RecA protein assisted selection reveals a low fidelity of recognition of homology in a duplex DNA by an oligonucleotide

Electrochemically mediated in situ growth of electroactive polymers for highly sensitive detection of double-stranded DNA without sequence-preference

The ability to directly detect double-stranded DNA (dsDNA) without sequence-preference continues to be a major challenge. Herein, we report an electrochemical method for the direct, highly sensitive detection of dsDNA based on the strand replacement of dsDNA by peptide nucleic acid (PNA) and the in situ growth of electroactive polymers through the surface-initiated electrochemically mediated atom transfer radical polymerization (SI-eATRP). Thiolated PNA molecules are firstly self-assembled onto gold electrode surface for the specific recognition of target dsDNA (dsDNA-T), which in turn leads to the formation of a high density of PNA/DNA heteroduplexes on the electrode surface for the subsequent attachment of ATRP initiators via the phosphate-Zr⁴⁺-carboxylate chemistry. By applying a negative potential to the electrode, the air-stable Cu^II deactivators can be reduced into the Cu^I activators so as to trigger the surface-initiated polymerization for the in situ growth of electroactive polymers. Due to the strand replacement of dsDNA by PNA, dsDNA can be directly detected without sequence-preference. Besides, the growth of polymers enables the modification of numerous electroactive probes, thereby greatly improving the electrochemical signal. Under optimal conditions, a good linearity between the electrochemical signal and the logarithm of dsDNA-T concentration over the range from 1.0 fM to 1.0nM, with a detection limit of 0.47 fM, can be obtained. Results indicate that it is highly selective, and holds high anti-interference capability in the presence of human serum samples. Therefore, this method offers great promises in providing a universal and efficient solution for the direct detection of dsDNA.

Reversibility, equilibration, and fidelity of strand exchange reaction between short oligonucleotides promoted by RecA protein from escherichia coli and human Rad51 and Dmc1 proteins

We demonstrate the reversibility of RecA-promoted strand exchange reaction between short oligonucleotides in the presence of adenosine 5'-O-(thiotriphosphate). The reverse reaction proceeds without the dissociation of RecA from DNA. The reaction reaches equilibrium and its yield depends on the homology between the reaction substrates. We estimate the tolerance of the RecA-promoted strand exchange to individual base substitutions for a comprehensive set of possible base combinations in a selected position along oligonucleotide substrates for strand exchange and find, in agreement with previously reported estimations, that this tolerance is higher than in the case of free DNA. It is demonstrated that the short oligonucleotide-based approach can be applied to the human recombinases Rad51 and Dmc1 when strand exchange is performed in the presence of calcium ions and ATP. Remarkably, despite the commonly held belief that the eukaryotic recombinases have an inherently lower strand exchange activity, in our system their efficiencies in strand exchange are comparable with that of RecA. Under our experimental conditions, the human recombinases exhibit a significantly higher tolerance to interruptions of homology due to point base substitutions than RecA. Finding conditions where a chemical reaction is reversible and reaches equilibrium is critically important for its thermodynamically correct description. We believe that the experimental system described here will substantially facilitate further studies on different aspects of the mechanisms of homologous recombination.

RecA-mediated strand invasion of DNA by oligonucleotides substituted with 2-aminoadenine and 2-thiothymine

Sequence-specific recognition of DNA is a critical step in gene targeting. Here we describe unique oligonucleotide (ON) hybrids that can stably pair to both strands of a linear DNA target in a RecA-dependent reaction with ATP or ATPγS. One strand of the hybrids is a 30-mer DNA ON that contains a 15-nt-long A/T-rich central core. The core sequence, which is substituted with 2-aminoadenine and 2-thiothymine, is weakly hybridized to complementary locked nucleic acid or 2′-OMe RNA ONs that are also substituted with the same base analogs. Robust targeting reactions took place in the presence of ATPγS and generated metastable double D-loop joints. Since the hybrids had pseudocomplementary character, the component ONs hybridized less strongly to each other than to complementary target DNA sequences composed of regular bases. This difference in pairing strength promoted the formation of joints capable of accommodating a single mismatch. If similar joints can form in vivo, virtually any A/T-rich site in genomic DNA could be selectively targeted. By designing the constructs so that the DNA ON is mismatched to its complementary sequence in DNA, joint formation might allow the ON to function as a template for targeted point mutation and gene correction.

