DNA triplex structures are stabilized by the incorporation of 3'-endo blocked pyrimidine nucleosides in the Hoogsteen strand

A short route to pyrimidine locked nucleosides has been developed for their incorporation in triplex forming oligonucleotides (TFO). Compared to oligonucleotides built with standard nucleosides, the modified TFOs containing 3'-endo blocked residues formed, with their corresponding DNA duplexes, more stable triple helix systems, an effect which might be ascribed to the 3'-endo pucker of the modified nucleoside residues.

Alveolar mononuclear cells can develop into multinucleated osteoclasts: an in vitro cell culture model

Previous studies have shown that osteoclasts are derived from mononuclear cells of hemopoietic bone marrow and peripheral blood. The purpose of this study was to demonstrate the presence of multinucleated osteoclasts after adding alveolar mononuclear cells to new-born rat calvaria osteoblasts in vitro. To utilize osteoclast-free bone, fetal calvariae were obtained from newborn Wistar-rats and cultured in DMEM medium for 14 days. On the day of osteoblast culture, alveolar mononuclear cells were isolated from newborn Wistar rats with a serial washing method and then co-cultured with the calvarial osteoblasts. Bone resorption characteristics were observed both with light and scanning electron microscopy. When alveolar mononuclear cells were cultured for 14 days on the calvarial osteoblasts in response to 1 alpha, 25-dihydroxyvitamin D3, they formed tartrate-resistant acid phosphatase (TRAP)-positive mononuclear and multinucleated cells. Resorption pits were seen in the 7-14 days long-term cultures. These results indicate that osteoclasts can be derived from alveolar mononuclear cells in vitro when a suitable microenvironment is provided by calvarial osteoblasts and vitamin D(3).

Mycobacterial infection of the upper extremities

BACKGROUND AND PURPOSE

Mycobacterial infection of the upper extremities is extremely rare. To make an early accurate diagnosis is often difficult, and the treatment is, therefore, frequently delayed in clinical practice. This paper describes the diagnosis and treatment of mycoabacterial infection of the upper extremities in a series of patients treated at National Taiwan University Hospital.

METHODS

The medical records of 15 patients with mycobacterial infection of the upper extremities treated between 1985 and 1998 were retrospectively analyzed. The diagnosis of mycobacterial infection was established by positive culture results, the presence of acid-fast bacilli, or characteristic histopathologic findings.

RESULTS

Mycobacterial infection was suspected on initial examination in only two patients. The duration between the onset of symptoms and correct diagnosis averaged 37.5 months (range, 3 wk to 209 mo). The involved sites of mycobacterial infection included the wrist in nine patients, the elbow in two, the hand in two, the humerus in two, the forearm in one, and the shoulder in one. Three patients suffered from multifocal musculoskeletal mycobacterial infection. Microbiologic studies identified Mycobacterium tuberculosis in four patients and nontuberculous mycobacteria (NTM) in four. Characteristic histopathologic findings of mycobacterial infection including caseation, granulomatous inflammation, eosinophilic epithelioid cells, Langhan's giant cells, and lymphocytic aggregates were noted in all 15 patients. All patients received chemotherapy and 14 patients underwent surgical treatment. The mean duration of follow-up was 46 months (range, 15-97 months). Treatment failed in two of the patients with multifocal NTM infection and in one patient whose mycobacterial infection was identified by histopathology.

CONCLUSIONS

Mycobacterial infection should be included in the differential diagnosis of infection of the upper extremities. Treatment failures are more frequent in patients with multifocal NTM infection.

Ipsilateral distal radius and scaphoid fractures

Simultaneous fractures of the distal radius and scaphoid are uncommon. Previous reports have outlined a variety of treatment methods for this condition. We describe the results in eight patients with simultaneous fractures of the distal radius and scaphoid, who were treated at National Taiwan University Hospital from 1987 to 1998. Treatments for the distal radius fractures included pin-in-cast in one patient, casting in one, external fixation in one, external fixation after pinning in three, and open reduction with internal fixation in two. All scaphoid fractures occurred at the scaphoid waist, and were treated with long-arm thumb spica in three patients, Herbert screw fixation in two, and percutaneous pinning in three. All of the fractures united, and none of the patients developed scaphoid avascular necrosis. One patient suffered from superficial radial nerve injury during external fixation. The functional results of the wrist were good in five patients and fair in three. To prevent the possible over-distraction of the scaphoid fracture, fixation of the scaphoid should be performed if a distraction force is to be applied during the treatment of the distal radius fracture. If no distraction force is to be applied, a thumb spica may provide adequate fixation for the scaphoid fracture.

