Gel fidelity assay measuring nucleotide misinsertion, exonucleolytic proofreading, and lesion bypass efficiencies.
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Base Sequence↗
Biomedical subjects
S Creighton
Publications and source records attributed to S Creighton.
Use of transvaginal ultrasonography with color Doppler imaging to determine an appropriate treatment regimen for uterine fibroids with a GnRH agonist before surgery: a preliminary study.
The aim was to obtain data that could be used to determine the most appropriate treatment regimen for uterine fibroids with a gonadotropin releasing hormone analog (goserelin) before surgery. Fifteen premenopausal women (aged 27-53 years; mean 40 years) were referred from a gynecological outpatients' clinic. They all had uterine fibroids and were awaiting hysterectomy or myomectomy. All women were scheduled to receive an implant of goserelin (3.6 mg), undergo transvaginal ultrasonography and have a sample of peripheral blood taken at monthly intervals for 6 months. The main outcome measures were fibroid size and indices of blood flow (the pulsatility index and peak systolic velocity) in both uterine arteries and the principal artery supplying the largest fibroid. The concentrations of follicle stimulating hormone, estradiol, luteinizing hormone and progesterone were measured in peripheral plasma. Twelve women (80%) completed 2 months of treatment, but only three (20%) completed the study (due to side-effects of the drug). After 2 months of treatment, the plasma hormone levels were all in the low-normal range; the mean fibroid volume had decreased by 53% and the mean peak systolic blood velocity in the fibroid artery had decreased by 45%. Mean changes in all indices were < 10% over the next 4 months of treatment. Six women (40%) had fibroids with an initial volume of > 100 ml; these tumors showed the largest reduction in size. We conclude that women with a uterine fibroid of > 100 ml are the best candidates for treatment with goserelin (3.6 mg/month) before surgery. Two months' treatment effects a marked reduction in fibroid volume and blood flow and is associated with good compliance.
Journal Article↗
Umbilical cord blood erythroblast count as an index of intrauterine hypoxia.
The relation of umbilical cord blood arterial pH, Apgar score, leucocyte count, and erythroblast count at delivery with the diagnosis of fetal distress in labour was studied prospectively in three groups of singleton pregnancies delivering at term vaginally (55 infants), by elective caesarean section (39 infants), or by emergency caesarean section for abnormal intrapartum fetal heart rate patterns (55 infants). In the emergency caesarean section group the umbilical cord blood arterial pH was significantly lower and the leucocyte and erythroblast counts were higher than in the elective caesarean section group. Comparison of the emergency caesarean section and spontaneous vaginal delivery groups showed significant differences for pH and erythroblast count, but not for leucocyte count. In the spontaneous vaginal delivery group erythroblastosis was associated with umbilical cord blood pH, whereas leucocytosis was associated with the length of labour. The five minute Apgar score was > or = 7 in all infants. This study suggests that leucocytosis is a non-specific response of the fetus to labour, whereas erythroblastosis reflects fetal tissue hypoxia.
Erythroblasts↗
Two cases of cervical pregnancy following in vitro fertilization and embryo transfer to the lower uterine cavity.
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Adult↗
Biochemical basis of DNA replication fidelity.
DNA polymerase is the critical enzyme maintaining genetic integrity during DNA replication. Individual steps in the replication process that contribute to DNA synthesis fidelity include nucleotide insertion, exonucleolytic proofreading, and binding to and elongation of matched and mismatched primer termini. Each process has been investigated using polyacrylamide gel electrophoresis (PAGE) to resolve 32P-labeled primer molecules extended by polymerase. We describe how integrated gel band intensities can be used to obtain site-specific velocities for addition of correct and incorrect nucleotides, extending mismatched compared to correctly matched primer termini and measuring polymerase dissociation rates and equilibrium DNA binding constants. The analysis is based on steady-state "single completed hit conditions", where polymerases encounter many DNA molecules but where each DNA encounters an enzyme at most once. Specific topics addressed include nucleotide misinsertion, mismatch extension, exonucleolytic proofreading, single nucleotide discrimination using PCR, promiscuous mismatch extension by HIV-1 and AMV reverse transcriptases, sequence context effects on fidelity and polymerase dissociation, structural and kinetic properties of mispairs relating to fidelity, error avoidance mechanisms, kinetics of copying template lesions, the "A-rule" for insertion at abasic template lesions, an interesting exception to the "A-rule", thermodynamic and kinetic determinants of base pair discrimination by polymerases.
Animals↗
A comparison of the fidelity of copying 5-methylcytosine and cytosine at a defined DNA template site.
