Cost-utility analysis of molnupiravir for high-risk, community-based adults with COVID-19: an economic evaluation of the PANORAMIC trial.

BACKGROUND: The cost-effectiveness of molnupiravir, an oral antiviral for early treatment of SARS-CoV-2, has not been established in vaccinated populations. AIM: To evaluate the cost-effectiveness of molnupiravir relative to usual care alone among mainly vaccinated community-based people at higher risk of severe outcomes from COVID-19 over 6 months. DESIGN AND SETTING: An economic evaluation of the PANORAMIC trial in the UK. METHOD: A cost-utility analysis that adopted a UK NHS and personal social services perspective and a 6-month time horizon was performed using PANORAMIC trial data. Cost-effectiveness was expressed in terms of incremental cost per quality-adjusted life year (QALY) gained. Sensitivity and subgroup analyses assessed the impacts of uncertainty and heterogeneity. Threshold analysis explored the price for molnupiravir consistent with likely reimbursement. RESULTS: In the base-case analysis, molnupiravir had higher mean costs of £449 (95% confidence interval [CI] = 445 to 453) and higher mean QALYs of 0.0055 (95% CI = 0.0044 to 0.0067) than usual care (mean incremental cost per QALY of £81 190). Sensitivity and subgroup analyses showed similar results, except for those aged ≥75 years, with a 55% probability of being cost-effective at a £30 000 per QALY threshold. Molnupiravir would have to be priced around £147 per course to be cost-effective at a £15 000 per QALY threshold. CONCLUSION: At the current cost of £513 per course, molnupiravir is unlikely to be cost-effective relative to usual care over a 6-month time horizon among mainly vaccinated patients with COVID-19 at increased risk of adverse outcomes, except those aged ≥75 years.

Cost-Effectiveness Analysis of Molnupiravir Versus Best Supportive Care for the Treatment of Outpatient COVID-19 in Adults in the US.

BACKGROUND AND AIMS: Coronavirus disease 2019 (COVID-19) imposes a substantial and ongoing burden on the US healthcare system and society. Molnupiravir is a new oral antiviral for treating COVID-19 in outpatient settings. This study evaluated the cost-effectiveness profile of molnupiravir versus best supportive care in the treatment of adult patients with mild-to-moderate COVID-19 at risk of progression to severe disease, from a US payer's perspective. METHODS: The model was developed using a decision tree for the short-term acute phase of COVID-19 and a Markov state transition model for the long-term post-acute phase. This model compared molnupiravir with best supportive care as consistent with the MOVe-OUT trial. Costs were reported in 2021 US dollars. Transition probabilities were derived from the phase III MOVe-OUT trial and the TriNetX real-world electronic health records database. Costs were derived from the TriNetX database and utility values from a de novo, vignette-based utility study. Deterministic and probabilistic sensitivity analyses (DSA/PSA) were conducted. Primary outcomes included proportion hospitalized, proportion who died overall and by highest healthcare setting at the end of the acute phase, quality-adjusted life-years (QALYs), and incremental costs per QALY gained over a lifetime (100 years) horizon, discounted at 3% annually and assessed at a willingness-to-pay (WTP) threshold of $100,000 per QALY. RESULTS: In this model, the use of molnupiravir led to an increase in QALYs (0.210) and decrease in direct total medical costs (-$895) per patient across a lifetime horizon, compared with best supportive care in COVID-19 outpatients. Molnupiravir was the dominant intervention when compared with best supportive care. Patients treated with molnupiravir were less likely to be hospitalized (6.38% vs. 9.20%) and more likely to remain alive (99.88% vs. 98.71%) during the acute phase. Through DSA, molnupiravir treatment effect of hospitalization reduction was identified to be the most influential parameter, and through PSA, molnupiravir remained dominant in 84% of the total simulations and, overall, 100% cost effective. CONCLUSION: This analysis suggests that molnupiravir is cost effective compared with best supportive care for the treatment of adult outpatients with COVID-19. However, our study was limited by the unavailability of the most recent information on the rapidly evolving pandemic, including new viral variants, patient populations affected, and changes in standards of care. Further research should explore the impact of vaccination on the cost effectiveness of molnupiravir and other therapies, based on real-world data, to account for these changes, including the impact of vaccination and immunity.