Preparation of betaTCP/HAP biphasic ceramics with natural bone structure by heating bovine cancellous bone with the addition of (NH(4))(2)HPO(4)

In this study, the calcined bovine bone (CBB)-removing the organic substance by a burning process-with addition of different quantities of ammonium phosphate [(NH(4))(2)HPO(4)] (AP) was heated to a high temperature to transform its crystalline phase constitution from hydroxyapatite (HAP) into a tricalcium phosphate (TCP)/HAP biphasic structure. Results revealed that the CBB without AP appeared to be mainly composed of an HAP type pattern when heated to 1300 degrees C. After adding doped AP to CBB, the HPO(4)(2-) ions of AP condensed into P(2)O(7)(4-) ions at temperatures of 400-600 degrees C. P(2)O(7)(4-) ions reacted with the OH(-) ions of HAP to form betaTCP at temperatures up to 600 degrees C. The conversion reaction of HAP to betaTCP finished at around 900 degrees C. With increasing AP in the CBB, HAP gradually converted into different phase compositions of TCP/HAP or TCP at high temperature. Mechanical testing results showed that there was no significant difference in sintered CBB with different quantities of AP. By heating calcined bovine cancellous bone with different quantities of AP, we obtained different crystalline phase compositions of bioceramics with a natural porous structure.

Linkage of a triple helix-forming oligonucleotide to amsacrine-4-carboxamide derivatives modulates the sequence-selectivity of topoisomerase II-mediated DNA cleavage

Amsacrine-4-carboxamide-oligonucleotide conjugates were synthesized and studied for their capacity to form DNA triple helices and to alter human topoisomerase II binding and cleavage properties. The intercalating agent was attached to the 3'- or the 5'-end of a 24 nt triple helix-forming oligonucleotide via linkers of different lengths. The stability of these DNA triple helices was investigated by gel retardation and melting temperature studies using a synthetic 70 bp DNA duplex target. The effect of the conjugates on DNA cleavage by topoisomerase II was evaluated using the 70 bp duplex and a 311 bp restriction fragment containing the same triple helix site. The conjugate with the amsacrine derivative linked to the 3' end of the TFO via a hexaethylene glycol linker modulates the extent of DNA cleavage by topoisomerase II at specific sites.

A new family of sequence-specific DNA-cleaving agents directed by triple-helical structures: benzopyridoindole-EDTA conjugates

Sequence-specific DNA recognition can be achieved by oligonucleotides that bind to the major groove of oligopyrimidine x oligopurine sequences. These intermolecular structures could be used to modulate gene expression and to create new tools for molecular biology. Here we report the synthesis and biochemical characterization of triple helix-specific DNA cleaving reagents. It is based on the previously reported triplex-specific ligands, benzo[e]pyridoindole (BePI) and benzo[g]pyridoindole (BgPI), covalently attached to ethylenediaminotetraacetic acid (EDTA). In the presence of iron, a reducing agent and molecular oxygen, BgPI-EDTA x FeII but not BePI-EDTA x FeII induced a double-stranded cut in a plasmid DNA at the single site where a triplex-forming oligonucleotide binds. At single nucleotide resolution, it was found that upon triplex formation BePI-EDTA x FeII led to cleavage of the pyrimidine strand and protection of the purine strand. BgPI-EDTA x FeII cleaved both strands with similar efficiency. The difference in cleavage efficiency between the two conjugates was rationalized by the location of the EDTA x FeII moiety with respect to the grooves of DNA (major groove: BePI-EDTA x FeII, minor groove: BgPI-EDTA x FeII). This work paves the way to the development of a new class of triple helix directed DNA cleaving reagents. Such molecules will be of interest for sequence-specific DNA cleavage and for investigating triple-helical structures, such as H-DNA, which could play an important role in the control of gene expression in vivo.

