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PubMed2001

Application of inductively coupled plasma sector field mass spectrometry for elemental analysis of urine.

An analytical method using double focusing sector field inductively-coupled plasma mass spectrometry (sector field ICP-MS) for rapid simultaneous determination of 42 elements in urine is described. Sample preparation consisted of 20-fold dilution with 0.14 mol/l nitric acid in ultrapure water. The importance of controlling possible contamination sources at different sample preparation and analysis stages in order to achieve adequate method detection limits (DL) is emphasized. Correction for matrix effects was made using indium and lutetium as internal standards. Different approaches for accuracy assessment in urine analysis are evaluated. Additional information on trace element concentrations in a urine reference material is given. Between-batch precision was assessed from the analysis of separately prepared aliquots of the reference material and was better than 10% RSD for 32 of the elements. The robustness of the procedure was tested by analysis of about 250 samples in one analytical run lasting more than 50 hours. A statistical summary of results for 19 urine samples from non-exposed subjects is presented. For a majority of the elements tested concentrations were higher than the detection limit of the method.

Calibration↗
PubMed2004

Attention-deficit/hyperactivity disorder: cognitive evoked potential (P300) topography predicts treatment response to methylphenidate.

OBJECTIVE: Auditory cognitive evoked potential (P300) topography predicts robust response to the stimulant pemoline in patients with attention-deficit/hyperactivity disorder (ADHD). Patients with a right fronto-central to parietal (FC2:P4) auditory P300 amplitude ratio >0.5 respond robustly to pemoline, whereas others do not. This study was performed to demonstrate whether the same test and ratio predict treatment response to methylphenidate. METHODS: Patients aged 6-12 with DSM-IV diagnosis of ADHD were administered auditory and visual cognitive evoked potential (P300) testing. They then underwent single-blind treatment with an extended-release version of methylphenidate. Robust response was defined as a 60% decrease from baseline in a parent rated ADHD rating scale. RESULTS: Nine of 20 subjects responded robustly. They did not differ from the non-robust responders in age, baseline attention or hyperactivity ratings, or any P300 parameter except auditory P300 topography. A FC2:P4 auditory P300 amplitude ratio >0.5 predicted robust response with a positive predictive value of 0.67 and a negative predictive value of 0.73. CONCLUSIONS: The ratio of right fronto-central to parietal auditory P300 amplitude predicts response to stimulants in patients with ADHD. As non-stimulant treatments are approved for the treatment of ADHD, tests such as this may help pinpoint whether to use a stimulant or a medicine with some other mechanism of action.

Attention Deficit Disorder with Hyperactivity↗
PubMed2000

Isolation of INS-1-derived cell lines with robust ATP-sensitive K+ channel-dependent and -independent glucose-stimulated insulin secretion.

The biochemical mechanisms involved in regulation of insulin secretion are not completely understood. The rat INS-1 cell line has been used to gain insight in this area because it secretes insulin in response to glucose concentrations in the physiological range. However, the magnitude of the response is far less than that seen in freshly isolated rat islets. In the current study, we have stably transfected INS-1 cells with a plasmid containing the human proinsulin gene. After antibiotic selection and clonal expansion, 67% of the resultant clones were found to be poorly responsive to glucose in terms of insulin secretion (< or =2-fold stimulation by 15 mmol/l compared with 3 mmol/l glucose), 17% of the clones were moderately responsive (2- to 5-fold stimulation), and 16% were strongly responsive (5- to 13-fold stimulation). The differences in responsiveness could not be ascribed to differences in insulin content. Detailed analysis of one of the strongly responsive lines (832/13) revealed that its potent response to glucose (average of 10-fold) was stable over 66 population doublings (approximately 7.5 months of tissue culture) with half-maximal stimulation at 6 mmol/l glucose. Furthermore, in the presence of 15 mmol/l glucose, insulin secretion was potentiated significantly by 100 pmol/l isobutylmethylxanthine (320%), 1 mmol/l oleate/palmitate (77%), and 50 nmol/l glucagon-like peptide 1 (60%), whereas carbachol had no effect. Glucose-stimulated insulin secretion was also potentiated by the sulfonylurea tolbutamide (threefold at 3 mmol/l glucose and 50% at 15 mmol/l glucose) and was abolished by diazoxide, which demonstrates the operation of the ATP-sensitive K+ channel (K(ATP)) in 832/13 cells. Moreover, when the K(ATP) channel was bypassed by incubation of cells in depolarizing K+ (35 mmol/l), insulin secretion was more effectively stimulated by glucose in 832/13 cells than in parental INS-1 cells, which demonstrates the presence of a K(ATP) channel-independent pathway of glucose sensing. We conclude that clonal selection of INS-1 cells allows isolation of cell lines that exhibit markedly enhanced and stable responsiveness to glucose and several of its known potentiators. These lines may be attractive new vehicles for studies of beta-cell function.

