Mechanical Properties of Smart Metal Matrix Composite by Shape Memory Effects

The thermomechanical behavior of TiNi shape memory alloy fiber reinforced 6061 aluminum matrix smart composite is investigated experimentally and analytically. The yield stress of the composite is observed to increase with prestrain given to the composite. Analytical model is developed by utilizing a shape memory alloy constitutive model of exponential type for the thermomechanical behavior of the composite. The model predicts that the composite yield stress increases with increasing prestrain, and the key parameters in affecting the composite yield stress are prestrain and matrix heat treatment. The model predicts reasonably well the experimental results of the enhanced composite yield stress.

Room-temperature, continuous-wave 1-W green power by single-pass frequency doubling in a bulk periodically poled MgO:LiNbO3 crystal

Continuous-wave high-power green light generation at room temperature is reported in a single-pass frequency-doubling configuration with bulk periodically poled MgO:LiNbO3 crystal placed outside a diode end-pumped Nd:GdVO4 laser. The MgO:LiNbO3 samples of 6.95-microm domain period, uniform periodicity, and 50% duty cycle along the entire crystal length are fabricated by use of a high-voltage multipulse poling method. A maximum power of 1.18 W at 531 nm with 16.8% conversion efficiency is obtained from a 2-mm-thick, 25-mm-long MgO:LiNbO3 crystal; the corresponding internal green power and conversion efficiency are 1.38 W and 19.6%, respectively, whereas the normalized conversion efficiency is 3.3%/W.

Wavelength stabilization of a distributed Bragg reflector laser diode by use of complementary current injection

We have demonstrated wavelength stabilization in an 821-nm AlGaAs three-section tunable distributed Bragg reflector (DBR) semiconductor laser diode (LD) that consists of active, phase-controlled, and DBR regions. We injected two separate, complementary currents into the active and the phase-controlled regions in the DBR-LD to suppress wavelength shift. This modulation method was applied to the LD fundamental wave in a second-harmonic-generation (SHG) laser, and the oscillating wavelength was maintained within the phase-matching acceptance range of the SHG device during modulation. A peak blue-violet light power of 62 mW was obtained for the ideal modulation waveform.

Barrier-to-autointegration factor (BAF) bridges DNA in a discrete, higher-order nucleoprotein complex

Barrier-to-autointegration factor (BAF) is a highly conserved cellular protein that was identified by its activity in protecting retroviral DNA against autointegration. We show that BAF has the property of bridging double-stranded DNA in a highly ordered nucleoprotein complex. Whereas BAF protein alone is a dimer in solution, upon binding DNA, BAF forms a dodecamer with DNA bound at multiple discrete sites in the complex. The interactions between BAF and DNA are entirely nonspecific with respect to DNA sequence. The dual interaction of BAF with DNA and LAP2, a protein associated with the nuclear lamina, suggests a role for LAP2 in chromosome organization. Consistent with this idea, RNA interference experiments with Caenorhabditis elegans reveal a defect in mitosis.

Single active site catalysis of the successive phosphoryl transfer steps by DNA transposases: insights from phosphorothioate stereoselectivity

The transposase family of proteins mediate DNA transposition or retroviral DNA integration via multistep phosphoryl transfer reactions. For Tn10 and phage Mu, a single active site of one transposase protomer catalyzes the successive transposition reaction steps. We examined phosphorothioate stereoselectivity at the scissile position for all four reaction steps catalyzed by the Tn10 transposase. The results suggest that the first three steps required for double-strand cutting at the transposon end proceed as a succession of pseudo-reverse reaction steps while the 3' end of the transposon remains bound to the same side of the active site. However, the mode of substrate binding to the active site changes for the cut transposon 3' end to target DNA strand joining. The phosphorothioate stereoselectivity of the corresponding steps of phage Mu transposition and HIV DNA integration matches that of Tn10 reaction, indicating a common mode of substrate-active site interactions for this class of DNA transposition reactions.

31%-efficient blue second-harmonic generation in a periodically poled MgO:LiNbO3 waveguide by frequency doubling of an AlGaAs laser diode

We present a method of controlling the shape of the domain-inverted structure in an off-cut MgO:LiNbO(3) crystal by utilizing a two-dimensional high-voltage application. With this technique a periodically domain-inverted structure with a period of 3.2 microm and a thickness of 2.0 microm was fabricated over a 10-mm interaction length. This structure has made possible sufficient overlaps between propagation modes and domain inversion in the waveguide. Using this structure, we demonstrated cw blue second-harmonic generation of 17.3 mW of power at a wavelength of 426 nm with single-pass 55-mW cw AlGaAs laser diode input, which corresponded to 31% power-conversion efficiency.