Recognition and cleavage of DNA by rebeccamycin- or benzopyridoquinoxaline conjugated of triple helix-forming oligonucleotides

Indolocarbazole and benzopyridoquinoxaline derivatives have been shown to have anti-tumor activity and to stimulate DNA topoisomerase I-mediated cleavage. Two indolocarbazole compounds (R-6 and R-95) and one benzopyridoquinoxaline derivative (BPQ(1256)) were covalently attached to the 3'-end of a 16mer triple helix-forming oligonucleotide (TFO). These conjugates bind to DNA with a higher affinity than the unsubstituted oligonucleotides. Furthermore, they induce topoisomerase I-mediated and triplex-directed DNA cleavage in a sequence-specific manner.

In vivo kinematic study of normal wrist motion: an ultrafast computed tomographic study

OBJECTIVE

To quantify in vivo carpal kinematics of a normal wrist in a dynamic continuous model.

DESIGN

The instantaneous changes in the radiocarpal and midcarpal joints during normal wrist motion were analyzed using ultrafast computed tomography (CT).

BACKGROUND

Wrist injuries account for a considerable and growing proportion of work-related disorders and disability. However, little is known about normal wrist kinematics.

METHODS

Ten uninjured subjects were studied using ultrafast CT to measure the continuous motion of the wrist from full flexion to full extension. Sagittal plane scanning was performed mediolaterally at six different locations as the wrists were moved slowly and repeatedly from full flexion to full extension. The data were printed to X-ray film and transferred to an independent work station with a video camera. The motion of the radiocarpal, midcarpal and wrist joints was determined by an image analyzing system.

RESULTS

Wrist motion was expressed as a ratio of capitate-lunate (C-L) (midcarpal) motion and radio-lunate (R-L) (radiocarpal) motion. In the volar flexion of normal wrists, the contribution of the radiocarpal joint and midcarpal joint were approximately equal; while dorsal flexion of the normal wrist occurred mainly at the midcarpal joint.

CONCLUSIONS

In normal wrists, the radiocarpal joint and midcarpal joint contribute equally to volar flexion, while the midcarpal joint is more important in dorsal flexion.

RELEVANCE

In this study, we demonstrated the suitability of using two-dimensional computed tomographic images in a quantitative study of flexion/extension kinematics of the normal wrist.

Cytokine and prostaglandin E2 release from leukocytes in response to metal ions derived from different prosthetic materials: an in vitro study

Cytokines produced by leukocytes in the periprosthetic membranes surrounding joint replacements have been implicated as causal agents in osteolysis and prosthetic loosening. In this study, we used an in vitro leukocyte culture system to monitor the response of leukocytes to various metal ions and their possible roles in the mechanism of aseptic loosening. Human peripheral leukocytes were isolated and incubated with various concentrations of Co2+, Cr3+, and Ti3+ ions. Leukocyte cell counts and the levels of the tumor necrosis factor-alpha (TNF-alpha), interleukin-1 (IL-1), interleukin-6 (IL-6) and prostaglandin E2 (PGE2) released into the media were analyzed at 1 h, 3 h, and 1, 3, and 7 day intervals. The results showed that adding different metal ions into leukocyte cultures did not affect the cell counts. Exposure of leukocytes to Co2+ ion increased the release of TNF-alpha, IL-6, and PGE2. Exposure of leukocytes to Cr3+ ion did not increase the release of TNF-alpha but increased the secretion of IL-6 and PGE2. In contrast, exposure of the leukocytes to Ti3+ ions was associated with a decrease in the release of TNF-alpha and PGE2 and a minimal change in IL-6 noted after 7 days' culture. The present study elucidated the possible mechanisms involved in periprosthetic osteolysis and the inflammatory response of human leukocytes to metal ions. We found that cobalt ion is the most potent stimulant for cytokines and prostaglandin secretion by leukocytes. This elucidation, in combination with other efforts to reduce the generation of wear debris and metal ions, may improve the longevity of orthopedic implants.

