Nuclear extracts promote gene correction and strand pairing of oligonucleotides to the homologous plasmid

We compared strand pairing and gene correction activities between different constructs of oligonucleotides, using homologous supercoiled DNA and eukaryotic nuclear extracts. The RNA-DNA chimeric oligonucleotide was more efficient in strand pairing and gene correction than its DNA-DNA homolog. Single-stranded deoxyoligonucleotides showed similar strand pairing and correction activity to the modified RNA-DNA chimeric oligonucleotides, whereas single-stranded ribooligonucleotides did not show either activity. However, the correlations were not always linear, suggesting that only a fraction of the joint molecules may be processed to cause the final gene correction. Several mammalian extracts with markedly different in vitro activity showed the similar amounts of the joint molecules. These results led us to conclude that strand pairing is a necessary event in gene correction but may not be the rate-limiting step. Furthermore, depletion of HsRad51 protein caused large decreases in both strand-pairing and functional activities, whereas supplementation of HsRad51 produced only a slight increase in the repair activity, indicating that HsRad51 participates in the strand pairing, but subsequent steps define the frequency of gene correction. In addition, we found that the structure and stability of intermediates formed by single-stranded deoxyoligonucleotides and RNA-DNA chimeric oligonucleotides were different, suggesting that they differ in their mechanisms of gene repair.     

Intrastrand base pairing in single-stranded deoxyribonucleic acid from ColE1-derived plasmid pCR1.

Single strands of EcoRI-cleaved pCR1 deoxyribonucleic acid were examined by electron microscopy for intrastrand base pairing by using partial denaturing conditions. The locations of three stem and loop structures were mapped relative to the inverted repeat of Tn903. Potential roles and origins of these loops are discussed.     

Origin pairing ('handcuffing') and unpairing in the control of P1 plasmid replication

The P1 plasmid origin has an array of five binding sites (iterons) for the plasmid-encoded initiator protein RepA. Saturation of these sites is required for initiation. Iterons can also pair via their bound RepAs. The reaction, called handcuffing, is believed to be the key to control initiation negatively. Here we have determined some of the mechanistic details of the reaction. We show that handcuffed RepA-iteron complexes dissociate when they are diluted or challenged with cold competitor iterons, suggesting spontaneous reversibility of the handcuffing reaction. The complex formation increases with increased RepA binding, but decreases upon saturation of binding. Complex formation also decreases in the presence of molecular chaperones (DnaK and DnaJ) that convert RepA dimers to monomers. This indicates that dimers participate in handcuffing, and that chaperones are involved in reversing handcuffing. They could play a direct role by reducing dimers and an indirect role by increasing monomers that would compete out the weaker binding dimers from the origin. We propose that an increased monomer to dimer ratio is the key to reverse handcuffing.     

Origin pairing ('handcuffing') as a mode of negative control of P1 plasmid copy number.

In one family of bacterial plasmids, multiple initiator binding sites, called iterons, are used for initiation of plasmid replication as well as for the control of plasmid copy number. Iterons can also pair in vitro via the bound initiators. This pairing, called handcuffing, has been suggested to cause steric hindrance to initiation and thereby control the copy number. To test this hypothesis, we have compared copy numbers of isogenic miniP1 plasmid monomer and dimer. The dimer copy number was only one-quarter that of the monomer, suggesting that the higher local concentration of origins in the dimer facilitated their pairing. Physical evidence consistent with iteron-mediated pairing of origins preferentially in the dimer was obtained in vivo. Thus, origin handcuffing can be a mechanism to control P1 plasmid replication.     

Centromere pairing precedes meiotic chromosome pairing in plants

Meiosis is a specialized eukaryotic cell division, in which diploid cells undergo a single round of DNA replication and two rounds of nuclear division to produce haploid gametes. In most eukaryotes, the core events of meiotic prophase I are chromosomal pairing,synapsis and recombination. To ensure accurate chromosomal segregation, homologs have to identify and align along each other at the onset of meiosis. Although much progress has been made in elucidating meiotic processes, information on the mechanisms underlying chromosome pairing is limited in contrast to the meiotic recombination and synapsis events. Recent research in many organisms indicated that centromere interactions during early meiotic prophase facilitate homologous chromosome pairing, and functional centromere is a prerequisite for centromere pairing such as in maize. Here, we summarize the recent achievements of chromosome pairing research on plants and other organisms, and outline centromere interactions, nuclear chromosome orientation,and meiotic cohesin, as main determinants of chromosome pairing in early meiotic prophase.     