Adenosine Triphosphate↗
PubMed2006

Automatic identification of the left ventricle in cardiac cine-MR images: dual-contrast cluster analysis and scout-geometry approaches.

PURPOSE: To evaluate the technical feasibility of two approaches--dual-contrast (DC) cluster analysis, and scout geometry (SG)--for automatic identification of the left ventricular (LV) cavity in short-axis (SA) cine-MR images. MATERIALS AND METHODS: The DC algorithm uses Fuzzy C-Means (FCM) cluster analysis of SA images from a black-blood double-inversion recovery turbo spin-echo (dual IR TSE) sequence, and bright-blood images from a steady-state free precession (SSFP) sequence. The SG algorithm employs geometric information from scout views (i.e., vertical long-axis (VLA) and four-chamber (4CH) views). Both algorithms incorporate additional geometric continuity constraints along with LV region segmentation to identify the LV. The performance of both algorithms was compared on images of eight healthy volunteers, and the SG algorithm was further evaluated on images of 13 clinical patients. RESULTS: The DC algorithm identified the LV in 89% (72/75 at end-diastole (ED) and 47/59 at end-systole (ES)) of the images from healthy volunteers, compared to 98% (74/75 at ED and 57/59 at ES) by the SG algorithm. Both methods are robust against interslice signal variations and misalignment. The DC method suffers from misregistration between the dual IR TSE and SSFP images near the apex at ES. The SG method identified the LV in 91% (112/122 at ED and 91/102 at ES) of the images from clinical patients. CONCLUSION: The SG method requires no additional scan, is robust and accurate, and performs better than the DC method for automatic identification of the LV.

Adult↗
PubMed2003

Chromium picolinate for reducing body weight: meta-analysis of randomized trials.

The aim of this meta-analysis was to assess the evidence of chromium picolinate for reducing body weight. Literature searches were conducted on Medline, Embase, The Cochrane Library, Amed and Ciscom. Nine experts and four manufacturers of commercial preparations containing chromium picolinate were asked to contribute published and unpublished studies. There were no restrictions regarding the language of publication. The screening of studies, selection, data extraction, validation and the assessment of methodological quality were performed independently by two reviewers. To be included, studies were required to state that they were randomized, double-blind and placebo-controlled, and report on body weight. Ten trials met all inclusion criteria and provided data, which were suitable for statistical pooling. For body weight a significant differential effect was found in favour of chromium picolinate (weighted mean difference: -1.1 kg; 95% confidence interval (CI): -1.8 to -0.4 kg, n=489). Sensitivity analysis suggests that this effect is largely dependent on the results of a single trial (weighted mean difference: -0.9 kg; 95% CI: -2.0 to 0.2 kg, n=335). Three of the reviewed trials reported on adverse events, indicating their absence in the treatment groups. In conclusion, our meta-analysis suggests a relatively small effect of chromium picolinate compared with placebo for reducing body weight. The clinical relevance of the effect is debatable and the lack of robustness means that the result has to be interpreted with caution.

Dietary Supplements↗
PubMed2006

Localization of chorionic pregnancy-associated glycoprotein family in the pig.

The objective of this study was to localize the immuno-positive porcine PAG (pPAG) proteins within chorionic cells throughout the intensive placenta development as pregnancy advances (16-61 days post coitum - dpc). Placental sections were used for double fluorescent histochemistry with selected primary rabbit anti-pPAG sera. The polyclonals were created against recombinant pPAG2 antigen or various secretory porcine native chorionic antigens produced in vitro. Among placental cells stained with fluorescent propidium iodine, the positive pPAG immuno-complexes were visualized by Alexa 488 fluorochrom - conjugated to secondary anti-rabbit goat immunoglobulins. This is the first report concerning cellular localization of the pPAG protein family within diffuse epitheliochorial placenta development throughout the first half of pregnancy in the pig. Fluorescent immuno-positive pPAG signals have been restricted to chorionic cell layers (branched mushroom-like and finger-like structures) that generate a epitheliochorial feto-maternal surface augmented by maternal endometrium interdigitations with the gestation progress in the pig. These results suggest that the pPAG proteins robustly expressed in chorionic cells are involved in the regulation of intensive development of diffuse porcine placenta during the first half of pregnancy.