A new method for determining the stereochemistry of DNA cleavage reactions: application to the SfiI and HpaII restriction endonucleases and to the MuA transposase

A new method was developed for tracking the stereochemical path of enzymatic cleavage of DNA. DNA with a phosphorothioate of known chirality at the scissile bond is cleaved by the enzyme in H218O. The cleavage produces a DNA molecule with the 5'-[16O,18O, S]-thiophosphoryl group, whose chirality depends on whether the cleavage reaction proceeds by a single-step hydrolysis mechanism or by a two-step mechanism involving a protein-DNA covalent intermediate. To determine this chirality, the cleaved DNA is joined to an oligonucleotide by DNA ligase. Given the strict stereochemistry of the DNA ligase reaction, determined here, the original chirality of the phosphorothioate dictates whether the 18O is retained or lost in the ligation product, which can be determined by mass spectrometry. This method has advantages over previous methods in that it is not restricted to particular DNA sequences, requires substantially less material, and avoids purification of the products at intermediate stages in the procedure. The method was validated by confirming that DNA cleavage by the EcoRI restriction endonuclease causes inversion of configuration at the scissile phosphate. It was then applied to the reactions of the SfiI and HpaII endonucleases and the MuA transposase. In all three cases, DNA cleavage proceeded with inversion of configuration, indicating direct hydrolysis of the phosphodiester bond by water as opposed to a reaction involving a covalent enzyme-DNA intermediate.

Waveguide second-harmonic generation device with broadened flat quasi-phase-matching response by use of a grating structure with located phase shifts

We report on a theoretical analysis and experiments for bandwidth broadening in quasi-phase-matched (QPM) second-harmonic generation (SHG).We used phase-shifted segments of a periodic grating to obtain a spectrally broadened, nearly flat response simultaneously with high conversion efficiency. We used an x-cut MgO:LiNbO(3) QPM waveguide in our analysis and experiments. The spectral range of the 850-nm fundamental for which SHG conversion exceeded 0.95 of the maximum value broadened from 0.02 to 0.12 nm when a 1-cm-long grating was divided into three segments with optimum phase shift. SHG conversion efficiency was 300%/W for this waveguide. The SHG efficiency and phase-matching characteristics showed good agreement with theoretical results.

Footprints on the viral DNA ends in moloney murine leukemia virus preintegration complexes reflect a specific association with integrase

Retroviral DNA integration is mediated by the preintegration complex, a large nucleoprotein complex derived from the core of the infecting virion. We previously have used Mu-mediated PCR to probe the nucleoprotein organization of Moloney murine leukemia virus preintegration complexes. A region of protection spans several hundred base pairs at each end of the viral DNA, and strong enhancements are present near the termini. Here, we show that these footprints reflect a specific association between integrase and the viral DNA ends in functional preintegration complexes. Barrier-to-autointegration factor, a cellular protein that blocks autointegration of Moloney murine leukemia virus DNA, also plays an indirect role in generating the footprints at the ends of the viral DNA. We have exploited Mu-mediated PCR to examine the effect of mutations at the viral DNA termini on complex formation. We find that a replication competent mutant with a deletion at one end of the viral DNA still exhibits a strong enhancement about 20 bp from the terminus of the mutant DNA end. The site of the enhancement therefore appears to be at a fixed distance from the ends of the viral DNA. We also find that a mutation at one end of the viral DNA, which renders the virus incompetent for replication, abolishes the enhancements and protection at both the U3 and U5 ends. A pair of functional viral DNA ends therefore are required to interact before the chemical step of 3' end processing.

A large nucleoprotein assembly at the ends of the viral DNA mediates retroviral DNA integration

We have probed the nucleoprotein organization of Moloney murine leukemia virus (MLV) pre-integration complexes using a novel footprinting technique that utilizes a simplified in vitro phage Mu transposition system. We find that several hundred base pairs at each end of the viral DNA are organized in a large nucleoprotein complex, which we call the intasome. This structure is not formed when pre-integration complexes are made by infecting cells with integrase-minus virus, demonstrating a requirement for integrase. In contrast, footprinting of internal regions of the viral DNA did not reveal significant differences between pre-integration complexes with and without integrase. Treatment with high salt disrupts the intasome in parallel with loss of intermolecular integration activity. We show that a cellular factor is required for reconstitution of the intasome. Finally, we demonstrate that DNA-protein interactions involving extensive regions at the ends of the viral DNA are functionally important for retroviral DNA integration activity. Current in vitro integration systems utilizing purified integrase lack the full fidelity of the in vivo reaction. Our results indicate that both host factors and long viral DNA substrates may be required to reconstitute an in vitro system with all the hallmarks of DNA integration in vivo.