Thermal decomposition and reconstitution of hydroxyapatite in air atmosphere

In this paper, the decomposition and reconstruction behavior of hydroxyapatite (HAP) during heating and cooling in air atmosphere were studied. The commercial HAP were chosen and gradually heated to 1500 degrees C and cooled to room temperature by a program controlled SiC heated furnace. X-ray diffraction (XRD) and Fourier-transformed infrared (FTIR) analysis were used to investigate the change of crystalline phases and functional groups of HAP at different temperatures. Weight change of samples was recorded by thermogravimetric analysis (TGA) during heating and cooling. The results revealed that HAP gradually releases its OH- ions and transforms into OHAP in the temperature of 1000-1360 degrees C. Above 1360 degrees C, the OHAP would decompose into TTCP and alpha TCP phase. The OH- stretching bands of HAP could be traced by FTIR even at the temperature of 1350 degrees C which indicates HAP decomposition. HAP does not dehydrate completely before decomposition. We speculated that some oxyapatite (OAP) might be formed during dehydration with a great amount of OHAP still left in the system even up to the temperature of decomposition. In the temperature range of 1400-1500 degrees C, there was no significant difference in XRD patterns, only TTCP and alpha TCP crystalline phases were observed. When the HAP gradually cools from 1500 degrees C, a part of TTCP and alpha TCP would directly reconstruct into OAP around 1350 degrees C. OAP existed in the temperature range of 1350-1300 degrees C during cooling. When the temperature decreased to 1290 degrees C, a part of TTCP and alpha TCP reconstructed into OHAP by rehydration reaction and OAP were rehydrated into OHAP as well. At 1100 degrees C, the rest of TTCP and alpha TCP reconstitutes into HAP. As the temperature decreases, the OHAP is gradually rehydrated and reconstituted into HAP.

Targeting topoisomerase I cleavage to specific sequences of DNA by triple helix-forming oligonucleotide conjugates. A comparison between a rebeccamycin derivative and camptothecin

Topoisomerase I is an ubiquitous DNA cleaving enzyme and an important therapeutic target in cancer chemotherapy for the camptothecins as well as for indolocarbazole antibiotics such as rebeccamycin and its synthetic derivatives, which stabilize the cleaved DNA-topoisomerase I complex. The covalent linkage of a triple helixforming oligonucleotide to camptothecin or to the indolocarbazole derivative R-6 directs DNA cleavage by topoisomerase I to specific sequences. Sequence-specific recognition of DNA is achieved by the triple helix-forming oligonucleotide, which binds to the major groove of double-helical DNA and positions the drug at a specific site. The efficacy of topoisomerase I-induced DNA cleavage mediated by the rebeccamycin-conjugate and the camptothecin-conjugate was compared and related to the intrinsic potency of the isolated drugs.

Optimization of alternate-strand triple helix formation at the 5"-TpA-3" and 5"-ApT-3" junctions

Alternate-strand triple helix formation was optimized at the two junction steps, the 5"-TpA-3" and 5"-ApT-3" junctions. Footprint experiments, gel retardation assays and thermal denaturation measures on a sequence appropriately designed with two adjacent alternate-strand polypurine tracts points out that the addition of an adenine residue and the removal of one nucleotide should facilitate the crossing strands at the 5"-TpA-3" junction and at the 5"-ApT-3" junction, respectively. These results provide a 'switch code' for the construction of alternate-strand triple helix forming oligonucleotides which open new possibilities for extending the range of applications of antigene strategy.

Bone defect healing enhanced by ultrasound stimulation: an in vitro tissue culture model