Animals↗
PubMed2002

Long-term effects of rivastigmine in moderately severe Alzheimer's disease: does early initiation of therapy offer sustained benefits?

Goals of the study included evaluating the long-term efficacy of rivastigmine in Alzheimer's disease (AD) patient categories stratified by baseline dementia severity, and post hoc investigation of particular benefits of early initiation of rivastigmine treatment in moderately severe AD. Both rivastigmine-treated groups (originally randomized to 1-4 or 6-12 mg/day) experienced significantly smaller declines in Alzheimer's Disease Assessment Scale-Cognitive subscale (ADAS-Cog) scores from baseline than the projected placebo group after 52 weeks. Patients receiving rivastigmine from Day 1 experienced significantly less decline compared with patients originally receiving placebo and then initiating rivastigmine treatment after a 6-month delay. Furthermore, cognitive benefits were more robust in patients with moderately severe disease compared with previous reports in mild to moderately severe AD. Findings suggest that early treatment with rivastigmine 6-12 mg/day is associated with sustained long-term cognitive benefits in patients with moderately severe AD. The results support the value of early treatment of AD patients, particularly those with moderately severe AD.

Aged↗
PubMed1998

Radical Nature of Cu-Catalyzed Controlled Radical Polymerizations (Atom Transfer Radical Polymerization).

Copper-catalyzed atom transfer radical polymerization (ATRP) is one of the most robust and precise techniques for controlling radical polymerization. The very good control of molecular weights, polydispersities, functionalities, chain composition, and topologies unusual for radical systems combined with the application of transition metals as catalysts requires more detailed mechanistic studies and proof of the radical nature of active species. The following results are in agreement with the radical nature of ATRP: reverse ATRP, chemoselectivities similar to those for conventional radical polymerization (effect of additives and inhibitors/scavengers, reactivity ratios, transfer coefficients), regioselectivities similar to those for conventional radical polymerization (low proportion of head-to-head units and expected structure of both tail and head end groups), stereoselectivities (tacticities) similar to that in conventional radical polymerization, EPR detection of X-Mtn+1 species resulting from the persistent radical effect, and confirmation of the termination by doubling molecular weights as well as cross-linking with multifunctional initiators and inimers. In addition, it seems that, in most ATRP systems, the contribution of degenerative transfer and reversible formation of organometallic intermediates is small and a halogen atom is transferred in the concerted process rather than in a two-step process with the involvement of radical anions.

Journal Article↗
PubMed2005

Secondary structures of short peptide chains in the gas phase: double resonance spectroscopy of protected dipeptides.

The conformational structure of short peptide chains in the gas phase is studied by laser spectroscopy of a series of protected dipeptides, Ac-Xxx-Phe-NH(2), Xxx=Gly, Ala, and Val. The combination of laser desorption with supersonic expansion enables us to vaporize the peptide molecules and cool them internally; IR/UV double resonance spectroscopy in comparison to density functional theory calculations on Ac-Gly-Phe-NH(2) permits us to identify and characterize the conformers populated in the supersonic expansion. Two main conformations, corresponding to secondary structures of proteins, are found to compete in the present experiments. One is composed of a doubly gamma-fold corresponding to the 2(7) ribbon structure. Topologically, this motif is very close to a beta-strand backbone conformation. The second conformation observed is the beta-turn, responsible for the chain reversal in proteins. It is characterized by a relatively weak hydrogen bond linking remote NH and CO groups of the molecule and leading to a ten-membered ring. The present gas phase experiment illustrates the intrinsic folding properties of the peptide chain and the robustness of the beta-turn structure, even in the absence of a solvent. The beta-turn population is found to vary significantly with the residues within the sequence; the Ac-Val-Phe-NH(2) peptide, with its two bulky side chains, exhibits the largest beta-turn population. This suggests that the intrinsic stabilities of the 2(7) ribbon and the beta-turn are very similar and that weakly polar interactions occurring between side chains can be a decisive factor capable of controlling the secondary structure.

Amino Acids↗
PubMed2004

Combined effect of vision and hearing impairment on depression in elderly Chinese.