Solution structure of the Mu end DNA-binding ibeta subdomain of phage Mu transposase: modular DNA recognition by two tethered domains

The phage Mu transposase (MuA) binds to the ends of the Mu genome during the assembly of higher order nucleoprotein complexes. We investigate the structure and function of the MuA end-binding domain (Ibetagamma). The three-dimensional solution structure of the Ibeta subdomain (residues 77-174) has been determined using multidimensional NMR spectroscopy. It comprises five alpha-helices, including a helix-turn-helix (HTH) DNA-binding motif formed by helices 3 and 4, and can be subdivided into two interacting structural elements. The structure has an elongated disc-like appearance from which protrudes the recognition helix of the HTH motif. The topology of helices 2-4 is very similar to that of helices 1-3 of the previously determined solution structure of the MuA Igamma subdomain and to that of the homeodomain family of HTH DNA-binding proteins. We show that each of the two subdomains binds to one half of the 22 bp recognition sequence, Ibeta to the more conserved Mu end distal half (beta subsite) and Igamma to the Mu end proximal half (gamma subsite) of the consensus Mu end-binding site. The complete Ibetagamma domain binds the recognition sequence with a 100- to 1000-fold higher affinity than the two subdomains independently, indicating a cooperative effect. Our results show that the Mu end DNA-binding domain of MuA has a modular organization, with each module acting on a specific part of the 22 bp binding site. Based on the present binding data and the structures of the Ibeta and Igamma subdomains, a model for the interaction of the complete Ibetagamma domain with DNA is proposed.

Site-specific recombination in plane view

Biochemists have worked long and hard on each reaction component and chemical step to reach the point of asking the question as to how protein and DNA molecules are arranged and rearranged in the process of site-specific recombination. The structures of several lambda integrase family members published recently have answered many of the questions about this process.

Solution structure of the I gamma subdomain of the Mu end DNA-binding domain of phage Mu transposase

The MuA transposase of phase Mu is a large modular protein that plays a central role in transposition. We show that the Mu end DNA-binding domain, I beta gamma, which is responsible for binding the DNA attachment sites at each end of the Mu genome, comprises two subdomains, I beta and I gamma, that are structurally autonomous and do not interact with each other in the absence of DNA. The solution structure of the I gamma subdomain has been determined by multidimensional NMR spectroscopy. The structure of I gamma comprises a four helix bundle and, despite the absence of any significant sequence identity, the topology of the first three helices is very similar to that of the homeodomain family of helix-turn-helix DNA-binding proteins. The helix-turn-helix motif of I gamma, however, differs from that of the homeodomains in so far as the loop is longer and the second helix is shorter, reminiscent of that in the POU-specific domain.

Second-harmonic generation with a high-index-clad waveguide

Theoretical and experimental analyses of second-harmonic generation (SHG) with a high-index-clad waveguide are reported. It was found that confinement of the propagation modes and the overlap between the fields of fundamental and second-harmonic waves could be increased in this waveguide. This structure was achieved in an x-cut MgO:LiNbO (3) quasi-phase-matched (QPM) waveguide by use of Nb(2)O(5) as a cladding layer. With the QPM SHG device, harmonic blue light of 5.5 mW at the 434-nm wavelength was generated with a normalized conversion efficiency of 1200%/W cm(2).

Polynucleotidyl transfer reactions in site-specific DNA recombination

Site-specific DNA rearrangement reactions are widespread among organisms. They are used, for example, by vertebrates to boost immune response diversity, and in turn by parasitic organisms to evade the host immune system by surface antigen switching. Parasitic genetic elements ubiquitous to most organisms invade new host genomic sites by a variety of types of site-specific recombination. Polynucleotidyl transfer reactions are central to these DNA recombination reactions. The recombinase of each reaction system that 'catalyses' such chemical reactions at specific DNA sites are apparently designed to accomplish unique DNA geometrical specificity, or delicate control over the extent or direction of the reaction, with the sacrifice of protein turnover. Here we discuss our current understanding of several issues that relate to the polynucleotidyl transfer steps in several of the better studied site-specific recombination reactions.

Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn

Integration host factor (IHF) is a small heterodimeric protein that specifically binds to DNA and functions as an architectural factor in many cellular processes in prokaryotes. Here, we report the crystal structure of IHF complexed with 35 bp of DNA. The DNA is wrapped around the protein and bent by >160 degrees, thus reversing the direction of the helix axis within a very short distance. Much of the bending occurs at two large kinks where the base stacking is interrupted by intercalation of a proline residue. IHF contacts the DNA exclusively via the phosphodiester backbone and the minor groove and relies heavily on indirect readout to recognize its binding sequence. One such readout involves a six-base A tract, providing evidence for the importance of a narrow minor groove.

