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H Torigoe

Publications and source records attributed to H Torigoe.

32 records · Page 2Linked to original sources
PubMed1995

Structural polymorphism and thermal stability of telomere DNAs (T2G4)n and (T4G4)n.

The ends of eukaryotic chromosomes, termed telomeres, contain a single-stranded 3' overhang composed of tandemly repeated guanine-rich sequences, such as (T2G4)n and (T4G4)n, along one strand. The sequences can form defined folded tetraplex structures. Here we have systematically examined structural polymorphism and thermal stability of a series of oligonucleotide sequences, Tet n: (T2G4)n and Oxy n: (T4G4)n (n = 1, 2, 3, 4), using circular dichroism (CD) spectroscopy. The CD spectra of Tet 1 and Oxy 1 are consistent with those observed in tetraplex structures consisting of four parallel strands (type I conformation); whereas the spectra of Tet 2, Oxy 2, Oxy 3, and Oxy 4 correspond with those observed for tetraplex conformations where the strands are antiparallel (type II conformation). The spectra of Tet 3 and Tet 4 suggests that Tet 3 and Tet 4 can adopt both type I and type II conformations and they are structurally polymorphic. The melting temperatures of Tet n and Oxy n (n = 1, 2, 3, 4) measured by CD melting are consistent with the previously reported values obtained from differential scanning calorimetry (DSC). Furthermore, the CD melting of Tet 4 suggests that the type II conformation of Tet 4 changes into type I conformation between 55 degrees C and 70 degrees C.

Base Sequence↗
PubMed1993

Thermodynamic and kinetic studies of DNA triplex formation of an oligohomopyrimidine and a matched duplex by filter binding assay.

The filter binding method was found to be a powerful method for studying the formation of triplexes composed of a single-stranded homopyrimidine and a duplex with a matched purine-pyrimidine tract. With this technique, we were able to determine thermodynamic and kinetic parameters for triplex formation between a homopyrimidine 19-mer (5'-TCCTCTTCTTTTCTTTCTT-3') and a duplex with sequence 5'-GCAGGAGAAGAAAAGAAAGAACG-3' for the purine strand. The experiments were performed over a wide pH range (3.8-7.4) and a temperature range of 0-35 degrees C. pH and temperature dependencies of the thermodynamic parameters were best explained in terms of a three-state model for triplex formation at low temperatures relative to the melting point. The main results were as follows: (1) pH dependence of the dissociation constants of the triplex is a result of the rapid acid-base equilibrium of pyrimidine single strands; (2) the association rate for triplex formation decreases with increasing pH in accordance with the dissociation constants; (3) the dissociation constant is virtually temperature-independent at low pH, while it becomes strongly temperature-dependent with increasing pH (these results can be explained in terms of a negative, non-zero delta Cp for triplex formation at low pH); (4) the association rate decreases with increasing temperature, and the resulting negative activation energy indicates that the triplex formation process involves a quasi-stable intermediate; (5) the triplex formation is a second-order reaction at low pH, whereas it can be interpreted as a third-order reaction at neutral pH, suggesting that different triplex formation pathways are observed depending on the pH.

Base Sequence↗
PubMed1993

Thermodynamic and kinetic analyses of DNA triplex formation: application of filter-binding assay.

We have developed a simple and efficient method for studying equilibrium thermodynamics and kinetics of DNA triplex formation, which utilizes a filter-binding procedure. The application of this method to the triplex formation between a double-stranded homopurine-homopyrimidine and a single-stranded homopyrimidine oligonucleotides has demonstrated its ability in the quantitative estimation of equilibrium binding constants and rate constants under various conditions. Thus, this simple method can serve as a powerful tool for the systematic analysis of sequence and environmental effects on the equilibrium and kinetic quantities in the triplex formation.

Base Sequence↗
PubMed1993

Mechanism of DNA triplex formation and its specificity as studied by filter binding assay.