In vitro assessment of a synergistic combination of gemcitabine and zebularine in pancreatic cancer cells.

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers with an extremely poor prognosis. Gemcitabine (Gem) is still the mainstay drug for the treatment of PDAC. However, rapid inactivation by cytidine deaminase (CDA) present in pancreatic cancer cells severely limits anticancer efficacy of Gem. In this study, we investigated the effect of a CDA inhibitor - Zebularine (Zeb) on anticancer activity of Gem in pancreatic cancer cell lines MiaPaCa-2, BxPC-3, and Panc-1. Zeb treatment synergistically increased Gem-induced cytotoxicity in all three pancreatic cancer cell lines. The strongest synergistic activity was found at 1:10 M ratio of Gem/Zeb (combination index 0.04-0.4). Additionally, Gem + Zeb treated cells showed marked decreased in the expressions of anti-apoptotic protein including Bcl-2 and survivin while significantly increased the cleaved caspase-3, and loss of mitochondrial membrane potential was observed. Multicellular 3D spheroids of MiaPaCa-2 cells treated with combination showed significant reduction (25-60%) in spheroid size, weight compared to single drug and control group. Live/dead cell imaging showed that Gem + Zeb treated spheroids exhibited a highly distorted surface with significantly higher number of dead cells (red). The results of the present study confirm that this synergistic combination is worthy of future investigations as a potential approach for the treatment of PDAC.

Intensive optimization and evaluation of global DNA methylation quantification using LC-MS/MS.

DNA methylation is a typical epigenetic phenomenon. Numerous methods for detecting global DNA methylation levels have been developed, among which LC-MS/MS has emerged as an excellent method from the viewpoint of sensitivity, reproducibility, and cost. However, LC-MS/MS methods have limitations due to a lack of the stability and the standardization required for a laboratory assay. The present study aimed to establish a robust assay that guarantees highly accurate measurements of global DNA methylation levels. There are at least three facets of the developed method. The first is discovery of the solvent conditions to minimize sodium adducts. The second is improvement of separation of nucleosides by LC using the columns that had not been used in previous similar studies. The third is success in reduction of the uncertainty of the measurement results, which was achieved by the calibration using the ratio of mdC but not the absolute amount in the presence of internal standards. These facets represent the advantage over methods reported previously. Our developed method enables quantification of DNA methylation with a short time length (8 min) for one analysis as well as with the high reproducibility of measurements that is represented by the inter-day CV% being less than 5%. In addition, data obtained from measuring global DNA methylation levels in cultured cell lines, with or without pharmacological demethylation, support its use for biomedical research. This assay is expected to allow us to conduct initial screening of epigenetic alterations or aberration in a variety of cells.

Quality assessment of cellular and tissue-based products using liquid chromatography-tandem mass spectrometry.

We are currently conducting clinical research on cell sheets for cartilage regeneration. One issue with the future use of chondrocyte sheets as cellular and tissue-based products is quality assessment. Currently, chondrocyte sheets are evaluated using invasive methods that cannot be performed on every sheet produced. We report here on our liquid chromatography-tandem mass spectrometry (LC-MS/MS) technique that allows the noninvasive assessment of every sheet using only 50 µl of culture medium. We found that LC-MS/MS could be used to confirm cell sheet viability through the measurement of glucose and glutamine uptake, to estimate extracellular matrix production by measuring serine consumption, to estimate cell kinetics by measuring cytidine and uracil concentrations, and to estimate melanoma inhibitory activity level by measuring pyridoxal concentration. LC-MS/MS may be useful for the noninvasive assessment of products to be used in regenerative medicine.