Amino acid pairing

A set of amino acid pairings are presented which may allow protein-to-protein information transfers. Amino acid pairing is only possible on a parallel β ribbon and involves both the polypeptide backbones and the side chains. Model building revealed that of the 210 possible amino acid pairs of the standard 20 amino acids, no more than 26 could be built to meet standard criteria for bonding. Of these 26, 14 were found to be genetically encoded when the codons are read as if they paired in a parallel manner (i.e. in a manner reflecting the structural parallelism of the amino acid pairings); the other 12 pairings were derivatives of the coded pairings in which a single base of the codon triplet had been varied in accordance with Crick's (1966) “wobble hypothesis.” Evidence for the pairings is presented from colligative studies of polyamino acids. Ways of testing the hypothesis further are suggested. Its implications for the Central Dogma and theories of the origin of life are discussed.     

Control of replication of plasmid R1: formation of an initial transient complex is rate-limiting for antisense RNA--target RNA pairing.

The replication frequency of plasmid R1 is determined by the availability of the initiator protein RepA. Synthesis of RepA is negatively controlled by an antisense RNA, CopA, which forms a duplex with the upstream region of the RepA mRNA, CopT. We have previously shown that the in vitro formation of the CopA-CopT duplex follows second-order kinetics and occurs in at least two steps. The first step is the formation of a transient (kissing) complex, which is subsequently converted to a persistent duplex. Here, we investigate the details of the reaction scheme and determine the rate constants of the pathway from the free RNAs to the complete duplex. Using a shortened CopA RNA (CopI) we have been able to determine the association and dissociation rate constants (k1,k-1) for the kissing complex (which are inferred to be the same for CopI-T and CopA-T), and measured the hybridization rate constant k2 (for CopA-T k2 is at least 1000-fold greater than for CopI-T). The analysis of CopA derivatives of mutant and wild-type origin shows that the rate of formation of the kissing complex is rate-limiting for the overall pairing reaction between CopA and CopT, both in vitro and in vivo. The biological implications of the kinetically irreversible RNA-RNA binding reaction scheme are discussed.     

Chromosome pairing in maize

This report summarizes our observations at pachytene on opposite-arms intercrosses between stocks of interchanges that involve chromosomes 1 and 5 in maize.—Pairing does not begin at the centromeres in these intercrosses.—We propose a model which assumes different probability values along each chromosome arm for the initial or primary site of pairing. Observations on the frequencies of the different types of configurations at pachytene were used to estimate probability values which satisfactorily fit the data.—There is a relatively low probability (of the order of.1 to.3) for the initial pairing to be in a short terminal segment (about.1 of the arm length). Initial pairing in the one or two short segments adjacent to the tip segment is much higher. Initial pairing is much lower in segments successively closer to the middles of the chromosome arms, and then zero or nearly zero in the proximal half of the arm. This means that the initial pairing may fail occasionally even in a relatively long interchanged segment and produce a T-shaped (3-armed) configuration.—After the initial pairing has occurred, the average probability that a secondary site of pairing is adjacent to the centromere in a segment.3 to.4 the length of an arm is low (.13, ranging from.02 to.29).—We can predict that in an intercross in which both breakpoints in both parental interchanges are far out on the chromosomes, "pairs" will be formed with nonhomologous ends (homologous differential segments paired). In these pairing could have begun at any point in the interstitial segments, but not likely in segments close to the centromeres.—Multiple secondary sites which vary in time or in order of pairing will explain the variation in position of the cross-shaped pachytene configuration in interchange heterozygotes.—The observed configuration in any one cell is the result of a particular combination of pairing events at the various sites. This is a very different concept of pairing from previous interpretations which described it as a result of zipper-like action, and the variation in position of the pachytene cross-configuration as the result of "shifts" in position.—Our cytogenetic results and their interpretation are in close agreement with reports on chromosome ultrastructure and molecular events in the early stages of meiosis, i.e. the attachment of chromosome ends to the nuclear membrane, the manner in which synaptonemal complexes develop, and the regions of DNA whose replication is delayed until zygonema.     

