Direct cost analysis of genetic testing for CYP2C19*2 and *3 loss of function variants in percutaneous coronary intervention patients

Background/Introduction

Patients with CYP2C19*2 or *3 loss of function (LOF) variants who undergo percutaneous coronary intervention (PCI) have an increased risk of ischemic events when treated with clopidogrel.

Purpose

A subgroup of patients who were included in the TAILOR-PCI trial were also enrolled in this study to determine if a genotype-guided (GG) approach based on CYP2C19*2 or *3 LOF variants is cost-effective.

Methods

Patients were randomized to the conventional therapy group with clopidogrel and to the GG group who underwent point of care genotype testing for CYP2C19*2 or *3 LOF variants. In the GG group, therapy was based on genotype results. Those identified as LOF carriers were prescribed ticagrelor while non-carriers were prescribed clopidogrel.

Results

There were no significant differences in direct medical costs between the conventional therapy group and GG group (mean $19,747 versus $20,682, p=0.11), however total costs were significantly greater in the GG group which was primarily driven by the outpatient cost of ticagrelor. Furthermore, there was no significant cost difference between ticagrelor treated LOF carriers and clopidogrel treated non-carriers.

Conclusion

These findings suggest that a GG approach with point of care testing for CYP2C19*2 or *3 LOF variants in patients undergoing PCI may be a cost-effective practice.

Funding Acknowledgement

Type of funding sources: Private grant(s) and/or Sponsorship. Main funding source(s): NIH grants

COMPARATIVE ANALYSIS OF CARBOXYMETHYL CELLULOSE AND PARTIALLY HYDROLYZED POLYACRYLAMIDE – LOW-SOLID NONDISPERSED DRILLING MUD WITH RESPECT TO PROPER-TY ENHANCEMENT AND SHALE INHIBITION

During drilling, different problems are encountered that can interfere with smooth drilling processes, including the accumulation of cuttings, reduced penetration rates, pipe sticking, loss of wellbore stability, and loss of circulation. These problems are generally encountered with conventional drilling mud, such as the bentonite–barite mud system. Formation damage is the most common problem encountered in bentonite mud systems with high solid content. In this work, we aimed to formulate two low-solid nondispersed (LSND) muds: carboxymethyl cellulose (CMC)–LSND mud and partially hydrolyzed polyacrylamide (PHPA)–LSND mud. A comparative analysis was performed to evaluate their property enhancements. LSND muds aid in maintaining hole stability and proper cutting removal. The results of this work show that the addition of both CMC and PHPA helps to improve drilling fluid properties; however, the PHPA–LSND mud was found to be superior. Shale swelling is a major concern in the petroleum industry, as it causes various other problems, such as pipe sticking, low penetration rates, and bit wear. The effect of these two LSND polymer muds in inhibiting shale swelling was analyzed using shale collected from the Champhai district of Mizoram, India.

Molecular typing of dengue viruses circulating in Assam, India during 2016-2017

BACKGROUND & OBJECTIVES

The global incidence of dengue has grown dramatically in recent decades and Assam, India has witnessed several outbreaks of dengue since 2015. Although during post-monsoon months (September to December), most cases of dengue in Assam are recorded but incidence of dengue in Assam has been slowly changing from being endemic to being hyper endemic. Therefore, this study was carried out to determine the serotypes and genotypes of dengue virus prevalent in Assam during the period of 2016-2017.

METHODS

This is a prospective study conducted for a period of two years from 2016 to 2017. Department of Microbiology, Gauhati Medical College and Hospital (GMCH) had received a total of ~12000 and ~9000 sera sample during 2016 and 2017 respectively for confirmation of clinically suspected dengue cases. For confirmation, dengue NS1 antigen and IgM antibody ELISA tests were performed. Multiplex RT-PCR was performed for serotyping of dengue viruses and representative samples found positive in PCR were sequenced to determine the genotypes of circulating dengue virus serotypes.