Intracavity second-harmonic generation with a periodically domain-inverted LiTaO(3) device

Efficient intracavity second-harmonic generation (SHG) based on a bulk-type quasi-phase-matched (QPM) SHG device in a LiTaO(3) crystal is demonstrated. The periodically domain-inverted regions were fabricated by a high-voltage application technique. The internal loss from the refractive-index change in the domain-inverted regions was reduced to less than 0.1% by an annealing technique. Intracavity frequency doubling of a Nd:YVO(4) laser with the QPM SHG device pumped by a laser diode was effected to generate 13-mW green light for a pump power of 130 mW without suffering transverse mode distortion from a photorefractive effect.

Mu transpositional recombination: donor DNA cleavage and strand transfer in trans by the Mu transposase

Central to the Mu transpositional recombination are the two chemical steps; donor DNA cleavage and strand transfer. These reactions occur within the Mu transpososome that contains two Mu DNA end segments bound to a tetramer of MuA, the transposase. To investigate which MuA monomer catalyzes which chemical reaction, we made transpososomes containing wild-type and active site mutant MuA. By pre-loading the MuA variants onto Mu end DNA fragments of different length prior to transpososome assembly, we could track the catalysis by MuA bound to each Mu end segment. The donor DNA end that underwent the chemical reaction was identified. Both the donor DNA cleavage and strand transfer were catalyzed in trans by the MuA monomers bound to the partner Mu end. This arrangement explains why the transpososome assembly is a prerequisite for the chemical steps.

Similarities between initiation of V(D)J recombination and retroviral integration

In the first step of V(D)J recombination, the RAG1 and RAG2 proteins cleave DNA between a signal sequence and the adjacent coding sequence, generating a blunt signal end and a coding end with a closed hairpin structure. These hairpins are intermediates leading to the formation of assembled antigen receptor genes. It is shown here that the hairpins are formed by a chemical mechanism of direct trans-esterification, very similar to the early steps of transpositional recombination and retroviral integration. A minor variation in the reaction is sufficient to divert the process from transposition to hairpin formation.

The wing of the enhancer-binding domain of Mu phage transposase is flexible and is essential for efficient transposition

A tetramer of the Mu transposase (MuA) pairs the recombination sites, cleaves the donor DNA, and joins these ends to a target DNA by strand transfer. Juxtaposition of the recombination sites is accomplished by the assembly of a stable synaptic complex of MuA protein and Mu DNA. This initial critical step is facilitated by the transient binding of the N-terminal domain of MuA to an enhancer DNA element within the Mu genome (called the internal activation sequence, IAS). Recently we solved the three-dimensional solution structure of the enhancer-binding domain of Mu phage transposase (residues 1-76, MuA76) and proposed a model for its interaction with the IAS element. Site-directed mutagenesis coupled with an in vitro transposition assay has been used to assess the validity of the model. We have identified five residues on the surface of MuA that are crucial for stable synaptic complex formation but dispensable for subsequent events in transposition. These mutations are located in the loop (wing) structure and recognition helix of the MuA76 domain of the transposase and do not seriously perturb the structure of the domain. Furthermore, in order to understand the dynamic behavior of the MuA76 domain prior to stable synaptic complex formation, we have measured heteronuclear 15N relaxation rates for the unbound MuA76 domain. In the DNA free state the backbone atoms of the helix-turn-helix motif are generally immobilized whereas the residues in the wing are highly flexible on the pico- to nanosecond time scale. Together these studies define the surface of MuA required for enhancement of transposition in vitro and suggest that a flexible loop in the MuA protein required for DNA recognition may become structurally ordered only upon DNA binding.

Generation of 340-nm light by frequency doubling of a laser diode in bulk periodically poled LiTaO(3)

Frequency doubling of a 680-nm laser diode in periodically poled LiTaO(3) is presented. By selective proton exchange followed by high-voltage pulse application, a second-order periodic domain inversion having uniform periodicity and optimum duty cycle was fabricated over a 10-mm interaction length in a 200-microm-thick LiTaO(3) substrate. A 340-nm wavelength of harmonic ultraviolet light was generated in a single pass through the domain-inverted structure.

Assembly of phage Mu transpososomes: cooperative transitions assisted by protein and DNA scaffolds

Transposition of phage Mu takes place within higher order protein-DNA complexes called transpososomes. These complexes contain the two Mu genome ends synapsed by a tetramer of Mu transposase (MuA). Transpososome assembly is tightly controlled by multiple protein and DNA sequence cofactors. We find that assembly can occur through two distinct pathways. One previously described pathway depends on an enhancer-like sequence element, the internal activation sequence (IAS). The second pathway depends on a MuB protein-target DNA complex. For both pathways, all four MuA monomers in the tetramer need to interact with an assembly-assisting element, either the IAS or MuB. However, once assembled, not all MuA monomers within the transpososome need to interact with MuB to capture MuB-bound target DNA. The multiple layers of control likely are used in vivo to ensure efficient rounds of DNA replication when needed, while minimizing unwanted transposition products.