5-Methylcytosine has been postulated to be an endogenous mutagen in procaryotes and eucaryotes leading to base substitution hot spots, C-->T transitions, resulting from spontaneous deamination of mC to T. The possibility remains, however, that a second mechanism involving mispairing of mC with A might also contribute to base substitution mutagenesis via G-->A transitions. Stimulation of the G-->A mutational pathway could involve preferential misincorporation of dAMP opposite template mC compared to C. To investigate this possibility, we synthesized a sequence containing mC at a defined template location. We compared the fidelity of copying mC versus C and the efficiency of extending mismatched base pairs at the mC position using three DNA polymerases, AMV reverse transcriptase, Drosophila DNA polymerase alpha, and mutant Escherichia coli Klenow fragment containing no proofreading exonuclease activity. Significant differences in misinsertion and mismatch extension efficiencies were observed only for the case of AMV reverse transcriptase. AMV reverse transcriptase was observed to incorporate dAMP 4 to 5-fold more efficiently opposite mC than C. Favored extension of a 5-MeC.A over C.A mispair was also observed with a difference of about 3-fold. In contrast to AMV reverse transcriptase, Klenow fragment showed no significant difference when copying either mC or C sites or when extending mispairs involving mC and C. Incorporation of dAMP opposite either C or mC was barely detectable using pol alpha, although pol alpha has been observed to form A.C mismatches in other sequences. While we cannot completely exclude the possibility that dAMP might be incorporated opposite mC in preference to C, our results suggest that contributions of the G-->A pathway to mC mutagenic hot spots are likely to be minor, lending additional support to the model invoking deamination of mC.
5-Methylcytosine↗
Base mispair extension kinetics. Binding of avian myeloblastosis reverse transcriptase to matched and mismatched base pair termini.
We investigate the enzymatic basis for the inefficient extension of single base mismatches by DNA polymerase compared with the extension of correct base pairs. Inefficient mismatch extension could result from either a reduced binding of the enzyme to mispaired versus correctly paired DNA template-primer termini, or from a lowered intrinsic rate of extension of mispairs by a bound enzyme, or from a combination of both factors. Avian myeloblastosis reverse transcriptase is used to measure the affinities (equilibrium dissociation constants) for the four matched and twelve mismatched base pair configurations situated at a primer 3'-terminus. The binding affinities are analyzed by two different assays employing polyacrylamide gels. The first assay uses steady-state kinetics to measure the efficiency of elongating correct and incorrect base pairs and to evaluate the enzyme's dissociation constants for matched and mismatched termini. The estimated KD values obtained in the steady-state analysis fall within a range of approximately 0.1-20 nM. The efficiencies of extending two of the mispairs, G.G and C.C, are too low to allow a determination of KD by the kinetics method. The second assay uses equilibrium binding to measure the ratio of polymerase bound to matched compared with mismatched termini, KDright/KDwrong. The affinity ratios, including values for G.G and C.C mispairs, are in the range of about 0.4-4.2. While around 1 order of magnitude difference is observed in the relative binding affinities of the polymerase for matched and mismatched primer termini, the relative extension efficiencies vary over more than 5 orders of magnitude. Therefore, it appears that inefficient mismatch extension is caused primarily by a kinetic block inhibiting elongation from mispaired primer 3'-termini rather than to a difference in binding.
Avian Myeloblastosis Virus↗
Role of arginine-38 in regulation of the cytochrome c oxidation-reduction equilibrium.
Arg-38 is an internal residue of mitochondrial cytochrome c that is close to heme propionate-7. Previous work comparing the behavior of cytochromes c from several species [Moore, G. R., Harris, D. E., Leitch, F. A., & Pettigrew, G. W. (1984) Biochim. Biophys. Acta 764, 331-342] has suggested that Arg-38 lowers the pKa of this propionate group and thereby accounts for the relative pH independence of the cytochrome c reduction potential from pH 5 to pH 8. The influence of Arg-38 on the oxidation-reduction equilibrium of yeast iso-1-cytochrome c has now been investigated by electrochemical, NMR, and theoretical analysis of six specifically mutated forms of this protein in which Arg has been replaced by Lys, His, Gln, Asn, Leu, or Ala. As the electron-withdrawing character of the residue at position 38 decreases, the reduction potential of the protein also decreases, with the largest decrease (ca. 50 mV) observed for the Ala variant. However, the variation in the reduction potentials of the mutants as a function of pH was similar to that observed for the wild-type protein. The effects of some of these mutations on the pKa values of His-33 and His-39 have been determined by NMR spectroscopy and found to be minimal. Calculations of the electrostatic free energy for the Leu-38 variant predict a decrease in the reduction potential of this mutant that is remarkably close to that observed experimentally. This work establishes that while Arg-38 contributes to the relatively high reduction potential of cytochrome c, this residue does not appear to be the sole functionality responsible for lowering the heme propionate-7 pKa.
Amino Acids↗
Integrated cystoscope: first rigid multipurpose operating cystoscope for local anesthetic endoscopy.