RESULTS

In the year 2016, 6157 sera samples and in 2017, 3386 sera samples were found positive in ELISA test. A total of 157 dengue positive sera samples representing 17 districts of Assam were further tested by multiplex RT-PCR for serotyping of the virus. In PCR, out of 157, 107 samples (68.15%) were found positive for the presence of dengue virus genome. Out of 107, 74 samples (69.15%) were positive for dengue virus serotype-1 (DENV-1), 32 samples (29.90%) for dengue virus serotype-2 (DENV-2) and one sample (0.93%) positive for dengue virus serotype-3 (DENV-3). Out of 107 PCR positive samples, 25 samples were sequenced to identify their genotypes. Phylogenetic analysis of sequenced dengue viruses revealed that all the seven DENV-1 strains were genotype V, 17 DENV-2 strains were genotype IV (Cosmopolitan genotype) and one DENV-3 strain was genotype III.

INTERPRETATION & CONCLUSION

These findings improve our knowledge of circulating dengue virus serotypes in Assam. Co-circulation of three serotypes of dengue virus highlights the need for establishment of active dengue surveillance. The genotypic data of our findings will be helpful for future dengue molecular epidemiology studies and to control the disease in the region.

Seroprevalence of Rotavirus infection in pig population of Arunachal Pradesh

AIM

This study was conducted to find out the seroprevalence of Rotavirus(RV) infection among the pig population of Arunachal Pradesh.

MATERIALS AND METHODS

Serums samples were collected from piglets of age ranging from 1 week to 6 months and the sows associated with the piglets that were reared under organized and unorganized system of management in six different districts of Arunachal Pradesh. The prevalence of RV specific antibodies was detected using a polyclonal antibody-based indirect enzyme-linked immunosorbent assay (i-ELISA).

RESULTS

The study revealed that out of 394 serum samples, 255 (64.72%) samples were found to be positive for RV-specific antibody in i-ELISA. Considering the samples from different districts, Papumpare district of Arunachal Pradesh showed highest numbers of seropositive animals (68.75%) followed by upper Subansiri (64.91%) while West Siang district showed lowest positivity rate (61.22%).

CONCLUSION

As considerable seropositivity was recorded among pig population of Arunachal Pradesh in this study, there is urgent need to establish high-impact and cost-effective public health intervention tools, key among them being the introduction of strict hygiene practice and RV vaccination program, to greatly reduce the number of deaths due to diarrheal diseases. To the authors' knowledge, this is the first report on the prevalence of RV infection from pigs of Arunachal Pradesh.

Development of an effective and efficient DNA isolation method for Cinnamomum species

Different species of Cinnamomum are rich in polysaccharide's and secondary metabolites, which hinder the process of DNA extraction. High quality DNA is the pre-requisite for any molecular biology study. In this paper we report a modified method for high quality and quantity of DNA extraction from both lyophilized and non-lyophilized leaf samples. Protocol reported differs from the CTAB procedure by addition of higher concentration of salt and activated charcoal to remove the polysaccharides and polyphenols. Wide utility of the modified protocol was proved by DNA extraction from different woody species and 4 Cinnamomum species. Therefore, this protocol has also been validated in different species of plants containing high levels of polyphenols and polysaccharides. The extracted DNA showed perfect amplification when subjected to RAPD, restriction digestion and amplification with DNA barcoding primers. The DNA extraction protocol is reproducible and can be applied for any plant molecular biology study.

Long-term risedronate treatment normalizes mineralization and continues to preserve trabecular architecture: sequential triple biopsy studies with micro-computed tomography