The phage Mu transpososome core: DNA requirements for assembly and function

The two chemical steps of phage Mu transpositional recombination, donor DNA cleavage and strand transfer, take place within higher order protein-DNA complexes called transpososomes. At the core of these complexes is a tetramer of MuA (the transposase), bound to the two ends of the Mu genome. While transpososome assembly normally requires a number of cofactors, under certain conditions only MuA and a short DNA fragment are required. DNA requirements for this process, as well as the stability and activity of the ensuing complexes, were established. The divalent cation normally required for assembly of the stable complex could be omitted if the substrate was prenicked, if the flanking DNA was very short or if the two flanking strands were non-complementary. The presence of a single nucleotide beyond the Mu genome end on the non-cut strand was critical for transpososome stability. Donor cleavage additionally required at least two flanking nucleotides on the strand to be cleaved. The flanking DNA double helix was destabilized, implying distortion of the DNA near the active site. Although donor cleavage required Mg2+, strand transfer took place in the presence of Ca2+ as well, suggesting a conformational difference in the active site for the two chemical steps.

Structure of the bacteriophage Mu transposase core: a common structural motif for DNA transposition and retroviral integration

The crystal structure of the core domain of bacteriophage Mu transposase, MuA, has been determined at 2.4 A resolution. The first of two subdomains contains the active site and, despite very limited sequence homology, exhibits a striking similarity to the core domain of HIV-1 integrase, which carries out a similar set of biochemical reactions. It also exhibits more limited similarity to other nucleases, RNase H and RuvC. The second, a beta barrel, connects to the first subdomain through several contacts. Three independent determinations of the monomer structure from two crystal forms all show the active site held in a similar, apparently inactive configuration. The enzymatic activity of MuA is known to be activated by formation of a DNA-bound tetramer of the protein. We propose that the connections between the two subdomains may be involved in the cross-talk between the active site and the other domains of the transposase that controls the activity of the protein.

Highly efficient quasi-phase-matched second-harmonic generation by frequency doubling of a high-frequency superimposed laser diode

We report highly efficient blue-light generation by frequency doubling of a high-frequency superimposed laser diode, stabilized by a grating feedback technique, in a periodically domain-inverted LiTaO(3) waveguide. To increase second-harmonic generation conversion efficiency, we enhanced the peak power of the laser diode by using a gain-switching method. Locking the oscillation wavelength of the laser diode by the grating feedback technique, we obtained 4.5 mW of average blue-light power with 13% conversion efficiency.

A novel class of winged helix-turn-helix protein: the DNA-binding domain of Mu transposase

BACKGROUND

Mu transposase (MuA) is a multidomain protein encoded by the bacteriophage Mu genome. It is responsible for translocation of the Mu genome, which is the largest and most efficient transposon known. While the various domains of MuA have been delineated by means of biochemical methods, no data have been obtained to date relating to its tertiary structure.

RESULTS

We have solved the three-dimensional solution structure of the DNA-binding domain (residues 1-76; MuA76) of MuA by multidimensional heteronuclear NMR spectroscopy. The structure consists of a three-membered alpha-helical bundle buttressed by a three-stranded antiparallel beta-sheet. Helices H1 and H2 and the seven-residue turn connecting them comprise a helix-turn-helix (HTH) motif. In addition, there is a long nine-residue flexible loop or wing connecting strands B2 and B3 of the sheet. NMR studies of MuA76 complexed with a consensus DNA site from the internal activation region of the Mu genome indicate that the wing and the second helix of the HTH motif are significantly perturbed upon DNA binding.

CONCLUSIONS

While the general appearance of the DNA-binding domain of MuA76 is similar to that of other winged HTH proteins, the connectivity of the secondary structure elements is permuted. Hence, the fold of MuA76 represents a novel class of winged HTH DNA-binding domain.

First-order quasi-phase-matched second-harmonic generation in a LiTaO(3) waveguide

We achieved improvement in conversion efficiency in a first-order quasi-phase-matched second-harmonic generation device that uses a LiTaO(3) waveguide by experimentally characterizing the device process and the performances. Efficient overlaps among propagation light modes and the first-order periodically domain-inverted region are gained in a strongly confined waveguide fabricated by use of proton exchange annealed by a quick heat treatment. A blue-light power of 22 mW is obtained for a conversion efficiency of 18% by using a Ti:Al(2)O(3) laser. The observed FWHM temperature and wavelength acceptance bandwidths for second-harmonic generation power are 2.5 °C and 0.13 nm, respectively. Using this device with antireflection coating on the input and output facets of the waveguide, we generate 1.3 mW of blue light for a conversion efficiency of 4% by direct diode-laser doubling.