The Miller Integrated Cystoscope is the first small-diameter (17 Ch), rigid, multipurpose, operating cystoscope (biopsy, urethrotomy, ureteric catheterization, cutting, retrieval of stones and foreign bodies, and injection) designed with patient comfort in mind. Despite a small outside diameter, the 8.7-Ch instrument channel conducts a 7.5-Ch accessory including the unique rigid Endoknife, which converts it into an optical urethrotome and rigid Endoneedle which can deliver local anesthetic and other pharmacologic agents into the bladder, prostate, and urethra of both male and female patients. The simplicity of design has dispensed with the need for more costly and conventional instrumentation (e.g., optical urethrotome, Albarron lever) at a fraction of the cost. The urologist can not only inspect the lower urinary tract (Cf fiberscopes) but also perform endoscopic procedures short of a full transurethral prostatectomy with maximum patient comfort.
Ambulatory Surgical Procedures↗
Enzymes work by solvation substitution rather than by desolvation.
Considerable attention has recently been drawn to the hypothesis that enzymes catalyze their reactions by displacing solvent and creating an environment similar to the gas phase for the reacting substrates. This "desolvation hypothesis" is reexamined in this paper by defining a common reference energy for reactions in various environments. It is argued that consistent attempts to describe the actual energetics of enzymatic reactions, taking either gas phase or solution as a reference, would contradict the above hypothesis. That is, the enzyme does remove water molecules from its substrate, but substitutes these molecules for another polar environment (namely, its active site). By taking amide hydrolysis as an example, we use experimentally estimated solvation energies and analyze the reaction profile in the gas phase, in solution, and in enzyme active sites. We show that the gas-phase reaction is characterized by an enormous activation barrier (associated with forming the charged nucleophile from neutral fragments), although the nucleophilic attack is essentially barrierless. On the other hand, the enzyme and solution reactions are found to have similar reaction profiles, with a lower activation barrier for the enzymatic reaction. Presumably, the fact that previous analyses of this problem did not involve the construction of the relevant thermodynamic cycles (and quantitative estimates of the corresponding solvation energies) led to the desolvation hypothesis. Our conclusion is that enzyme active sites provide specific polar environments that do not resemble the gas phase but that are designed for electrostatic stabilization of ionic transition states and that "solvate" these states more than water does.
Binding Sites↗
A combined 2D-NMR and molecular dynamics analysis of the structure of the actinomycin D: d(ATGCAT)2 complex.
We present a comparative analysis of an NMR experiment and molecular and harmonic dynamics simulations of an actinomycin D: d(ATGCAT)2 complex. A comparison of NOE measurements and 1/R6 weighted proton-proton distances confirm the general correctness of the Actinomycin D-DNA model proposed by Sobell. There are, however, some substantial differences between the proton-proton distances inferred from the NOE results and the molecular and harmonic dynamics simulations. The remaining discrepancies could either come from contributions of other conformations to the average properties of the complex or from uncertainties in the NMR distance analysis. An analysis of the molecular dynamics helix properties, sugar puckers, hydrogen bonding, rms fluctuations and torsional properties are qualitatively consistent with those from previous simulations, but the presence of an intercalated drug leads to some new structural and dynamical features.
Chemical Phenomena↗
Artificial urinary sphincters--early experience.
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Adolescent↗
Computer modeling of actinomycin D interactions with double-helical DNA.
We have performed molecular mechanical calculations on intercalation complexes of actinomycin D with a series of base-paired hexanucleoside pentaphosphates; d(GCGCGC)2, d(GCCGGC)2, d(GCATGC)2, d(GCTAGC)2 and d(ATGCAT)2. Our results are in good agreement with previous experimental work on sequence selectivity. The results provide a rationalization for the strong preference of actinomycin D to intercalate on the 3' side of guanine residues, consistent with previously proposed models. Finally, the computed structures for d(ATGCAT)2-actinomycin D complexes have been compared with two-dimensional nuclear magnetic resonance nuclear Overhauser effect experimental results. To our knowledge, this is the first extensive comparison of molecular mechanical model structures for a drug-DNA complex with experimental solution phase data. We find generally good agreement between our computational models and the experimental solution phase structures.
Computers↗
Deaths from non-accidental injury in children.
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Child↗
Changes in lateral differentiation of head posture in the human neonate.
Developmental changes in the relationship between lateral differences in responsiveness and the assumption of asymmetrical head postures were examined. The head turning of 70 infants ranging in age from 0-72 hr was observed following a procedure (maintenance of the head in a midline position) known to reduce or eliminate lateral differences in the infant's response to stimulation. Even following this procedure infants older than 12 hr made significantly more right than left head turns whereas younger infants exhibited no such difference. When lateral differences in sensitivity were not interfered with in 0 to 12 hr old infants (n=20) they, kile the older infants, made significantly more right than left turns. These results are discussed in terms of possible developmental consequences of a reciprocity between asymmetric head position and lateral differences in sensitivity.
Age Factors↗