Tratamento da dor neuropática: Eficácia, segurança e custo-efetividade de pregabalina ® e da associação vitamina B12, uridina e citidina (ETNA) / Treatment of diabetic neuropathic pain: Efficacy, safety and cost-effectiveness of pregabalin and the association of vitamin B12, uridine and cytidine / Tratamiento del dolor neuropático diabético: Eficacia, seguridad y coste-efectividad de pregabalina y de la asociación de la vitamina B12, uridina y citidina

TECNOLOGIAS: Medicamento Pregabalina e medicamento com Vitamina B12 associada à citidina e uridina (ETNA®). INDICAÇÃO: Tratamento da dor neuropática diabética. CARACTERIZAÇÃO DAS TECNOLOGIAS: A pregabalina é um anticonvulsivante indicado, entre outros, para o tratamento da dor neuropática em adultos. Seu mecanismo de ação é a redução do influxo de cálcio para regular a transmissão de mensagens excitatórias entre as células nervosas. O medicamento ETNA® é uma combinação de vitamina B12, e nucleotídeos uridina e citidina e é indicado para o tratamento de doenças dos nervos periféricos. PERGUNTA: As intervenções pregabalina e ETNA® são seguras, eficazes e custo-efetivas no tratamento da dor neuropática diabética, em relação às alternativas gabapentina e amitriptilina já disponíveis no SUS? BUSCA E ANÁLISE DE EVIDÊNCIAS CIENTÍFICAS: Foi realizada uma busca por revisões sistemáticas e estudos econômicos nas bases de dados The Cochrane Library (via Bireme), Medline (via Pubmed), LILACS e Centre for Reviews and Dissemination (CRD). Foi realizada também busca manual na internet e nas referências dos estudos encontrados. Foram selecionadas avaliações de tecnologias em saúde (ATS) em sites de agências internacionais e na Rede Brasileira de Avaliação de Tecnologias em Saúde (REBRATS). Foram selecionados estudos publicados em inglês, português ou espanhol. RESUMO DOS RESULTADOS DOS ESTUDOS SELECIONADOS: Foram incluídos nove estudos: quatro revisões sistemáticas, um ensaio clínico e quatro estudos econômicos. As revisões sistemáticas que consideraram a eficácia e segurança da pregabalina avaliaram como desfechos a redução na intensidade da dor, a taxa de resposta ao tratamento (≥50% na redução da dor), a impressão do paciente em relação à melhora e eventos adversos. Essas revisões apresentaram resultados a favor da pregabalina, porém em relação ao placebo. O ensaio clínico que avaliou a eficácia e segurança do medicamento ETNA® mostrou resultados a favor dessa intervenção, porém comparado somente à vitamina B12. Os resultados de custo-efetividade para a pregabalina consideraram como medida de efetividade o número de dias sem dor ou com dor leve, o número de dias com 30% e 50% de redução de dor e QALY (Anos de Visa Ajustados por Qualidade) ganhos. Apenas um estudo de custo-efetividade não favoreceu a pregabalina. RECOMENDAÇÕES: O tratamento da dor neuropática diabética é contemplado pelo Protocolo Clínico e Diretrizes Terapêuticas da Dor Crônica, o qual recomenda o medicamento amitriptilina em monoterapia (primeira escolha) ou a associação desta com gabapentina, em caso de falha terapêutica da monoterapia. As evidências avaliadas neste PTC permitem recomendar (fracamente) a pregabalina em substituição à gabapentina apenas em casos de falha terapêutica dos esquemas citados anteriormente, uma vez que nenhum estudo incluiu comparações diretas entre pregabalina e amitriptilina ou gabapentina, não comprovando haver superioridade terapêutica da tecnologia em relação aos medicamentos já disponíveis no SUS. Quanto ao ETNA®, a recomendação é contra o seu uso devido à escassez de estudos com evidências de qualidade suficiente para garantir a eficácia e segurança terapêutica dessa intervenção e justificar o gasto.(AU)