Division of labor among monomers within the Mu transposase tetramer

A single tetramer of Mu transposase (MuA) pairs the recombination sites, cleaves the donor DNA, and joins these ends to a target DNA by strand transfer. Analysis of C-terminal deletion derivatives of MuA reveals that a 30 amino acid region between residues 575 and 605 is critical for these three steps. Although inactive on its own, a deletion protein lacking this region assembles with the wild-type protein. These mixed tetramers carry out donor cleavage but do not promote strand transfer, even when the donor cleavage stage is bypassed. These data suggest that the active center of the transposase is composed of the C-terminus of four MuA monomers; one dimer carries out donor cleavage while all four monomers contribute to strand transfer.

DNA-promoted assembly of the active tetramer of the Mu transposase

A stable tetramer of the Mu transposase (MuA) bound to the ends of the Mu DNA promotes recombination. Assembly of this active protein-DNA complex from monomers of MuA requires an intricate array of MuA protein-binding sites on supercoiled DNA, divalent metal ions, and the Escherichia coli HU protein. Under altered reaction conditions, many of these factors stimulate assembly of the MuA tetramer but are not essential, allowing their role in formation of the complex to be analyzed. End-type MuA-binding sites and divalent metal ions are most critical and probably promote a conformational change in MuA that is necessary for multimerization. Multiple MuA-binding sites on the DNA contribute synergistically to tetramer formation. DNA superhelicity assists cooperativity between the sites on the two Mu DNA ends if they are properly oriented. HU specifically promotes assembly involving the left end of the Mu DNA. In addition to dissecting the assembly pathway, these data demonstrate that the tetrameric conformation is intrinsic to MuA and constitutes the form of the protein active in catalysis.

Assembly of the active form of the transposase-Mu DNA complex: a critical control point in Mu transposition

Discovery and characterization of a new intermediate in Mu DNA transposition allowed assembly of the transposition machinery to be separated from the chemical steps of recombination. This stable intermediate, which accumulates in the presence of Ca2+, consists of the two ends of the Mu DNA synapsed by a tetramer of the Mu transposase. Within this stable synaptic complex (SSC), the recombination sites are engaged but not yet cleaved. Thus, the SSC is structurally related to both the cleaved donor and strand transfer complexes, but precedes them on the transposition pathway. Once the active protein-DNA complex is constructed, it is conserved throughout transposition. The participation of internal sequence elements and accessory factors exclusively during SSC assembly allows recombination to be controlled prior to the irreversible chemical steps.

HIV-1 DNA integration: mechanism of viral DNA cleavage and DNA strand transfer

Retroviral DNA integration involves a coordinated set of DNA cutting and joining reactions. Linear viral DNA is cleaved at each 3' end to generate the precursor ends for integration. The resulting recessed 3' ends are inserted into target DNA by a subsequent DNA strand transfer reaction. Purified HIV-1 integration protein carries out both of these steps in vitro. Two novel forms of the dinucleotide cleaved from HIV-1 DNA were identified and one, a cyclic dinucleotide, was used to analyze the stereochemical course of viral DNA cleavage. Both viral DNA cleavage and DNA strand transfer display inversion at chiral phosphorothioates during the course of the reaction. These results suggest that both reactions occur by a one-step mechanism without involvement of a covalent protein-DNA intermediate.

DNase protection analysis of the stable synaptic complexes involved in Mu transposition

Several critical steps in phage Mu transposition involve specialized protein-DNA complexes. Cleavage of Mu donor DNA by MuA protein leads to the formation of the stable cleaved donor complex (CDC), in which the two Mu DNA ends are held together by MuA. In the subsequent strand-transfer reaction the CDC attacks a target DNA to generate the strand-transfer complex, in which the donor and the target DNAs are covalently joined. We have carried out DNase I protection experiments on these protein-DNA complexes and found that only three MuA binding sites (L1, R1, and R2 of the six total) at the two Mu ends are stably bound by MuA to maintain the paired Mu end structure. The protection extends beyond the ends of the Mu sequence for different lengths (7-20 nucleotides) depending on the strand and the type of complex. After formation of the CDC, the other MuA binding sites (L2, L3, and R3) and internal activation sequence become dispensable for the subsequent strand-transfer reaction.