Ultrasound has many medical applications. Previous animal and clinical studies have clearly shown a positive effect of ultrasound on the rate of osseous repair. The present in vitro study was designed to elucidate the specific response of bony tissue to ultrasound treatment. Bilateral femora were obtained from 36 mature male Wistar rats. A bone defect was created at the center of each distal metaphysis. The femora were maintained for either 7 or 14 days in in vitro tissue culture and received 15 min of ultrasound stimulation or a sham exposure. The ultrasound intensity used was either 320 or 770 mW/cm2. Healing of the bone defect was evaluated by histomorphological examination and by analysis for the synthesis and secretion of prostaglandin E2. The results showed that ultrasound stimulation can accelerate both defect healing and trabecular bone regeneration. All experimental femoral defects treated with ultrasound healed faster than the untreated cortical defects, but only the defects receiving 770 mW/cm2 reached a level that was significantly different. The healing rate for the 320-mW/cm2 stimulated defects was intermediate between that of the 770-mW/cm2 and sham-exposed defects. With ultrasound stimulation, prostaglandin E2 secretion by the experimental femora decreased significantly. Changes in the prostaglandin synthesis and concentration were found to correspond to changes in the amount of trabecular regeneration and to acceleration of bone healing. This highly controlled and well-studied model of ultrasound stimulation of bone healing in vitro can be used to further examine the biological mechanisms involved.

Antioxidant status following acute ischemic limb injury: a rabbit model

Although ischemic injury to skeletal muscle is a matter of great clinical importance, relatively little is known about the mechanisms which determine systemic responses. One purpose of this study is to elucidate the systemic antioxidant status following an episode of acute ischemic limb injury and subsequent reperfusion. Twelve New Zealand white rabbits were used in this study. After the animals were anesthetized, an ischemic insult was created in the right hind limb for twelve hours, followed by four hours of reperfusion. Several series of blood samples were obtained. At the end of the experiment, the animals were killed and necropsies undertaken in order to evaluate the antioxidant status of various visceral organs. The results link ischemia and reperfusion injury to a significant decline in antioxidative activity in various tissues. The weakening in antioxidant status after ischemic limb injury was most pronounced in the heart tissue, followed in descending order by the spleen, skeletal muscle, lung, liver, and kidney tissue. The levels of specific antioxidants and reactive oxygen species in various organs changed significantly, and the changes were tissue specific. Endogenous radical scavenging systems were not entirely overwhelmed in most of the tissues studied. But higher levels of malondialdehyde (MDA) found in cardiac tissue suggest that the production of oxygen free radicals is accelerated by an ischemic injury. Based on the study, we believe that the cardiac tissue is particularly susceptible to the effects of ischemia and reperfusion injury. Damage to cardiac tissue is probably the major cause of mortality following acute ischemic injury in a limb.

The influence of hydroxyapatite particles on osteoclast cell activities

Aseptic loosening after total joint arthroplasty is a major problem in orthopedic surgery. Small particles from material wear have been reported as the main cause of implant failure. For this reason, investigation into possible wear particles from the materials used in the implant may lead to longevity after arthroplasty. Hydroxyapatite (HA) has been extensively investigated and reported as an excellent biomaterial with excellent biocompatibility. In this study, we used an in vitro osteoblast/osteoclast model to test the biocompatibility of various-sized HA particles. Primary osteoclasts/osteoblasts were co-cultured with different-sized HA particles (0.5-3.0 microm, 37-53 microm, 177-205 microm, and 420-841 microm) for 3 h, 1 day, 3 days, and 7 days. Cellular responses to the HA particles were evaluated by changes in cell counts and the secretion of transforming growth factor (TGF-beta1), alkaline phosphatase (ALP), tumor necrosis factor (TNF-alpha), prostaglandin (PGE2), and lactate dehydrogenase (LDH) in the supernatant of the culture media. The results showed that osteoblasts/osteoclasts co-cultured with HA particles smaller than 53 microm undergo the most significant changes. Cellular counts significantly decreased, and the changes were more obvious in the osteoblast population. There also was a significant decrease in TGF-beta1 concentration and a significant increase in PGE2 and LDH concentration, but there were no changes in the TNF-alpha or ALP titer. It can be concluded that larger HA particles may be quite compatible with bone cells while smaller-sized HA particles can both activate the osteoclasts and decrease the cell population of the osteoblasts. Justification for the additional expense incurred with the use of hydroxyapatite in primary total hip arthroplasty should be further evaluated.