BACKGROUND: Sensory impairment and depression are common in old age and the relation between depression and vision as well as hearing impairment have been established. However, few studies have directly compared their effects and examined the impact of dual sensory loss. The purpose of this study is to compare impacts of self-reported hearing and vision loss as well as the effect of double sensory impairment on depression. METHOD: This article analyzes cross-sectional data collected from a representative community sample of 2,003 Chinese elderly people aged 60 or above in Hong Kong. Respondents were interviewed in a face-to-face format and data including vision and hearing impairment, socio-demographic variables, health indicators, family support, and depression were obtained. RESULTS: Logistic regression analyses revealed that visual impairment was significantly related to depression even after age, gender, marital status, education, self-reported health status, the presence of 11 diseases, functional limitation and family support were controlled but hearing loss was not. Hearing impairment did not add to the likelihood of depression where visual impairment was already present. CONCLUSION: The impact of visual impairment on psychological well-being among elderly Chinese is more robust than hearing loss. Therefore, aged care service practitioners must take this risk factor into consideration in their preventive intervention and treatment for psychological well-being.

Age Distribution↗
PubMed1985

Regional multiparameter estimation from tomographic diffusible tracer clearance curves: modification of the double-integral method.

Measurement of regional CBF in transverse section using inert, diffusible tracers can be carried out using a double-integral form of the Kety-Schmidt equation. An implementation of this form proposed by Kanno and Lassen (the K-L estimator) is utilized by the Tomomatic 64, a dynamic single-photon computed tomography system that records washin-washout data during and following inhalation of 133Xe gas. Advantages of the algorithm include noninvasive calibration of the input function and excellent depiction of ischemia: disadvantages are sensitivity to errors in input function delay (delta), the inability to estimate the partition coefficient (lambda) (hence, only the clearance index, k, is estimated), and a noise sensitivity proportional to k. A modification of the method is proposed that not only accounts for delta variations, but also provides an estimate of relative lambda (hence, the perfusion, f, is estimated). The proposed estimator is shown to be robust in the presence of noise with error variances equal to or better than those with the K-L estimator, yet estimates of both relative f and lambda are provided by the modification. New simulation results implicate the Compton scatter fraction as a major contributor in the overestimation of white matter perfusion values using both the K-L and proposed estimators, and illustrate the need for hardware and software scatter fraction reduction and control.

Cerebrovascular Circulation↗
PubMed2001

The molecular logic of olfaction in Drosophila.

Drosophila fruit flies display robust olfactory-driven behaviors with an olfactory system far simpler than that of vertebrates. Endowed with 1300 olfactory receptor neurons, these insects are able to recognize and discriminate between a large number of distinct odorants. Candidate odorant receptor molecules were identified by complimentary approaches of differential cloning and genome analysis. The Drosophila odorant receptor (DOR) genes encode a novel family of proteins with seven predicted membrane-spanning domains, unrelated to vertebrate or nematode chemosensory receptors. There are on the order of 60 or more members of this gene family in the Drosophila genome, far fewer than the hundreds to thousands of receptors found in vertebrates or nematodes. DOR genes are selectively expressed in small subsets of olfactory neurons, in expression domains that are spatially conserved between individuals, bilaterally symmetric and not sexually dimorphic. Double in situ RNA hybridization with a number of pairwise combinations of DOR genes fails to reveal any overlap in gene expression, suggesting that each olfactory neuron expresses one or a small number of receptor genes and is therefore functionally distinct. How is activation of such a subpopulation of olfactory receptor neurons in the periphery sensed by the brain? In the mouse, all neurons expressing a given receptor project with precision to two of 1800 olfactory bulb glomeruli, creating a spatial map of odor quality in the brain. We have employed DOR promoter transgenes that recapitulate expression of endogenous receptor to visualize the projections of individual populations of receptor neurons to subsets of the 43 glomeruli in the Drosophila antennal lobe. The results suggest functional conservation in the logic of olfactory discrimination from insects to mammals.

Animals↗
PubMed2003

Correlation between anatomy and electrical activation in canine pulmonary veins.

