RNA secondary structure and are often involved in RNA-protein or RNA-RNA recognition. Because of the self-complementarity of stems, a stem-loop structure can also adopt an alternative duplex structure containing unpaired nucleotides. This hairpin-duplex equilibrium also represents a major problem in structural studies of nucleic acids by NMR and x-ray crystallography, both requiring concentrated samples. Strategies using a mixture of unlabeled and 15 N-labeled oligonucleotides were developed to discriminate between the two species by NMR (1, 2). However, many attempts at crystallizing RNA or DNA stem-loop structures led unexpectedly to duplex crystal structures (3-6). This was even the case for the unusually stable RNA tetraloops belonging to the GNRA, UNCG, and CUUG families, which are supposed to be nucleation points for RNA folding because of their stability and quick folding kinetics (see "Discussion" in Ref. 7). Significantly, this problem does not seem to spread to NMR studies because several RNA stem-loop structures were successfully solved by using this technique, whereas most of the hairpin structures described by x-ray crystallography were obtained from complexes with proteins (8 -10) or were embedded in a larger RNA context, as for tRNAs, hammerhead ribozyme, and ribosome structures. The only notable exception is the GAGA tetraloop found in the sarcin-ricin loop, successfully crystallized as a hairpin (11,12).The present study focuses on the dimerization initiation site (DIS) 4 of HIV-1 genomic RNA that has been extensively studied by several biochemical and biophysical methods. This strongly conserved stem-loop sequence (13) (Fig. 1a) was shown to be cruc...

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Section: ͑1͒supporting

confidence: 87%

Mechanism of Hairpin-Duplex Conversion for the HIV-1 Dimerization Initiation Site

Bernacchi

Ennifar

Tóth

et al. 2005

Journal of Biological Chemistry

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“…This issue is in accordance with data of Renaldo et al (28) that the strand exchange process between ds and ss DNA at physiological conditions occurs by a sequential displacement mechanism. On the whole, the results of this experiment in combination with our previous electron microscopy data (3) show that in solutions of homologous duplexes the strand exchange process occurs via formation of HJs followed by branch migration resulting in the resolution into new or previously existing duplexes.…”

Section: Discussionsupporting

confidence: 69%

“…Previously, we revealed DNA-DNA interaction using gel electrophoresis of solutions of purified PCR products by appearance of the additional bands corresponding to double size DNA fragments (3). The efficiency of PCR product purification was demonstrated, and the double-stranded (ds) structure of DNA fragments interacting was confirmed using several consecutive purifications and S1 nuclease analysis.…”

mentioning

confidence: 98%

Mechanism of Spontaneous DNA−DNA Interaction of Homologous Linear Duplexes

Neschastnova¹,

Markina²,

Попенко³

et al. 2002

Biochemistry

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Previously, we demonstrated the interaction of homologous linear duplexes with formation of four-way DNA structures on the model of five PCR products. We propose that homologous duplex interaction is initiated by the nucleation of several dissociated base pairs of the complementary ends of two fragments with Holliday junction formation, in which cross point migration occurs via spooling of DNA strands from one duplex to the other one, finally resulting in complete resolution into new or previously existing duplexes. To confirm that DNA-DNA interaction involves formation of four-way DNA structures with strand exchange at the cross point, we have demonstrated the strand exchange process between identical duplexes using homologous fragments, harboring either biotin label or (32)P-label. Incubation of the mixture resulted in the addition of (32)P-label to biotin-labeled fragments, and the intensity of (32)P-labeling of biotinylated fragments was dependent upon the incubation duration. DNA-DNA interaction is not based on surface-dependent denaturing, as Triton X-100 does not decrease the formation of complexes between DNA duplexes. The equilibrium concentration of Holliday junctions depends on the sequences of the fragment ends and the incubation temperature. The free energy of Holliday junction formation by the fragments with GC and AT ends differed by 0.6 kcal/mol. Electron microscopic analysis demonstrated that the majority of Holliday junctions harbor the cross point within a 300 base pair region of the fragment ends. This insight into the mechanism of homologous duplex interaction extends our understanding of different DNA rearrangements. Understanding of DNA-DNA interaction is of practical use for better interpretation and optimization of PCR-based analyses.

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“…Indeed, junctions have been observed to form at high concentrations in the PCR products of the p53 gene. 23 The stacked-X junctions seen in the crystal structures of d(CCGGGACCGG) and d(CCGGTA-CCGG) have an interduplex angle of ~41°, which is shallower than had been estimated by gel electrophoresis, fluorescence resonance energy transfer (FRET), and atomic force microscopy. 24 -26 Although there are some uncertainties in the estimates from the gel and spectroscopic methods, this discrepancy has led to some discussion as to whether the crystal structures say anything about the geometry of the junction in solution.…”

Section: Discussionmentioning

confidence: 95%

The Inherent Properties of DNA Four-way Junctions: Comparing the Crystal Structures of Holliday Junctions

Eichman

Ortiz-Lombardı́a

Aymamı́

et al. 2002

Journal of Molecular Biology

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Holliday junctions are four-stranded DNA complexes that are formed during recombination and related DNA repair events. Much work has focused on the overall structure and properties of fourway junctions in solution, but we are just now beginning to understand these complexes at the atomic level. The crystal structures of two all-DNA Holliday junctions have been determined recently from the sequences d(CCGGGACCGG) and d(CCGGTACCGG). A detailed comparison of the two structures helps to distinguish distortions of the DNA conformation that are inherent to the cross-overs of the junctions in this crystal system from those that are consequences of the mismatched dG·dA base-pair in the d(CCGGGACCGG) structure. This analysis shows that the junction itself perturbs the sequence-dependent conformational features of the B-DNA duplexes and the associated patterns of hydration in the major and minor grooves only minimally. This supports the idea that a DNA four-way junction can be assembled at relatively low energetic cost. Both structures show a concerted rotation of the adjacent duplex arms relative to B-DNA, and this is discussed in terms of the conserved interactions between the duplexes at the junctions and further down the helical arms. The interactions distant from the strand cross-overs of the junction appear to be significant in defining its macroscopic properties, including the angle relating the stacked duplexes across the junction.

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Interaction of linear homologous DNA duplexes via Holliday junction formation

Cited by 17 publications

References 49 publications

Mechanism of Hairpin-Duplex Conversion for the HIV-1 Dimerization Initiation Site

Mechanism of Hairpin-Duplex Conversion for the HIV-1 Dimerization Initiation Site

Mechanism of Spontaneous DNA−DNA Interaction of Homologous Linear Duplexes

The Inherent Properties of DNA Four-way Junctions: Comparing the Crystal Structures of Holliday Junctions

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