TECHNOLOGIES: Pregabalin and vitamin B12 associated with uridine and cytidine (ETNA®) . INDICATION: Treatment of diabetic neuropathic pain. TECHNOLOGIES CHARACTERIZATION: Pregabalin is an anticonvulsant indicated for the treatment of neuropathic pain in adults. Its mechanism of action is the reduction of calcium influx to regulate transmission of excitatory messages between nerve cells. ETNA ® is a combination of vitamin B12, uridine and cytidine nucleotides and it is indicated for the treatment of peripheral nerves diseases. QUESTION: Are ETNA ® and pregabalin safe, effective and cost-effective options in the treatment of diabetic neuropathic pain, regarding the alternatives amitriptyline and gabapentin available at SUS? SEARCH AND ANALYSIS OF SCIENTIFIC EVIDENCE: a search for systematic reviews and economic studies was performed in the databases The Cochrane Library (via Bireme), Medline (via Pubmed), LILACS and Centre for Reviews and Dissemination (CRD). Manual search was also conducted on the internet and in the references of the studies found. Health Technology Assessments (HTA) have been selected in international agencies and in Brazilian Network for Health Technology Assessment (REBRATS). Studies published in English, Portuguese or Spanish were selected. SUMMARY OF RESULTS OF THE SELECTED STUDIES: Nine studies were included, four systematic reviews, one clinical trial and four economic studies. Systematic reviews considering efficacy and safety of pregabalin evaluated the following outcomes: reduction in pain intensity, treatment response rate (≥50% on pain reduction), the Patient Global Impression of Change and adverse events. These reviews showed results in favor of pregabalin compared to placebo. The ETNA® Clinical trial showed results in favor of the intervention but compared to vitamin B12 alone. The results of cost-effectiveness for pregabalin considered as a measure of effectiveness the number of days with no pain or mild pain, the number of days with 30% and 50% reduction in pain and QALY gains. Only one cost-effectiveness study has not favored pregabalin. RECOMMENDATIONS: The treatment for neuropathic pain is contemplated in the therapeutic guideline for chronic disease, which recommends the use of amitriptyline in monotherapy as first choice or its association with gabapentin in cases of therapeutic failure with the monotherapy. The evidences appraised here allow recommending (weakly) the use of pregabalin in replacement of gabapentin only in cases of therapeutic failure of the schemes mentioned above, since no study included direct comparisons between pregabalin and amitriptyline or gabapentin, making it impossible to support the therapeutic superiority of pregabalin compared to other drugs already used in Brazil. The recommendation is against ETNA® use due to lack of studies with sufficient evidence of quality to ensure the efficacy and safety of this intervention and justify the expense.(AU)