The objective of the study was to assess the time course of changes in bone mineralization and architecture using sequential triple biopsies from women with postmenopausal osteoporosis (PMO) who received long-term treatment with risedronate. Transiliac biopsies were obtained from the same subjects (n = 7) at baseline and after 3 and 5 years of treatment with 5 mg daily risedronate. Mineralization was measured using 3-dimensional (3D) micro-computed tomography (CT) with synchrotron radiation and was compared to levels in healthy premenopausal women (n = 12). Compared to the untreated PMO women at baseline, the premenopausal women had higher average mineralization (Avg-MIN) and peak mineralization (Peak-MIN) by 5.8% (P = 0.003) and 8.0% (P = 0.003), respectively, and lower ratio of low to high-mineralized bone volume (BMR-V) and surface area (BMR-S) by 73.3% (P = 0.005) and 61.7% (P = 0.003), respectively. Relative to baseline, 3 years of risedronate treatment significantly increased Avg-MIN (4.9 +/- 1.1%, P = 0.016) and Peak-MIN (6.2 +/- 1.5%, P = 0.016), and significantly decreased BMR-V (-68.4 +/- 7.3%, P = 0.016) and BMR-S (-50.2 +/- 5.7%, P = 0.016) in the PMO women. The changes were maintained at the same level when treatment was continued up to 5 years. These results are consistent with the significant reduction of turnover observed after 3 years of treatment and which was similarly maintained through 5 years of treatment. Risedronate restored the degree of mineralization and the ratios of low- to high-mineralized bone to premenopausal levels after 3 years of treatment, suggesting that treatment reduced bone turnover in PMO women to healthy premenopausal levels. Conventional micro-CT analysis further demonstrated that bone volume (BV/TV) and trabecular architecture did not change from baseline up to 5 years of treatment, suggesting that risedronate provided long-term preservation of trabecular architecture in the PMO women. Overall, risedronate provided sustained benefits on mineralization and architecture, two key determinants of bone strength, over 5 years lending support for its long-term efficacy in fracture risk reduction.

Risedronate preserves bone architecture in early postmenopausal women in 1 year as measured by three-dimensional microcomputed tomography

Risedronate reduces the risk of vertebral fractures by up to 70% within the first year of treatment. Increases in bone mineral density or decreases in bone turnover markers explain only a portion of the anti-fracture effect, suggesting that other factors, such as changes in trabecular bone architecture, also play a role. Our objective was to determine the effects of risedronate on bone architecture by analyzing iliac crest bone biopsy specimens using three-dimensional microcomputed tomography (3-D micro CT). Biopsy specimens were obtained at baseline and after 1 year of treatment from women enrolled in a double-blind, placebo-controlled study of risedronate 5 mg daily for the prevention of early postmenopausal bone loss. Trabecular architecture deteriorated in the placebo group (n = 12), as indicated by a 20.3% decrease in bone volume (25.1% vs. 20.0%, P = 0.034), a 13.5% decrease in trabecular number (1.649 vs. 1.426 mm(-1), P = 0.052), a 13.1% increase in trabecular separation (605 vs. 684 microm, P = 0.056), and an 86.2% increase in marrow star volume (3.251 vs. 6.053 mm(3), P = 0.040) compared with baseline values. These changes in architectural parameters occurred in the presence of a concomitant decrease from baseline in lumbar spine bone mineral density (-3.3%, P = 0.002), as measured by dual energy x-ray absorptiometry. There was no statistically significant ( P < 0.05) deterioration in the risedronate-treated group (n = 14) over the 1-year treatment period. Comparing the actual changes between the two groups, the placebo group experienced decreases in bone volume (placebo, -5.1%; risedronate, +3.5%; P = 0.011), trabecular thickness (placebo, -20 microm; risedronate, +23 microm; P = 0.032), and trabecular number (placebo, -0.223 mm(-1); risedronate, +0.099 mm(-1); P = 0.010), and increases in percent plate (placebo, +2.79%; risedronate, -3.23%; P = 0.018), trabecular separation (placebo, +79 microm; risedronate, -46 microm; P = 0.010) and marrow star volume (placebo, +2.80 mm(3); risedronate, -2.08mm(3); P = 0.036), compared with the risedronate group. These data demonstrate that trabecular architecture deteriorated significantly in this cohort of early postmenopausal women, and that this deterioration was prevented by risedronate. Although there is no direct link in this study between fracture and preservation of architecture, it is reasonable to infer that the preservation of bone architecture may play a role in risedronate's anti-fracture efficacy.