The filter binding method was found to be a very useful method for triple-helical formation of oligo DNA duplexes with homoprymidine single-strands. Using this method, we have obtained dissociation constants of triplexes and association rates of triple-helical formation of a variety of combinations of double-strands (23-mer) and pyrimidine single-strands as functions of pH and temperature. pH dependences of dissociation constants and association rates are theoretically discussed in terms of acid-base equilibrium of pyrimidine strands. Temperature-dependence of dissociation constants and association rates were considerably different between acidic and neutral pH range, suggesting that mechanism of triple-helical formation differs between two pH ranges. The results were best interpreted in terms of a three-state model for the triple-helical formation. Furthermore, the effect of mismatched sequences on the stability of the triplexes were also discussed.

Base Sequence↗
PubMed1993

Thermodynamics of tetraplex DNAs, (T2G4)n and (T4G4)n.

The ends of eukaryotic chromosomes, termed telomeres, contain stretches of tandemly repeated guanine-rich sequences, such as (T2G4)n and (T4G4)n, along one strand. These sequences can form defined folded tetraplex structures in solution. Here we have systematically investigated the thermodynamic properties of a series of sequences, Tet n: (T2G4)n and Oxy n: (T4G4)n (n = 1, 2, 3, 4), in 10mM NaPi, 250mM NaCl, pH7.0, using differential scanning calorimetry (DSC). The melting process of all tetraplex DNAs is reversible. Tet n and Oxy n are similar in the dependence of melting temperature, Tm, and transition calorimetric enthalpy per strand, delta Hcal, on the number of the tandem sequence. The total delta Hcal value of Tet n is similar in magnitude to that of Oxy n, whereas the Tm value of the main fraction of Tet n is greater than that of Oxy n. These results suggest that Tet n and Oxy n form similar tetraplex DNA configuration, and the difference in Tm values between Tet n and Oxy n is attributed to the length of the T strings.

Calorimetry, Differential Scanning↗
PubMed1992

Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures.

The three-dimensional solution structure of the recombinant B domain (FB) of staphylococcal protein A, which specifically binds to the Fc portion of immunoglobulin G, was determined by NMR spectroscopy and hybrid distance geometry-dynamical simulated annealing calculations. On the basis of 692 experimental constraints including 587 distance constraints obtained from the nuclear Overhauser effect (NOE), 57 torsion angle (phi, chi 1) constraints, and 48 constraints associated with 24 hydrogen bonds, a total of 10 converged structures of FB were obtained. The atomic root mean square difference among the 10 converged structures is 0.52 +/- 0.10 A for the backbone atoms and 0.98 +/- 0.08 A for all heavy atoms (excluding the N-terminal segment from Thr1 to Glu9 and the C-terminal segment from Gln56 to Ala60, which are partially disordered). FB is composed of a bundle of three alpha-helices, i.e., helix I (Gln10-His19), helix II (Glu25-Asp37), and helix III (Ser42-Ala55). Helix II and helix III are antiparallel to each other, whereas the long axis of helix I is tilted at an angle of about 30 degrees with respect to those of helix II and helix III. Most of the hydrophobic residues of FB are buried in the interior of the bundle of the three helices. It is suggested that the buried hydrophobic residues form a hydrophobic core, contributing to the stability of FB.(ABSTRACT TRUNCATED AT 250 WORDS)

Amides↗
PubMed1992

A dopamine D1 receptor antagonist, SCH 23390, selectively blocks vasopressin release after noxious stimuli in the rat.

Effects of a dopamine D1 receptor antagonist, SCH 23390, were investigated on plasma level of vasopressin after stressful stimuli in rats. The antagonist markedly attenuated the increase in plasma level of vasopressin after electric footshocks but not after s.c. injected hypertonic saline. The antagonist, however, did not significantly change the suppressive vasopressin response to fear-related emotional stress, though the drug suppressed motor behavior of the rat during testing period. These data suggest that dopamine D1 receptors play an important role selectively in the facilitatory vasopressin response to noxious stimuli in rats.

Animals↗
PubMed1990

Sequential 1H NMR assignments and secondary structure of the B domain of staphylococcal protein A: structural changes between the free B domain in solution and the Fc-bound B domain in crystal.