TECNOLOGÍAS: Pregabalina y vitamina B12 asociado a uridina y citidina (ETNA®). INDICACIÓN: Tratamiento de la neuropatía diabética. CARACTERIZACIÓN DE LAS TECNOLOGÍAS: La pregabalina es un anticonvulsivo indicado, entre otras cosas, para el tratamiento de la neuropatía diabética en adultos. Su mecanismo de acción es la reducción de la afluencia de calcio para regular la transmisión de mensajes excitatorios entre las células nerviosas. ETNA ® es una combinación de vitamina B12 y de nucleótidos de uridina y citidina y está indicado para el tratamiento de enfermedades de los nervios periféricos. PREGUNTA: ¿Las intervenciones pregabalina y ETNA ® son seguros, eficaces y coste-efectiva en el tratamiento de la neuropatía diabética, en comparación con las alternativas gabapentina y amitriptylina ya disponible en el SUS? BÚSQUEDA Y ANÁLISIS DE LA EVIDENCIA CIENTÍFICA: una búsqueda de revisiones sistemáticas y estudios económicos se realizó en las bases de datos de la Cochrane Library (vía Bireme), MEDLINE (vía PubMed), LILACS y Centre for Reviews and Dissemination (CRD). Búsqueda manual también se llevó a cabo. Comentarios de las tecnologías de la salud han sido seleccionadas en las agencias internacionales y en la Red Brasileña de Evaluación de Tecnologías Sanitarias (REBRATS). Se seleccionaron los estudios publicados en inglés, portugués o español. RESUMEN DE LOS RESULTADOS DE LOS ESTUDIOS SELECCIONADOS: Se incluyeron nueve estudios, cuatro revisiones sistemáticas, un ensayo clínico y cuatro estudios económicos. Revisiones sistemáticas de eficacia e seguridad de pregabalina encontraron como resultados la reducción de la intensidad del dolor, la tasa de respuesta al tratamiento, la impresión del paciente con respecto a la mejora y los eventos adversos. Estos exámenes mostraron resultados a favor de la pregabalina, pero en relación con el placebo. El ensayo clínico que evaluó la eficacia de la droga ETNA ® mostró resultados a favor de la intervención, pero en comparación con la vitamina B12 en monoterapia. Los resultados de coste-efectividad de pregabalina han considerado como una medida de efectividad el número de días sin dolor o dolor leve , el número de días con 30 % y 50% de reducción en el dolor y AVAC (años de vida ajustado por calidad) . Sólo un estudio de costo-efectividad no ha favorecido la pregabalina. RECOMENDACIONES: El tratamiento de la neuropatía diabética se contempla en las guías clínicas y terapéuticas del dolor crónico, que recomienda el uso de amitriptylina en monoterapia (primera elección) o asociado con la gabapentina, en caso de fracaso terapéutico con la monoterapia. Las evidencias evaluadas aquí permiten recomendar (débilmente) el uso de pregabalina en el reemplazo de la gabapentina sólo en casos de fracaso terapéutico de los sistemas antes mencionados, ya que ningún estudio incluyó comparaciones directas entre pregabalina y amitriptilina o gabapentina, no probando superioridad terapéutica de la pregabalina en comparación con otros fármacos ya utilizados en Brasil. En cuanto a ETNA, la recomendación es contra su uso debido a la falta de estudios con pruebas de calidad suficiente para garantizar la eficacia y seguridad de esta intervención y justificar el gasto.(AU)

Eficacia y seguridad del uso de decitabina: 5-AZA2': deoxicitidina para el tratamiento del síndrome mielodisplásico / Efficacy and safety of the use of decitabine: 5-AZA2': deoxycytidine for the treatment of myelodysplastic syndrome

INTRODUCCIÓN: Síndrome Mielodisplásico (myelodysplastic syndrome, SMD) se denomina a un grupo de afecciones que ocurren cuando se dañan las células productoras de sangre en la médula ósea. Su prevalencia es de 4.4 casos por cada 100.000 personas. OBJETIVO: Determinar la eficacia y la seguridad de DECITABINA: 5-AZA-2´-DEOXICITIDINA, en el tratamiento del Síndrome Mielodisplásico, para su posible incorporación al FTM. METODOLOGÍA: La búsqueda de información científica se realizó accediendo a la base de Revisiones de la Colaboración Cochrane, en Pubmed, NICE, Centro de Revisiones y Diseminación de la Universidad de York (Database HTA) y se obtuvieron publicaciones derivadas de las referencias bibliográficas de las publicaciones encontradas por estos medios. RESULTADOS: Los estudios comparados con el mejor tratamiento de soporte indican que la Decitabina muestra, en algunos parámetros, un avance en el tratamiento del paciente con síndrome Mielodisplásico (mediana de sobrevida libre de progresión 6.6 meses versus 3.0 meses), aunque no modifica la Sobrevida Global. La evidencia publicada sobre eventos adversos indicó que el tratamiento con Decitabina muestra un porcentaje significativamente mayor de efectos secundarios al tratamiento comparado con el mejor tratamiento de soporte (neutropenia febril grado 3-4, 25% versus 7% con el MTS; hipoplasia, 14% versus 0% en el MTS). La comparación de Decitabina con tratamiento con quimioterapia se evaluó en un estudio no aleatorizado mostrando beneficios para la Decitabina en la sobrevida y en la mortalidad a 3 meses. Se encontró poca evidencia comparando la Decitabina a otros agentes hipometilantes, y una comparación indirecta con la 5-azacitidina favoreció a esta última. DISCUSIÓN: La evidencia obtenida del uso de la Decitabina en el SMD no mostró resultados concluyentes para varias de las medidas evaluadas hasta el presente, frente a otras alternativas médicas. Las investigaciones realizadas hasta ahora son escasas y en algunos casos no tienen la calidad necesaria para indicar una diferencia importante en el tratamiento con este fármaco. CONCLUSIÓN: Se considera que la evidencia existente es insuficiente hasta el momento para concluir sobre la eficacia de este fármaco en el tratamiento de los Síndromes Mielodisplásicos especialmente al compararlo con otros fármacos como ser los hipometilantes que también se han evaluado para su ingreso al FTM.(AU)