The influence of nutritional and environmental conditions on the accumulation of poly-beta-hydroxybutyrate in Bacillus mycoides RLJ B-017

AIMS

To optimize the nutritional and environmental conditions for growth of and poly-beta-hydroxybutyrate (PHB) accumulation in Bacillus mycoides RLJ B-017.

METHODS AND RESULTS

An isolate, identified as B. mycoides, was grown on different sources of carbon and nitrogen. Among these, sucrose, beef extract and di-ammonium sulphate were found to be the most suitable for growth and PHB accumulation. The overall maximum value of PHB (%) in cells, PHB yield (Yp/s) and productivities (Qp and qp) were 69.4 +/- 0.4% dry cell weight (DCW), 0.21 gp gS(-1), 0.104 +/- 0.012 gp l(-1) h(-1) and 0.03 gp gx(-1) h(-1), respectively when grown in a medium containing 20 gs l(-1) sucrose, supplemented with di-ammonium sulphate. The addition of beef extract increased the value of PHB (%) in cells, PHB yield and productivities by 17.58 +/- 0,3, 23.8, 19.23 +/- 0.3 and 13.8 +/- 0.2% , respectively. The overall maximum values of PHB (% DCW), PHB yield and productivities were obtained at pH 7.0 +/- 0 .1, temperature 30 +/- 0.5 degrees C, agitation 650 rev min(-1) and oxygen transfer rate 3.8 mmol O(2) l(-1) h(-1).

CONCLUSIONS

Sucrose, glucose and fructose were found to be more suitable for cell growth and PHB accumulation, but sucrose was less expensive than glucose. Among the nitrogen sources, beef extract and di-ammonium sulphate promoted PHB synthesis. The accumulation of PHB was observed to be growth associated.

SIGNIFICANCE AND IMPACT OF THE STUDY

Gram-positive bacteria have not been reported to accumulate large amounts of polyhydroxyalkanoate and hence have not been considered as potent candidates for industrial production. A number of Bacillus spp. have been reported to accumulate 9-44.5% DCW PHB. By comparison, Bacillus RLJ B-017 contained 69.4 +/- 0.4% DCW PHB. Therefore, this strain has been considered as a potent organism for industrial interest. A relatively high yield of PHB was obtained in this wild strain and PHB synthesis was independent of nutrient limitation. The conditions for the higher PHB yield and productivity will be optimized in the next phase using fed-batch culture.

Three-dimensional microimaging (MRmicroI and microCT), finite element modeling, and rapid prototyping provide unique insights into bone architecture in osteoporosis

With the proportion of elderly people increasing in many countries, osteoporosis has become a growing public health problem, with rising medical, social, and economic consequences. It is well recognized that a combination of low bone mass and the deterioration of the trabecular architecture underlies osteoporotic fractures. A comprehensive understanding of the relationships between bone mass, the three-dimensional (3D) architecture of bone and bone function is fundamental to the study of new and existing therapies for osteoporosis. Detailed analysis of 3D trabecular architecture, using high-resolution digital imaging techniques such as magnetic resonance microimaging (MRmicroI), micro-computed tomography (microCT), and direct image analysis, has become feasible only recently. Rapid prototyping technology is used to replicate the complex trabecular architecture on a macroscopic scale for visual or biomechanical analysis. Further, a complete set of 3D image data provides a basis for finite element modeling (FEM) to predict mechanical properties. The goal of this paper is to describe how we can integrate three-dimensional microimaging and image analysis techniques for quantitation of trabecular bone architecture, FEM for virtual biomechanics, and rapid prototyping for enhanced visualization. The integration of these techniques provide us with an unique ability to investigate the role of bone architecture in osteoporotic fractures and to support the development of new therapies.