High fidelity of RecA-catalyzed recombination: a watchdog of genetic diversity

Homologous recombination plays a key role in generating genetic diversity, while maintaining protein functionality. The mechanisms by which RecA enables a single-stranded segment of DNA to recognize a homologous tract within a whole genome are poorly understood. The scale by which homology recognition takes place is of a few tens of base pairs, after which the quest for homology is over. To study the mechanism of homology recognition, RecA-promoted homologous recombination between short DNA oligomers with different degrees of heterology was studied in vitro, using fluorescence resonant energy transfer. RecA can detect single mismatches at the initial stages of recombination, and the efficiency of recombination is strongly dependent on the location and distribution of mismatches. Mismatches near the 5′ end of the incoming strand have a minute effect, whereas mismatches near the 3′ end hinder strand exchange dramatically. There is a characteristic DNA length above which the sensitivity to heterology decreases sharply. Experiments with competitor sequences with varying degrees of homology yield information about the process of homology search and synapse lifetime. The exquisite sensitivity to mismatches and the directionality in the exchange process support a mechanism for homology recognition that can be modeled as a kinetic proofreading cascade.

Sequence-universal recognition of duplex DNA by oligonucleotides via pseudocomplementarity and helix invasion

The well-known Watson-Crick complementarity rules, which were discovered 50 years ago, elegantly direct the specific pairing of two DNA single strands. On the contrary, once formed, the double-stranded (ds) DNA lacks such a simple and sequence-universal recognition principle, since most of the characteristic chemical groups of nucleobases are now buried deep inside the double helix, the major DNA form. We report a promising versatile approach for highly selective recognition of designated sites within dsDNA featuring considerable practical potential for a variety of molecular-biological, biotechnological, gene-therapeutic, and diagnostic applications. It may also have implications for prebiotic evolution of genetic machinery at the primordial stages of the origin of life. Our design synergistically employs the robust helix-invasion ability of recently developed DNA mimics and analogs, pseudocomplementary peptide nucleic acids and pseudocomplementary oligonucleotides, thus enabling the sequence-unrestricted recognition of chosen DNA duplexes by nucleobase oligomers. Using this basically general approach, we selectively tagged a unique mixed-base site on the target dsDNA fragment with streptavidin and/or multiply labeled this site with fluorophores via the primer-extension reaction.

Influence of DNA sequence on the positioning of RecA monomers in RecA-DNA cofilaments

We show that certain DNA sequences have the ability to influence the positioning of RecA monomers in RecA-DNA complexes. A tendency for RecA monomers to be phased was observed in RecA protein complexes with several oligonucleotides containing a recombinational hotspot sequence, the chi-site from Escherichia coli. This influence was observed in both the 5' to 3' and 3' to 5' directions with respect to chi. A 5'-end phosphate group and probably some other features in DNA also influence the phasing of RecA monomers. We conclude that natural DNAs contain a number of features that influence the positioning of RecA monomers. The ability of specific DNA sequences to influence the positioning of RecA monomers demonstrates some specificity in the binding of individual bases at different sites within a RecA monomer and, most likely, reflects the stereochemical non-equivalence of these sites. The possible biological implications of the phasing of RecA monomers in presynaptic DNA-protein cofilaments are discussed.