Measuring topology of low-intensity DNA methylation sites for high-throughput assessment of epigenetic drug-induced effects in cancer cells.

Epigenetic anti-cancer drugs with demethylating effects have shown to alter genome organization in mammalian cell nuclei. The interest in the development of novel epigenetic drugs has increased the demand for cell-based assays to evaluate drug performance in pre-clinical studies. An imaging-based cytometrical approach that can measure demethylation effects as changes in the spatial nuclear distributions of methylated cytosine and global DNA in cancer cells is introduced in this paper. The cells were studied by immunofluorescence with a specific antibody against 5-methylcytosine (MeC), and 4,6-diamidino-2-phenylindole (DAPI) for delineation of methylated sites and global DNA in nuclei. In the preprocessing step the segmentation of nuclei in three-dimensional images (3-D) is followed by an automated assessment of nuclear DAPI/MeC patterns to exclude dissimilar entities. Next, low-intensity MeC (LIM) and low-intensity DNA (LID) sites of similar nuclei are localized and processed to obtain specific nuclear density profiles. These profiles sampled at half of the total nuclear volume yielded two parameters: LIM(0.5) and LID(0.5). The analysis shows that zebularine and 5-azacytidine-the two tested epigenetic drugs introduce changes in the spatial distribution of low-intensity DNA and MeC signals. LIM(0.5) and LID(0.5) were significantly different (p<0.001) in 5-azacytidine treated (n=660) and zebularine treated (n=496) vs. untreated (n=649) DU145 human prostate cancer cells. In the latter case the LIM sites were predominantly found at the nuclear border, whereas treated populations showed different degrees of increase in LIMs towards the interior nuclear space, in which a large portion of heterochromatin is located. The cell-by-cell evaluation of changes in the spatial reorganization of MeC/DAPI signals revealed that zebularine is a more gentle demethylating agent than 5-azacytidine. Measuring changes in the topology of low-intensity sites can potentially be a valuable component in the high-throughput assessment of demethylation and risk of chromatin reorganization in epigenetic-drug screening tasks.

Combinations of 2'-C-methylcytidine analogues with interferon-alpha2b and triple combination with ribavirin in the hepatitis C virus replicon system.