Growth-associated production of poly-3-hydroxybutyrate by Bacillus mycoides

Bacillus mycoides strain RIJ B-017, a growth-associated poly-3-hydroxybutyrate (PHB) producer was grown on sucrose-containing media. PHB accumulated in cells up to 72% of dry cell mass. The overall maximum value of PHB yield (Yp/s) and productivities (Qp and qp) 250 mgp/gs, 120 mgp L-1 h-1 and 30 mgp gx-1 h-1, respectively, were obtained at 15 g/L sucrose. Differential scanning calorimeter heating curve showed two peaks, one at 95.9 degrees C and another at 165.4 degrees C with a shoulder around 154.6 degrees C. The viscosity-average molar mass in chloroform at 27 degrees C was 505 kDa. The carbon content of PHB was 55.4% of the mass.

Evaluation of changes in trabecular bone architecture and mechanical properties of minipig vertebrae by three-dimensional magnetic resonance microimaging and finite element modeling

The study objective was to analyze the three-dimensional (3D) trabecular architecture and mechanical properties in vertebral specimens of young and mature Sinclair minipigs to assess the relative contribution of architecture to bone strength. We used 3D magnetic resonance microimaging (MRmicroI) and direct image analysis to evaluate a set of standard structural measurements and new architectural descriptors of trabecular bone in biopsy specimens from L2, L3, and L4 vertebrae (n = 16 in each group) from young (mean age, 1.2 years) and mature (mean age, 4.8 years) minipigs. The measurements included bone volume/tissue volume (BV/TV), marrow star volume (Ma.St.V), connectivity density (ConnD), and two new parameters, percent platelike trabeculae (% plate) and percent bone in the load direction (% boneLD). The % plate, calculated from surface curvature, allowed the delineation of plates from rods. The % boneLD quantified the percentage of bone oriented along the long axis of the vertebral body. We showed that 3D MRmicroI can detect the subtle changes in trabecular architecture between the two age groups. ConnD, star volume, % plate, % boneLD, and BV/TV were found to be more effective than the model-based, derived indices (trabecular thickness [Tb.Th], trabecular separation [Tb.Sp], and trabecular number [Tb.N]) in differentiating the structural changes. BV/TV, % plate, and % boneLD significantly increased (p < 0.05) in all three vertebral sites of the mature minipigs. The significant decrease in ConnD and star volume in the mature vertebra was consistent with the concurrent increase of platelike trabecular bone (p < 0.05). Overall, ConnD, star volume, % plate, and % boneLD provided a coherent picture of the architectural changes between the two age groups. Apparent modulus and maximum stress were determined experimentally on biopsy specimens from L2 vertebrae (n = 16). When apparent modulus was predicted using 3D MRmicroI data sets as input for finite element modeling (FEM), the results were similar to the experimentally determined apparent modulus (p = 0.12). Both methods were then used to compare the young and the mature animals; the experimental and predicted apparent modulus were significantly higher for the mature group (p = 0.003 and 0.012, respectively). The experimental maximum stress in the vertebra of the mature animals was twice as high as that for the young animals (p = 0.006). Bone quantity (BV/TV or bone mineral content [BMC]) alone could explain approximately 74-85% of the total variability in stress and modulus. The inclusion of either ConnD or % boneLD with BV/TV in a multiple regression analysis significantly improved the predictability of maximum stress, indicating that architecture makes additional contributions to compressive strength in normal minipig vertebra.

Bone architecture and image synthesis

3-D bone architecture can now be measured by micro-computer tomography or micro-magnetic resonance imaging. The principles of the micro-computer technique is reviewed and new architectural parameters can be computed. In addition, the method allows the contruction of polymer models by stereolithography, a method that can be used to perform repetitive mechanical studies on the same bone sample. These non destructive methods are interesting in the pre-clinical studies on bone diseases and in the investigation of animal trials on new pharmacological compounds active on bone.