RecA realigns suboptimally paired frames of DNA repeats through a process that requires ATP hydrolysis

Microsatellite repeats such as mono-, di-, and trinucleotides are highly abundant and viable targets for homologous recombination in the genome. However, if recombination ensues in such repetitive regions, they are intrinsically prone to frame misalignments during pairing and might eventually give rise to genetic instabilities. Suboptimally paired frames lead to an abrogation of branch migration at the junctions of mixed sequences and repeats, due to a heterologous register. If so, can recombination machinery rectify such misalignments in order to avoid subsequent arrest in branch migration? We analyzed Escherichia coli RecA, the universal prototype of a recombinase, for its pairing abilities across repeats. We used a complementary pairing assay to test whether RecA can mediate realignments of stochastically paired suboptimal frames to a maximally aligned register. Here, we demonstrate that RecA-single stranded DNA filament indeed facilitates such a realignment, probably by sliding the paired strands across mono- and di- as well as trinucleotide repeats. These realignments apparently have no net directional bias. Such a putative "motor" function of RecA seems to be ATP hydrolysis-dependent.

DNA sequence similarity requirements for interspecific recombination in Bacillus

Gene transfer in bacteria is notoriously promiscuous. Genetic material is known to be transferred between groups as distantly related as the Gram positives and Gram negatives. However, the frequency of homologous recombination decreases sharply with the level of relatedness between the donor and recipient. Several studies show that this sexual isolation is an exponential function of DNA sequence divergence between recombining substrates. The two major factors implicated in producing the recombinational barrier are the mismatch repair system and the requirement for a short region of sequence identity to initiate strand exchange. Here we demonstrate that sexual isolation in Bacillus transformation results almost exclusively from the need for regions of identity at both the 5' and 3' ends of the donor DNA strand. We show that, by providing the essential identity, we can effectively eliminate sexual isolation between highly divergent sequences. We also present evidence that the potential of a donor sequence to act as a recombinogenic, invasive end is determined by the stability (melting point) of the donor-recipient complex. These results explain the exponential relationship between sexual isolation and sequence divergence observed in bacteria. They also suggest a model for rapid spread of novel adaptations, such as antibiotic resistance genes, among related species.

Gene targeting for gene therapy: prospects

Ideally, gene therapy involves the correction of genetic defects through the natural means of gene targeting. This therapy possesses a number of conceptual advantages. However, a major obstacle to successful gene therapy is the relative inefficiency of the targeting process in mammalian cells. Gene targeting may be accomplished by two different mechanisms: the homologous recombination and the mismatch correction of DNA heteroduplexes. Based on the model of homologous recombination for the well-studied prokaryotic and the less studied eukaryotic systems, three approaches have been employed to improve the efficiency and accuracy of homologous recombination events. These are: (1) artificial double-strand breaks in both the exogenous and the chromosomal DNA, (2) a contiguous long homology between the exogenous and chromosomal DNA, and (3) a transient overproduction of an active recombinase, the bacterial RecA or mammalian RecA-like proteins, in mammalian cell nuclei. Combining these approaches can result in more effective gene targeting protocols. The second mechanism has been improved based on recent observations of recombinogenic activity of oligonucleotides and, especially, specifically designed chimeric RNA/DNA oligonucleotides. The use of RecA-like proteins to stimulate searching for homology and forming stable DNA heteroduplexes between oligonucleotides and chromosomal DNA remains an attractive idea for additional improvement of gene targeting events.

PNA openers as a tool for direct quantification of specific targets in duplex DNA

We report a new approach for target quantification directly within DNA duplex. Our assay is based on the formation of a new biomolecular structure, the PD-loop. The approach takes advantage of a selective hybridization of a probe to double-stranded DNA (dsDNA), which is locally opened by a pair of bis-PNA oligomers. To optimize the technique, several experimental formats are tested with the use of PNA and oligonucleotide probes. The highest sensitivity is achieved when the hybridized probe is extended and multiply labeled with 125I-dCTP by DNA polymerase via strand displacement in the presence of single-strand binding (SSB) protein. In this case, the PNA-assisted probe hybridization combined with the method of multiphoton detection (MPD) allows to monitor sub-attomolar amounts of the HIV-1 target on the background of unrelated DNA at sub-nCi level of radioactivity. The developed robust methodology is highly discriminative to single mutations, thus being of practical use for DNA analysis.