BACKGROUND: Hepatitis C virus (HCV) polymerase is an essential enzyme for HCV replication and has multiple inhibitor binding sites making it a major target for antiviral intervention. It is apparent that no single drug can inhibit HCV replication in humans. Hence, combinations of nucleoside analogues beta-D-2'-C-methylcytidine (2'-C-MeC; NM-107) or beta-D-2'-deoxy-2'-fluoro-2'-C-methyleytidine (2'-F-C-MeC; PSI-6130) with interferon-alpha2b (IFN-alpha2b) or triple combination with ribavirin (RBV) were evaluated. METHODS: Huh-7 cells containing the self-replicating subgenomic HCV replicon (Clone B) were used for drug combination studies. After drug treatment for 5 days, total cellular RNA was then extracted and both ribosomal RNA and HCV replicon RNA were amplified in a single-step multiplex real-time PCR assay. Drug interaction analyses were performed using the CalcuSyn program. RESULTS: Double combinations of 2'-C-MeC or 2'-F-C-MeC with IFN-alpha2b at all ratios tested had weighted average combination index (Cl(wt)) values <1 indicating synergistic inhibition of HCV replication in the replicon system. For the triple combinations of IFN-alpha2b plus RBV with either 2'-C-MeC or 2'-F-C-MeC, the Cl(wt) values at 1:1:1 ratio tested were 0.5 and 0.8, respectively, indicating synergistic antiviral effects. No apparent cytotoxicity effects were observed with any of the combinations tested. CONCLUSION: These promising in vitro data warrant clinical investigation of the nucleosides analogues such as 2'-C-MeC or 2'-F-C-MeC in their prodrug forms, together with IFN-alphac2b and RBV, for successful treatment of HCV infections.

Numerical characterization of DNA sequences based on the k-step Markov chain transition probability.

A DNA sequence can be regarded as a discrete-time Markov chain. Based on k-step transition probabilities, we construct a series of 4 x 4 k-step transition matrices to characterize the DNA primary sequences. According to the properties of Markov chains, we obtain distributions of A, T, C and G, and analyze the changes among them from yesterday to tomorrow. We can calculate the probabilities of nucleotide triples of DNA primary sequences. Finally, we introduce a correlation of this kind of transition matrices and consider it as an invariant to analyze the similarities/dissimilarities of DNA sequences.

DNA mismatch correction by Very Short Patch repair may have altered the abundance of oligonucleotides in the E. coli genome.

A base mismatch correction process in E. coli K-12 called Very Short Patch (VSP) repair corrects T:G mismatches to C:G when found in certain sequence contexts. Two of the substrate mismatches (5'-CTWGG/3'-GGW'CC; W = A or T) occur in the context of cytosine methylation in DNA and reduce the mutagenic effects of 5-methylcytosine deamination to thymine. However, VSP repair is also known to repair T:G mismatches that are not expected to arise from 5-methylcytosine deamination (example--CTAG/GGT-C). In these cases, if the original base pair were a T:A, VSP repair would cause a T to C transition. We have carried out Markov chain analysis of an E. coli sequence database to determine if repair at the latter class of sites has altered the abundance of the relevant tetranucleotides. The results are consistent with the prediction that VSP repair would tend to deplete the genome of the 'T' containing sequences (example--CTAG), while enriching it for the corresponding 'C' containing sequences (CCAG). Further, they provide an explanation for the known scarcity of CTAG containing restriction enzyme sites among the genomes of enteric bacteria and identify VSP repair as a force in shaping the sequence composition of bacterial genomes.

Ammonium ion representation in Monte Carlo simulations of biomolecular solutions.

Monte Carlo computer simulation techniques may be used to predict structural properties of solvent networks in helical fragments of nucleic acids, provided that suitable potential functions are available to describe the interactions between nucleic acid atoms, water and counterions. Previous studies have shown that simple non-bonded and point charge parameters are adequate for mononuclear ions such as sodium and calcium. In this study a model interaction potential for the polynuclear ammonium ion is evaluated. The parameters used take account of the distribution of charge over the constituent atoms in the ion. Simulations are carried out on the ammonium salt of a small nucleic acid crystal hydrate and a comparison is made between the predicted and experimental results. It is shown that the simulated structure is in reasonable agreement with experiment. It is therefore feasible to use this potential in studies of ammonium-containing bimolecular systems.