Milliwatt-order blue-light generation in a periodically domain-inverted LiTaO(3) waveguide

We report the characterization of a quasi-phase-matched second-harmonic generation device in LiTaO(3) that has a periodically domain-inverted region and a proton-exchanged channel waveguide. A blue-light power of 2.4 mW was obtained at a 424-nm wavelength. The observed temperature bandwidth for FWHM power is approximately 3 degrees C-cm, which is three times wider than that in a similar device in LiNbO(3). It is also shown that diffraction-limited focusing of the generated blue light may be obtained.

Inversion of the phosphate chirality at the target site of Mu DNA strand transfer: evidence for a one-step transesterification mechanism

Central to transposition of phage Mu are two reactions mediated by the MuA protein. First, MuA introduces single-stranded cuts at the ends of the Mu DNA to generate 3' OH termini. In the subsequent strand-transfer step, the MuA-Mu DNA end complex cuts a target DNA and joins the Mu 3' ends to the 5' ends of the target. DNA containing chiral phosphorothioates was used to demonstrate inversion of the chirality during the course of strand transfer. This result strongly supports a one-step transesterification mechanism in which the 3' OH of the cleaved donor DNA is the attacking nucleophile. Furthermore, this donor 3' OH group was essential for target DNA cleavage. In contrast, during lambda integration the phosphate chirality was retained, as expected for a two-step transesterification involving a covalent protein-DNA intermediate.

MuB protein allosterically activates strand transfer by the transposase of phage Mu

The MuA and MuB proteins collaborate to mediate efficient transposition of the phage Mu genome into many DNA target sites. MuA (the transposase) carries out all the DNA cleavage and joining steps. MuB stimulates strand transfer by activating the MuA-donor DNA complex through direct protein-protein contact. The C-terminal domain of MuA is required for this MuA-MuB interaction. Activation of strand transfer occurs irrespective of whether MuB is bound to target DNA. When high levels of MuA generate a pool of free MuB (not bound to DNA) or when chemical modification of MuB impairs its ability to bind DNA, MuB still stimulates strand transfer. However, under these conditions, intramolecular target sites are used exclusively because of their close proximity to the MuA-MuB-donor DNA complex.

A rapid in vitro assay for HIV DNA integration

Retroviruses synthesize a double stranded DNA copy of their RNA genome after infection of a permissive cell and subsequent integration of this DNA copy into the host genome is necessary for normal viral replication. Integration occurs by a specialized DNA recombination reaction, mediated by the viral IN protein. Because this reaction has no known cellular counterpart, it is a particularly attractive target in the search for specific inhibitors with low toxicity that may serve as therapeutic antiviral agents. We present a simple assay system that is suitable for screening potential inhibitors of HIV DNA integration. Only short oligonucleotides matching one end of HIV DNA and purified HIV IN protein are required as substrates. Furthermore, since each step of the assay can be carried out in the wells of microtiter plates, large numbers of reactions can be processed simultaneously.

Steady-state kinetic analysis of ATP hydrolysis by the B protein of bacteriophage mu. Involvement of protein oligomerization in the ATPase cycle

The DNA strand-transfer reaction of bacteriophage Mu requires Mu B protein and ATP for high efficiency. These factors facilitate the capture of target DNA by the donor protein-DNA complex. To understand the mechanism of the Mu B ATPase cycle in the Mu DNA strand-transfer reaction, we undertook a steady-state kinetic analysis of Mu B ATPase. The results reveal complex properties of the ATPase activity; Mu B protein oligomerizes in the presence of ATP, and ATP hydrolysis by the Mu B ATPase is stimulated by the protein oligomerization and shows a positive cooperativity with respect to ATP concentration. Mu B ATPase activity is also modulated by DNA and Mu A protein. DNA alone suppresses the catalytic activity of Mu B ATPase, whereas DNA enhances the apparent binding affinity for ATP. In the presence of Mu A protein together with DNA, however, the catalytic activity is greatly stimulated. Based on these results, we propose a working hypothesis in which oligomerization of Mu B protein plays a key role in its ATPase cycle.

Efficient Mu transposition requires interaction of transposase with a DNA sequence at the Mu operator: implications for regulation

Phage Mu transposition is initiated by the Mu DNA strand-transfer reaction, which generates a branched DNA structure that acts as a transposition intermediate. A critical step in this reaction is formation of a special synaptic DNA-protein complex called a plectosome. We find that formation of this complex involves, in addition to a pair of Mu end sequences, a third cis-acting sequence element, the internal activation sequence (IAS). The IAS is specifically recognized by the N-terminal domain of Mu transposase (MuA protein). Neither the N-terminal domain of MuA protein nor the IAS is required for later reaction steps. The IAS overlaps with the sequences to which Mu repressor protein binds in the Mu operator region; the Mu repressor directly inhibits the Mu DNA strand-transfer reaction by interfering with the interaction between MuA protein and the IAS, providing an additional mode of regulation by the repressor.