Branch migration through DNA sequence heterology

Branch migration of a DNA Holliday junction is a key step in genetic recombination. Previously, it was shown that a single base-pair heterology between two otherwise identical DNA sequences is a substantial barrier to passage of a Holliday junction during spontaneous branch migration. Here, we exploit this inhibitory effect of sequence heterology to estimate the step size of branch migration. We also devise a simulation of branch migration through mismatched base-pairs to arrive at the underlying molecular basis for the block to branch migration imposed by sequence heterology. Based on the observation that two adjacent sequence heterologies exert their effects on branch migration more or less independently, we conclude that the step size of branch migration is quite small, of the order of one or two base-pairs per migratory step. Comparison of branch migration experiments through a single base-pair heterology with simulations of a random walk through sequence heterology suggests that the inhibition of branch migration is largely attributable to a thermodynamic barrier arising from the formation of unpaired or mispaired bases in heteroduplex DNAs.

PD-loop: a complex of duplex DNA with an oligonucleotide

A stable complex between duplex DNA and an oligonucleotide is assembled with the aid of a DNA synthetic mimic, peptide nucleic acid (PNA). Homopyrimidine PNAs are known to invade into short homopurine tracts in duplex DNA forming P-loops. We have found that P-loops, formed at two closely located purine tracts in the same DNA strand separated by a mixed purine-pyrimidine sequence, merge and open the double helix between them. The opposite DNA strand, which is not bound with PNA, exposes and becomes accessible for complexing with an oligonucleotide via Watson-Crick pairing. As a result, the PD-loop emerges, which consists of locally open duplex DNA, PNA "openers," and an oligonucleotide. The PD-loop stability and sequence specificity are demonstrated by affinity capture of duplex DNAs by using biotinylated oligonucleotides and streptavidin-covered magnetic beads. The type of complex formed by PNAs, an oligonucleotide and duplex DNA we describe, opens ways for development of various in vitro and in situ hybridization techniques with duplex DNA and may find applications in DNA nanotechnology and genomics.

Dissociation kinetics of RecA protein-three-stranded DNA complexes reveals a low fidelity of RecA-assisted recognition of homology

We determined that the incorporation of one mismatch into RecA mediated synaptic complexes between oligonucleotide single-stranded DNAs and target duplex DNAs destabilizes the complex by 0.8 to 1.9 kcal/mol. This finding supports our previous result, that RecA binding per se can significantly decrease the loss in free energy associated with mismatch incorporation even in the absence of ATP hydrolysis. We show that the specificity is mostly driven by the dissociation process. We found that the relative destabilization induced by different mismatches depends on their position. Thus, while there is a good correlation between the ranking order of mismatches at the 5' end of synaptic complexes and mismatches in heteroduplexes (D-loops), there is no correlation between the ranking order for mismatches at the 3' end and mismatches in various DNA structures. This difference between the 5' and 3' ends of synaptic complexes agrees well with the established 5' to 3' polarity of the strand exchange promoted by RecA protein. The lack of a correlation between mismatches at the 3' end of synaptic complexes and mismatches in D-loops suggests the intermediate is probably not a canonical protein-free D-loop.

Non-Watson-Crick base pairs modulate homologous alignments in RecA pairing reactions

Complementary pairing by RecA was examined in vitro to investigate how homology is deciphered from non-homology. Somewhere in a window of 40-50% sequence complementarity, RecA pairing begins to manifest the specificity of homology. Quantitation reveals a hierarchy among non-Watson-Crick mispairs: RecA reaction treats six out of 12 possible mispairs as good ones and three each of the remaining ones as moderate and bad pairs. The mispairs seem to function as independent pairing units free of sequence context effects. The overall strength of pairing is simply the sum of the constituent units. RecA mediated gradation of mispairs, free of sequence context effects, might offer a general thumb-rule for predicting the pairing strength of any alignment that carries multiple mispairs.