Application of LC-NMR and LC-MS to the identification of degradation products of a protease inhibitor in dosage formulations

LC-NMR and LC-MS were applied to the characterization of six degradation products of a protease inhibitor, N-hydroxy-1,3-di-[4-ethoxybenzenesulphonyl]-5,5-dimethyl-[1,3]c yclohexyldiazine-2-carboxamide, in a dosage formulation. A reversed-phase HPLC method was developed for the separation of the parent compound and its six degradation products. LC-MS was then utilized to obtain the molecular weight and fragmentation information using an electrospray ionization (ESI) interface in the positive ion mode. LC-NMR was employed to acquire detailed structural information using a selective solvent suppression pulse sequence in the stop flow mode. This work demonstrated the usefulness of this integrated approach for the rapid and unambiguous identification of drug compounds and their degradation products in dosage formulations.

Effect of prostaglandin and bisphosphonate on cancellous bone volume and structure in the ovariectomized rat studied by quantitative three-dimensional nuclear magnetic resonance microscopy

The purpose of this work was to evaluate the potential of nuclear magnetic resonance microscopy (NMRM) in conjunction with a processing technique to monitor the effect of preventive agents in an ovariectomized (OVX) rat. Twenty-five female Sprague-Dawley rats were OVX at 6 months of age (except for the intact control group), allowed to lose bone for 60 days, and then treated for 60 days. During treatment, animals were administered vehicle, prostaglandin E2 (PGE2; 6 mg/kg), or alendronate (3 microg/kg) subcutaneously once a day. Subsequently, tibiae were harvested and the marrow removed. NMRM was carried out at 9.4 T, with the specimens immersed in 1.2 mM diethylenetriaminepentaacetic acid-gadolinium salt (Gd-DTPA) aqueous solution. A three-dimensional (3D) partial flip-angle pulse sequence was used, providing a 1283 array of (46 microm)3 isotropic voxels. Fifty of the 128 axial images in the 3D data set comprising approximately 2.4 mm volume distal to the growth plate were processed from each specimen using a probability-based method for determining bone volume fraction (BVF), tubularity, contiguity, as well as the mean trabecular plate thickness and separation. PGE2 and alendronate altered BVF consistently at all tibial regions. The effect of alendronate was to keep BVF about midway between intact and OVX, whereas PGE2 returned BVF to intact levels. The other parameters showed similar responses to treatment. The strongest discriminator was trabecular BVF, which could obviously differentiate the groups. The study establishes NMRM as a nondestructive histomorphometric method for the quantitative evaluation of drug response in a rat ovariectomy model.

A quantitative one-dimensional magnetic resonance imaging technique in adjuvant arthritis: the assessment of disease progression and indomethacin efficacy

OBJECTIVE

To demonstrate the use of a one-dimensional proton (1H) nuclear magnetic resonance (NMR) imaging technique to noninvasively monitor the progression of adjuvant arthritis and its response to indomethacin treatment in Lewis rat leg joints.

METHODS

The total hydrogen content of a defined volume of the joint was quantitated at selected time points. The differences in proton T2 relaxation times allowed for characterization and quantitative separation of the fluid (relatively long T2) and nonfluid (relatively short T2) components of hydrogen content in the defined volume. The estimates of hydrogen content of both long and short T2 tissue components were used to assess the severity of the disease and its regression with indomethacin treatment.

RESULTS

A progressive increase of the 2 components of hydrogen content in saline treated arthritic rats is consistent with histological examinations. After 19 days of treatment, 0.1 mg/kg/day and 0.5 mg/kg/day of indomethacin reduced the fluid component (primarily from inflammatory edema) in arthritic leg joints by 39 and 77% respectively, compared to the saline treated arthritic rats. The higher dose of indomethacin also significantly reduced the nonfluid component (primarily from cellular content) suggesting a reduced influx of inflammatory cells into the affected areas. The paw volume measurements, radiologic changes, and histopathology also showed the regression of adjuvant arthritis on treatment.

CONCLUSION

The study demonstrated that the NMR method has the sensitivity required to assess the treatment efficacy in adjuvant arthritis and suggests its possible utility in early diagnosis and monitoring of therapy in clinical arthritis on human extremities.