Scavenging effect of benzophenones on the oxidative stress of skeletal muscle cells

Benzophenone is an ultraviolet (UV)-absorbing agent that has been used in industry and medicine for more than 30 years. Consumers of cosmetics and sunscreens containing UV-absorbers are exposed to benzophenones on a daily basis, owing to the widespread use of these compounds. However, the efficacy of these compounds as scavengers of oxidative stress is still not well established. In the present study, we investigate the antioxidative capacity of six sunscreen benzophenone compounds. A primary myoblast culture was mixed in vitro with 100 microM menadione. The cytotoxic effect by menadione-induced oxidative stress was monitored by the lucigenin- or luminol-amplified chemiluminescence, methylthiotetrazole (MTT) assay, and the antioxidative effects of various benzophenone compounds were evaluated. The results showed that the addition of menadione can induce oxidative stress on myoblasts by superoxide and hydrogen peroxide production, which can be eradicated by superoxide dismutase (SOD) and catalase, respectively, in a dose-dependent mode. The catalase has a protective effect on the cytotoxicity induced by menadione as measured by the MTT assay, while the SOD does not. The selected benzophenones also have a significant scavenging effect on the menadione-induced cell death on the myoblasts. The ortho-dihydroxyl structure and other hydroxy groups in the same ring have a stronger scavenging effect on the superoxide anion on myoblasts; thus, a stable penoxy radical may be formed. The mechanism of this effect remains to be clarified.

The effect of sintered beta-dicalcium pyrophosphate particle size on newborn Wistar rat osteoblasts

During recent years, sintered dicalcium phosphate (SDCP) has been shown to be an effective artificial bone filler for repairing bone defects. The goal of this study was to elucidate the effect of SDCP particle size on osteoblasts. Osteoblasts were mixed and cultured with various sized SDCP particles (0.5-3.0, 37-63, 177-250, and 420-841 microns) for 1 h, 3 h, 1 day, 3 days, and 7 days and then analyzed. The results show that the adding of smaller sized SDCP particles (0.5-3.0 and 37-63 microns) into osteoblast culture can significantly affect the cell counts of osteoblasts. The secretion of transforming growth factor-beta 1, alkaline phosphatase, and prostaglandin E2 in culture medium increased significantly. The changes were most significant and persisted longer in smaller particle groups. Small sintered dicalcium phosphate particles can inhibit the proliferation of the osteoblasts. The inhibitory effects of the smaller sized SDCP particles on the osteoblasts were mediated by the promotion of osteoblast differentiation and the increased synthesis of prostaglandin E2.

Preparation of a biphasic porous bioceramic by heating bovine cancellous bone with Na4P2O7.10H2O addition

Sintered bovine cancellous bone exhibited excellent biocompatiblity, high porosity and have an interconnecting porous structure allowing for bone ingrowth. However, the main mineral constitution of sintered bovine bone-hydroxyapatite (Ca10(PO4)6(OH)2, HAP) seems to be too stable in vivo. For improving its bioactivity, the calcined bovine bone removing the organic substance by burning process-with different quantities of sodium pyrophosphate (Na4P2O7.10H2O, NP) addition was heated to a high temperature to transform its crystalline phase constitution from HAP into TCP/HAP biphasic or other multiphasic structures. Results revealed that the calcined bovine bone without NP addition, exhibited a pure form of HAP characterized pattern during heating. Its thermal behavior was similar to stoichiometric HAP, it gradually lost its OH- ions and transformed into oxyhydroxyapatite at high temperature. After being doped into calcined bovine bone, NP would react with HAP to form betaBTCP and NaCaPO4 around 600 degrees C. At 900 degrees C, doped NP would completely react with HAP and the NaCaPO4 would further react with HAP to form more betaBTCP in the system. With NP increasing in the calcined bovine bone, HAP would gradually convert into different crystalline phase compositions of TCP/HAP, TCP/HAP/NaCaPO4 or TCP/NaCaPO4 at high temperature. By heating calcined bovine cancellouse bone with different quantities of NP we could obtain different crystalline phase compositions of natural porous bioceramic in this study.