V(D)J recombination: a functional definition of the joining signals

Two conserved DNA sequences serve as joining signals in the assembly of immunoglobulins and T-cell receptors from V-, (D)-, and J-coding segments during lymphoid differentiation. We have examined V(D)J recombination as a function of joining signal sequence. Plasmid substrates with mutations in one or both of the heptamer-spacer-nonamer sequences were tested for recombination in a pre-B-cell line active in V(D)J recombination. No signal variant recombines more efficiently than the consensus forms of the joining signals. We find the heptamer sequence to be the most important; specifically, the three bases closest to the recombination crossover site are critical. The nonamer is not as rigidly defined, and it is not important to maintain the five consecutive As that distinguish the consensus nonamer sequence. Both types of signals display very similar sequence requirements and have in common an intolerance for changes in spacer length greater than 1 bp. Although the two signal types share sequence motifs, we find no evidence of a role in recombination for homology between the signals, suggesting that they serve primarily as protein recognition and binding sites.

Interaction of proteins located at a distance along DNA: mechanism of target immunity in the Mu DNA strand-transfer reaction

DNA molecules carrying a Mu end(s) are inefficient targets in the Mu DNA strand-transfer reaction. This target immunity is due to preferential dissociation of Mu B protein from DNA molecules that have Mu A protein bound to the Mu end; free DNA is a much poorer target than DNA with Mu B protein bound. We show that Mu B protein, which binds nonspecifically to DNA, is immobile once bound. An encounter between Mu A and Mu B proteins, bound some distance apart along DNA, is necessary to facilitate the Mu B dissociation. Experiments which show that DNA without a Mu end can acquire immunity, by catenation to DNA with a Mu end(s), are consistent with a model of Mu A-Mu B interaction by DNA looping, but not by linear movement of protein(s) along DNA.

Novel strand exchanges in V(D)J recombination

We describe novel products of V(D)J recombination in which signal sequences become joined to coding elements, in contrast to the standard reaction whose products are junctions of two signal sequences or two coding elements. In this variant reaction, the recombination machinery evidently recognizes signal sequences and introduces strand breaks at the normal positions, but then connects the elements in unusual combinations. The lack of fixed directionality indicates that recombination sites are not uniquely aligned when strand exchange occurs. The discovery of these variant junctions suggests a model for the evolution of the antigen receptor loci.

Lymphoid V(D)J recombination: nucleotide insertion at signal joints as well as coding joints

The coding regions of antigen receptor genes assembled by variable-diversity-joining region [V(D)J] recombination are known in many cases to have undergone deletions of several nucleotides and also to contain insertions of noncoded nucleotides at the recombined junction (the coding joint). By using extrachromosomal recombination substrates to transfect lymphoid cell lines, we show that the signal joint (the fusion of the corresponding recognition signal sequences) can also contain insertions; however, nucleotide loss from the signals is very rare. The frequency of nucleotide addition varies among pre-B-cell lines in a manner proportional to their content of terminal deoxynucleotidyltransferase. We also find frequent nucleotide additions (and deletions) at coding joints, but in this case there is no strong correlation with the level of terminal deoxynucleotidyltransferase activity. Inserts at both signal and coding joints are rich in G + C, consistent with the base utilization preference of this enzyme.

The defect in murine severe combined immune deficiency: joining of signal sequences but not coding segments in V(D)J recombination

Pre-B and pre-T cell lines from mutant mice with severe combined immune deficiency (scid mice) were transfected with plasmids that contained recombination signal sequences of antigen receptor gene elements (V, D, and J). Recovered plasmids were tested for possible recombination of signal sequences and/or the adjacent (coding) sequences. Signal ends were joined, but recombination was abnormal in that half of the recombinants had lost nucleotides from one or both signals. Coding ends were not joined at all in either deletional or inversional V(D)J recombination reactions. However, coding ends were able to participate in alternative reactions. The failure of coding joint formation in scid pre-B and pre-T cells appears sufficient to explain the absence of immunoglobulin or T cell receptor production in scid mice.

Retroviral DNA integration: structure of an integration intermediate

The structure of a presumptive DNA intermediate in the integration of retroviral DNA was studied in a cell-free reaction with exogenously added target DNA. The product made by viral core particles of Moloney murine leukemia virus (Mo-MLV) containing linear viral DNA has a structure consistent with an integration mechanism similar to that observed during bacteriophage Mu transposition. In this intermediate, the 3' ends of the LTR sequences are joined to the target DNA, while the 5' ends of the viral DNA remain unjoined. The 5' ends of the LTR sequences in the intermediate are exactly the same as those found in the unintegrated linear double-stranded viral DNA. This result demonstrates that the linear form of Mo-MLV DNA can integrate directly without prior circularization.