Quantification of fluid changes in rat leg joints with adjuvant arthritis by a one-dimensional magnetic resonance imaging experiment

A simple and reliable method for quantifying the fluid content and characterizing the tissue T2 relaxation properties of animal extremities has been devised. This one-dimensional magnetic resonance imaging experiment, applied to the adjuvant arthritis model in rats, provides a useful, noninvasive monitor of the course of the disease in vivo. Tissue is characterized through the analysis of the biexponential T2 decay of the NMR-active hydrogen in the rat leg joint tissue. Long and short T2 components are identified, both of which are sensitive to the arthritic process. The long component is suggested to come from edema and increases by a factor of ca. 9 during the course of the disease, whereas the short T2 component may represent cellular influx into the joint and increases by a factor of ca. 3. These changes correlate with the severity of the disease and can be used to monitor therapeutic response. The main advantage of the technique over the more traditional two-dimensional imaging approach is that only one spatial variable has to be resolved, resulting in shorter imaging time.

Mechanism of oligonucleotide loop formation in solution

We have studied the tridecadeoxynucleotide CGCGAATTACGCG (I), which contains an additional A at position 9 compared to the dodecanucleotide of which the crystal structure has been determined. Sequence I exhibits no distinct melting curve and also has a concentration-dependent pattern of peaks on reverse-phase chromatography. This behavior is explained by a slow equilibration between loop and duplex forms in solution. We have characterized this equilibrium by proton NMR spectroscopy and shown that it is fully reversible by monitoring the two thymine methyl resonances, each of which occurs in two environments. Lower temperature and higher concentration favor the duplex; the midpoint of the transition is such that the loop predominates at room temperature. We have measured the van't Hoff enthalpy of formation of the duplex and the activation energy by temperature-jump and saturation-transfer experiments. The results are compared with those for the 17-mer sequence CGCGCGAATTACGCGCG (II), which contains two additional base pairs in the stem of the loop. The thermodynamic parameters and the effect of increasing salt concentration on the rate of conversion of the loop and duplex forms lead us to presume that the mechanism of interconversion involves complete strand separation and re-formation rather than cruciform formation and branch migration.

Conversions of poly(2-aminodeoxyadenylate-5-halodeoxyuridylate) from B to A forms in high salt. An NMR and circular dichroism study

Proton one- and two-dimensional nuclear Overhauser enhancement (1D and 2D NOE) spectroscopy has been used to demonstrate that poly(d2NH2A-d5IU) and poly(d2NH2A-d5BrU) are converted from the B to the A conformation in high salt, as found previously for poly(d2NH2A-dT) [Borah, B., Cohen, J. S., Howard, F. B., & Miles, H. T. (1985) Biochemistry 24, 7456-7462]. The 2D NOE and 1D NOE spectra exhibit strong base proton (H8,H6)-H3' cross relaxation, suggesting short interproton distances. These results are indicative of a C3'-endo sugar pucker for both purine and pyrimidine residues in an A or closely related structure. The circular dichroism and UV spectra are consistent with the interpretation of an A conformation in high salt.

Unique pyrimidine 2D-COSY aromatic cross-peaks as monitors of pyrimidine environments and mobility in oligo- and polynucleotides

Only cytosine contains two adjacent aromatic protons that give rise to cross-peaks in the aromatic region of 2D-COSY spectra of oligodeoxynucleotides. In two GC-containing sequences several such cross-peaks were resolved. The intensity of these cross-peaks is a sensitive monitor of local mobility, and upon the addition of the intercalating drug daunomycin selective intensity losses were observed, indicating binding to specific GC base pairs. We have also monitored the 2D-COSY cross-peaks from mobile pyrimidine bases in tRNA (Phe) as a function of temperature.

Poly(d2NH2A-dT): two-dimensional NMR shows a B to A conversion in high salt

Poly(d2NH2A-dT) forms a structure in high salt that is clearly distinct from the B form present in low salt. Two-dimensional nuclear Overhauser effect (2D NOE) NMR spectra establish that the conformation of the high-salt form is not Z. Correlations of observed cross peaks in the 2D NOE spectra and estimated interproton distances of the common DNA conformations are consistent only with an A form or closely related structure. This interpretation is also consistent with the negative circular dichroic band observed in the high-salt form of poly(d2NH2A-dT) and in A-form ribohomopolymer helices containing 2NH2A.