New junction models for alternate-strand triple-helix formation

BACKGROUND

[corrected] Oligonucleotide-directed triple-helix (triplex) formation can interfere with gene expression but only long tracts of oligopyrimidine*oligopurine sequences can be targeted. Attempts have been made to recognize short oligopurine sequences alternating on the two strands of double-stranded DNA by the covalent linkage of two triplex-forming oligonucleotides. Here we focus on the rational optimization of such an alternate-strand triplex formation on a DNA duplex containing a 5'-GpT-3'/3'-CpA-5' or a 5'-TpG-3'/3'-ApC-5' step by combination of (G,T)- and (G,A)-containing oligonucleotides that bind to the oligopurine strands in opposite orientations.

RESULTS

The deletion of one nucleotide in the reverse Hoogsteen region of the oligonucleotide provides the best binding at the 5'GpT-3'/3'-CpA-5' step, whereas the addition of two cytosines as a linker between the two oligonucleotides is the best strategy to cross a 5'-TpG-3'/3'-ApC-5' step. Energy minimization and experimental data suggest that these two cytosines are involved in the formation of two novel base quadruplets.

CONCLUSIONS

These data provide a rational basis for the design of oligonucleotides capable of binding to oligopurine sequences that alternate on the two strands of double-stranded DNA with a 5'-GpT-3'/3'-CpA-5' or a 5'-TpG-3'/3'-ApC-5' step at the junction.

Triple helix formation by (G,A)-containing oligonucleotides: asymmetric sequence effect

Sequence effects on the stability of purine-motif (also called (G, A)-motif) triple helix have been investigated through two symmetry-related systems: one of them had a 5'(GGA)43' core sequence of triplex-forming oligonucleotides (TFOs), whereas the other one had a reversed 5'(AGG)43' core sequence. These (G,A)-containing TFOs were prone to self-associate into intermolecular complexes at room temperature. The competition of TFOs' self-association with triple helix formation was assessed, and minimized. By varying the lengths and the terminal base sequences of TFOs, the following were found that (1) The stability of two triple helices with identical length and base composition but reverse strand orientation may be significantly different (up to a factor of 6). (2) When the 5'(GGA)43' core sequence was extended at the 3'-end by a G, the 13-nt TFO exhibited 3- and 5-fold higher affinity toward the target double-stranded DNA (dsDNA) than the longer 14-nt and 15-nt TFOs in which one and two A(s) were added at the 3'-end of the 13-nt TFO, respectively. In contrast, when the similar extensions occurred at the 5'-end of the 5'(AGG)43' core sequence, the length increase provided a higher binding affinity of TFOs toward the target duplex. (3) The nature of the base triplets involved at the ends of triple helices may have great influence on triplex stability. The observed asymmetric sequence effect of the (G,A)-motif triple helix formation is discussed in terms of the binding strength of the first base triplet(s) at the 3' end which seems to be deeply involved in the nucleation step of triple helix formation and therefore to be a determining factor for triplex stability.

Distinct gene arrangement in the Buzura suppressaria single-nucleocapsid nucleopolyhedrovirus genome

The genome organization of the Buzura suppressaria single-nucleocapsid nucleopolyhedrovirus (BusuNPV) was largely elucidated and compared to those of other baculoviruses. A detailed physical map was constructed for the restriction enzymes BamHI, BglI, BglII, EcoRI, HindIII, KpnI, PstI, XbaI and XhoI. The 120.9 kbp viral genome was cloned as restriction fragments into a plasmid library from which about 43.5 kbp of dispersed sequence information was generated. Fifty-two putative open reading frames homologous to those of other baculoviruses were identified and their location in the genome of BusuNPV was determined. Although the gene content of BusuNPV is similar to that of Autographa californica multiple-nucleocapsid nucleopolyhedrovirus, Bombyx mori nucleopolyhedrovirus and Orgyia pseudotsugata multiple-nucleocapsid nucleopolyhedrovirus, the gene order is, however, significantly different from that observed in the other viruses, which have a high degree of collinearity. A new approach (GeneParityPlot) was developed to represent the differences in gene order among baculoviruses when limited sequence information is available and to take advantage of the high degree of gene conservation. The data obtained show that BusuNPV is a distinct baculovirus species and the analyses suggest that gene distribution along baculovirus genomes may be used as a phylogenetic marker.