Mathematics of chromosome pairing

Analysis of frequencies of chromosome configurations in wheat-related species hybrids is extended to include cases involving homoeologous groups of size six. Further, the expected frequencies of the various configurations emanating from homologous and homoeologous pairing events have been determined for groups consisting of two and three homoeologous pairs of homologous chromosomes. Analysis of configuration frequencies of nullisomic 5B of wheat, in which both homologous and homoeologous pairing occurs, led to estimation of the relative frequencies of homologous and homoeologous pairing events as 17.9:1. In the samples analyzed, slightly less than one homoeologous exchange occurred per gamete.     

A pairing process.

A stochastic model for the formation of parasite pairs in the definite host is considered. An explicit expression for the expected number of pairs is derived and compared with alternative models.     

Homologous chromosome pairing.

Commonly accepted precepts are challenged: (1) that homologous chromosome pairing is normally mediated by nuclear envelope attachment sites; (2) that crossover site establishment awaits synaptic completion; and (3) that it is the function of the synaptonemal complex to hold homologues in register so that equal crossing over can occur, and perhaps to provide machinery for the crossover process. Although these views may eventually be shown to be true, it is felt that currently available evidence does not warrant their full acceptance, and that alternatives should be considered. As examples of alternatives the following ideas, with some supporting evidence, are suggested: (1) homologous chromosome pairing (in non-haplont organisms) may be accomplished by chance meeting of homologue segments (followed by establishment of invisible, elastic connectors) at congression for a mitotic metaphase (in many cases perhaps the premeiotic mitosis); (2) crossover sites may be established before, during, or immediately following initiation of synapsis; and (3) the synaptonemal complex may somehow function in the crossover process at the inception of its formation, but its complete deployment throughout each normal bivalent may serve some other role, such as mediation of the binding of sister chromatids apparently required for chiasma maintenance until anaphase I.     

Efficient DNA pairing in a Neurospora mutant defective in chromosome pairing

Summary A Neurospora crassa mutation, mei-2, affecting recombination and pairing of homologous chromosomes during meiosis, was characterized for its effect on repeat-induced point mutation (RIP). We found that RIP, which depends on recognition of DNA sequence homology, is not inhibited by mei-2, suggesting that the defect in chromosome pairing of this mutant is not due to a defect in DNA pairing and that DNA pairing is not dependent on chromosome pairing.     

Segmentation and the pairing hypothesis

The effect of stimulus contiguity and response contingency on responding in chain schedules was examined in two experiments. In Experiment 1, four pigeons were trained on two simple three-link chain schedules that alternated within sessions. Initial links were correlated with a variable-interval 30s schedule, and middle and terminal links were correlated with interdependent variable-interval 30s variable-interval 30s schedules. The combined duration of the interdependent schedules summed to 60s. The two chains differed with respect to signaling of the schedule components: a two-stimulus chain had one stimulus paired with the initial link and one stimulus paired with both the middle and the terminal link, while a three-stimulus chain had a different stimulus paired with the each of the three links. The results showed that the two-stimulus chain maintained lower initial-link responding than the three-stimulus chain. In Experiment 2, four pigeons were exposed to three separate conditions, the two- and three-stimulus chains of Experiment 1 and a three-stimulus chain that had a 3s delay to terminal-link entry from the middle-link response that produced it. The two-stimulus chain maintained lower initial-link responding than the three-stimulus chain, as in Experiment 1, and a similar initial-link responding was maintained by the two-stimulus chain and the three-stimulus chain with the delay contingency. The results demonstrate that a stimulus noncontiguous with food can maintain responding that is sometimes greater than a stimulus contiguous with food, depending on the response contingency for terminal-link entry. The results are contrary to the pairing hypothesis of conditioned reinforcement.