Nuclear magnetic resonance and neutron diffraction studies of the complex of ribonuclease A with uridine vanadate, a transition-state analogue

The complex of ribonuclease A (RNase A) with uridine vanadate (U-V), a transition-state analogue, has been studied with 51V and proton NMR spectroscopy in solution and by neutron diffraction in the crystalline state. Upon the addition of aliquots of U-V at pH 6.6, the C epsilon-H resonances of the two active-site histidine residues 119 and 12 decrease in intensity while four new resonances appear. Above pH 8 and below pH 5, these four resonances decrease in intensity as the complex dissociates. These four resonances are assigned to His-119 and His-12 in protonated and unprotonated forms in the RNase-U-V complex. These resonances do not titrate or change in relative area in the pH range 5-8, indicating a slow protonation process, and the extent of protonation remains constant with ca. 58% of His-12 and ca. 26% of His-119 being protonated. The results of diffraction studies show that both His-12 and His-119 occupy well-defined positions in the RNase-U-V complex and that both are protonated. However, while the classic interpretation of the mechanism of action of RNase based on the proposal of Findlay et al. [Findlay, D., Herries, D. G., Mathias, A. P., Rabin, B. R., & Ross, C. A. (1962) Biochem. J. 85, 152-153] requires both His-12 and His-119 to be in axial positions relative to the pentacoordinate transition state, in the diffraction structure His-12 is found to be in an equatorial position, while Lys-41 is close to an axial position. Hydrogen exchange data show that the mobility and accessibility of amides in the RNase-U-V complex do not significantly differ from what was observed in the native enzyme. The results of both proton NMR in solution and neutron diffraction in the crystal are compared and interpreted in terms of the mechanism of action of RNase.

Deuterium NMR of water in immobilized protein systems

Deuterium NMR spectra are reported for lysozyme crystals, powders, and frozen solutions. At high water contents the spectrum is a superposition of a narrow central component and a quadrupole doublet. The quadrupole splitting and the relaxation rates of both components, monitored as a function of water content and temperature, are discussed in terms of models for the water-protein interaction. The anisotropy of the water molecule motion is clearly demonstrated by the deuterium quadrupole splitting observed in the protein single crystal, but such splittings were not found in protein powders and frozen protein solutions. We therefore suggest that the most useful view of such data is to consider the water-protein interactions at the surface to be mixed rapidly and that a distribution of interactions be invoked rather than an oversimplified view often taken of a two or n-site mixing where n is small.

Complex hydrogen bonded cations. The benzimidazole benzimidazolium cation

The complex salts (Bz2H)+Y−, Bz = benzimidazole, Y = PF6− or BF4− have been identified in solution, and the molecularity of the fluoroborate, which has been crystallised, confirmed gravimetrically. Infrared and Raman spectra, together with those of the deuterated systems, indicate a similar structure in solution and the crystal, viz., an asymmetric single minimum bridging proton potential, in conformity with the X-ray structure, proving that the pronounced doublet observed in the vs band of the H bridged system is not due to proton tunnelling. The origin of the asymmetric structure is discussed.

Complex hydrogen bonded cations. The imdazole/imidazolium complex cation

The salts (ImH+)X−, Im = imidazole, X− = PF6−, BF4−, or ClO4− have been prepared in solution, and the perchlorate salt has been crystallised. The molecularity implied by the formula is confirmed in solution by Job's method, and for the crystals gravimetrically. In MeCN the association constant is ∼8 M−1. Infrared spectra of solution and crystals are similar, independent of counter ion, and indicate an asymmetric single minimum proton potential. The pronounced doublet in the NH stretching band of the H bridged complex, and replaced by a single band in the D bridged analogue, is not indicative of proton tunnelling. The X-ray structure is compatible with this interpretation of the spectra.