Optimization of alternate-strand triple helix formation at the 5'CpG3' and 5'GpC3' junction steps

Oligonucleotide-directed triple helix formation normally requires a long tract of oligopyrimidine.oligopurine sequence. This limitation can be partially overcome by alternate-strand triple helix (or switch triple helix) formation which enables recognition of alternating oligopurine/oligopyrimidine sequences. The present work is devoted to the optimization of switch triple helix formation at the 5'CpG3' and 5'GpC3' junction steps by combination of base triplets in Hoogsteen and in reverse Hoogsteen configurations. Rational design by molecular mechanics was first carried out to study the geometrical constraints at different junction steps and to propose a "switch code" which would optimize the interactions at junctions. These predictions were further checked and validated experimentally by gel retardation and DNase I footprinting assays. It was shown that the choice of an appropriate linker nucleotide in the switching third strand plays an important role in the interaction between oligonucleotides and alternating oligopurine/oligopyrimidine target sequences at different junctions: (i) the addition of a cytosine at the junction level in the oligonucleotide optimizes the crossover at the 5'CpG3' junction, whereas (ii) the best crossover at the 5'GpC3' junction step is achieved without any additional nucleotide. These results provide a useful guideline to extend double-stranded DNA sequence recognition by switch triple helix formation.

Preparation of high-temperature stabilized beta-tricalcium phosphate by heating deficient hydroxyapatite with Na4P2O7 x 10H2O addition

In this paper, the high-temperature stabilized beta-tricalcium phosphate (betaTCP, beta-Ca3(PO4)2) were prepared by heating the deficient HAP (d-HAP, Ca10-x(HPO4)x(PO4)6-x(OH)2-x) with tetra-sodium diphosphate decahydrate (NP, Na4P2O7 x 10H2O) addition. The betaTCP, d-HAP and d-HAP doped with 2.5, 5, 7.5 and 10 wt % NP were heated to different temperatures and were investigated by X-ray diffraction analysis (XRD) and Fourier-transformed infrared spectroscopy (FTIR). The results demonstrated that the HPO4(2-) of d-HAP condensed into P2O7(4-) occurred before 650 degrees C. The P2O7(4-) ions could be traced in the FTIR spectrum when the d-HAP was heated up to 750 degrees C. The reaction of P2O7(4-) with OH- did not occur instantly but over a wide range of temperatures. The d-HAP doped with NP would decrease the decomposition temperature of d-HAP. NP doped into d-HAP not only induced the d-HAP decomposition at lower temperature but also stabilized the betaTCP crystal structure at higher-temperature. It could also increase the conversion temperature of betaTCP to alphaTCP from 1180 degrees C up to 1300 degrees C. We could successfully prepare high-temperature (up to 1300 C) stabilized ffTCP by heating NP doped d-HAP.

Genetic organization of the HindIII-I region of the single-nucleocapsid nucleopolyhedrovirus of Buzura suppressaria

In order to investigate the genomic organization of the single-nucleocapsid nucleopolyhedrovirus (SNPV) of Buzura suppressaria (BusuNPV), the HindIII-I fragment located at map units (mu) 26.6-29.4 of the viral genome was sequenced. The fragment contained two partial and three complete open reading frames (ORFs) representing the 3' end of a polyhedron envelope protein gene (pep), a homologue of the AcMNPV ORF117, a conotoxin-like protein gene (ctl), an inhibitor of apoptosis gene (iap) and a superoxide dismutase gene (sod), respectively. These five genes were identified for the first time in a SNPV. Sequence analysis further revealed that these ORFs have the same conserved motifs and gene structure as those observed in their homologues from other baculoviruses. Between ctl and iap, an intergenic region of about 700 basepairs with structure similar to non-hr origins of DNA replication was observed. The genomic arrangement of the ORFs in the BusuNPV HindIII-I fragment is very different from the arrangement of their homologues in the genome of Autographa californica multiple nucleocapsid (M) NPV and other baculoviruses to date. Our data suggest that on the basis of gene arrangement, BusuNPV belongs to a distinct taxon within the Baculoviridae family, corroborating our previous conclusions derived from phylogeny analysis of several BusuNPV genes.