The recombinant B domain (FB) of staphylococcal protein A, which specifically binds to the Fc portion of immunoglobulin G (IgG), has been investigated with the use of two-dimensional proton nuclear magnetic resonance spectroscopy. All backbone and side-chain proton resonances of FB (60 amino acid residues), except the amide proton resonance of Ala2, were assigned by the sequential assignment procedures by using double-quantum-filtered correlated spectroscopy (DQF-COSY), homonuclear Hartmann-Hahn spectroscopy (HOHAHA), and nuclear Overhauser enhancement spectroscopy (NOESY). On the basis of the NOESY data, three helical regions, Glu9-His19, Glu25-Asp37, and Ser42-Ala55, were identified in the free FB in solution. Existence of two of the three helical regions, Glu9-His19 and Glu25-Asp37, in consistent with the X-ray crystallographic structure of the Fc-bound FB [Deisenhofer, J. (1981) Biochemistry 20, 2361-2370]. By contrast, in the Fc-bound FB as revealed by the X-ray analysis, the Ser42-Glu48 segment is extended and no structural information has been available in the Ala49-Ala55 segment. We suggest that a significant conformation change is induced in the C-terminal region of FB when it is bound to the Fc portion of IgG.

Amino Acid Sequence↗
PubMed1990

15N nuclear magnetic resonance studies of the B domain of staphylococcal protein A: sequence specific assignments of the imide 15N resonances of the proline residues and the interaction with human immunoglobulin G.

15N nuclear magnetic resonance (NMR) studies of the B domain (FB) of Staphylococcus protein A, which is uniformly labeled with 15N, are reported. The alpha CH(i)-15N(i) connectivity in the 1H-15N HMBC spectrum and the 13C(i-1)-15N(i) spin coupling in the 15N spectrum of a 13C-, 15N-doubly labeled FB were used to establish the assignments of the imide 15N resonances for all three Pro residues that exist in FB. Addition of human IgG caused a significant downfield shift of the Pro-39 resonance. This result is quite consistent with our previous suggestion that a significant conformation change is induced in the Ser-42-Ala-55 helical region of FB when it is bound to human IgG.

Binding Sites↗
PubMed1989

Experience with the ultrasonic surgical aspirator in a cavernous hemangioma of the cavernous sinus.

A patient with a cavernous hemangioma of the cavernous sinus was operated upon using the Cavitron Ultrasonic Surgical Aspirator (CUSA). Intracapsular subtotal removal of the tumor was accomplished efficiently with the CUSA. At the end of the procedure, however, the CUSA penetrated not only the capsule of the tumor, but also the wall of the internal carotid artery. Advantages and disadvantages of CUSA surgery for cavernous hemangiomas of the cavernous sinus are discussed.

Adult↗
PubMedDate not supplied

Novel class of DNA binding motifs based on bistetrahydrofuran and bisfuran skeleton with long alkyl chains.

Small molecules with DNA-binding affinity within the minor groove have become of great interest. In this paper, new DNA binding molecules; diamino-bistetrahydrofuran (bisTHF) and diamino-bisfuran are reported. The bisTHF ligand with RR configuration at the amino groups and C8 alkyl chains (RR8) stabilized GC-rich duplex. In contrast, bisfuran compounds stabilized AT-rich duplex. The binding affinity of RR8 with 12 mer duplex DNA was determined by isothermal titration calorimetry to be 3.3 x 10(8) M-1.

Binding Sites↗
PubMedDate not supplied

Promotion of triplex formation by 2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA) modification: thermodynamic and kinetic studies.

We analyzed the effect of 2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA) modification of triplex-forming oligonucleotide (TFO) on pyrimidine motif triplex formation at neutral pH, a condition where pyrimidine motif triplexes are unstable. The binding constant of the pyrimidine motif triplex formation at pH 6.8 with 2',4'-BNA modified TFO was about 20 times larger than that observed with unmodified TFO. The observed increase in the binding constant at neutral pH by the 2',4'-BNA modification resulted from the considerable decrease in the dissociation rate constant.

DNA↗