BACKGROUND: The roles of complex muscle sleeve geometry and fiber orientation in the pulmonary veins (PVs) in wave-front propagation are poorly understood. METHODS AND RESULTS: We mapped the left superior PV (LSPV, n=7) and left inferior PV (LIPV, n=4) of dogs with 420 bipolar electrodes (1-mm resolution) and performed detailed histological examination. In the anterior LSPV-left atrial (LA) junction, myocardial muscle fibers were oriented perpendicular to PV blood flow. A wedge filled with connective tissues led to a complete muscle separation or an abrupt increase in muscle thickness between the PV and LA (0.42+/-0.12 versus 2.0+/-0.31 mm, P<0.01). Distal LSPV pacing resulted in conduction block at the anterior PV-LA junction, with double potentials. In contrast, the posterior LSPV-LA junction showed gradual muscle thickening and a fiber orientation parallel to the blood flow. The maximum PV muscle thickness in the anterior PV-LA junction is thinner than that in the posterior junction (0.83+/-0.15 versus 1.3+/-0.38 mm, P<0.01). Distal LIPV pacing showed multiple PV-LA breakthroughs, with segmental conduction block in the anterior PV-LA junction. The conduction block corresponded to segmental PV-LA muscle disconnection. Complex fiber orientations in the PV muscle sleeves away from the PV-LA junction were responsible for intra-PV conduction delay or block during rapid PV pacing. CONCLUSIONS: We conclude that segmental muscle disconnection and differential muscle narrowing at PV-LA junctions and complex fiber orientations within the PV provide robust anatomical bases for conduction disturbance at the PV-LA junction and complex intra-PV conduction patterns.

Animals↗
PubMed2006

A rapid, direct measurement of bacterial growth rate in anaerobic wastewater treatment.

Reliable design and operation of biological wastewater treatment systems demand robust models of biological degradation processes. However, methods to directly measure key bacterial growth kinetics have not been readily available. Those methods that are available rely on the classic measurement of aerobic respiration using oxygen uptake take rates. This paper shows how the thymidine assay can be used as a rapid and direct measurement of bacterial specific growth rates (mu) in situ for an anaerobic treatment process, independent of aerobic respiration. A filtration-based assay is applied and evaluated a dispersed-phase high-rate anaerobic treatment process, with results obtained in less than an hour. The chemical oxygen demand (COD) biomass in the reactor was 0.52 kg COD m(-3) and the specific growth rate of these anaerobic bacteria was 0.8 +/- 0.2 d(-1). It took the bacterial populations 21.6 hours to double. This is an important advancement from existing methods that use aerobic respiration as a pseudo measurement of bacterial specific growth rates. The method allows rapid and direct measures of microbial growth rates for anaerobic treatment processes.

Bacteria, Anaerobic↗
PubMed2026

Protein persulfidation emerges as a conserved component of the redox response to DNA damage.

Genotoxic stress is frequently accompanied by alterations in cellular redox homeostasis; however, the mechanisms linking redox regulation to the DNA damage response (DDR) remain incompletely understood. Here, we investigated the early redox response to DNA damage induced by methyl methanesulfonate (MMS) in Saccharomyces cerevisiae, focusing on cysteine oxidative post-translational modifications (PTM). We show that activation of the DNA damage response is accompanied by rapid redox changes that occur in the absence of a generalized oxidative stress response. MMS exposure promotes selective remodeling of cysteine oxidative modifications, characterized by decreased free thiols, robust induction of protein persulfidation, and comparatively modest changes in sulfenylation. These alterations are accompanied by increased intracellular hydrogen sulfide levels, supporting the involvement of reactive sulfur species in the cellular response to DNA damage. Proteome-wide analyses revealed that cysteine oxidative modifications preferentially target proteins involved in central metabolism, nucleotide biosynthesis, and genome maintenance. Consistent with these observations, MMS-induced genotoxic stress promotes metabolic adaptation characterized by increased mitochondrial respiration, elevated ATP production, and mitochondrial morphological remodeling, linking bioenergetic adaptation to redox regulation. Importantly, perturbation of intracellular redox balance using N-acetylcysteine compromises survival under DNA-damaging conditions, supporting a functional role for redox signaling during the DDR. Finally, MMS treatment also induces protein persulfidation in mammalian cells. Moreover, exposure to etoposide, a mechanistically distinct genotoxic agent that induces DNA double-strand breaks through topoisomerase II inhibition, showed a similar trend, suggesting that protein persulfidation may not be restricted to alkylation-induced DNA damage. Together our findings identify protein persulfidation as a prominent component of the redox response to DNA damage and provide new insight into the functional interplay between mitochondrial metabolism, cysteine-based redox regulation, and genome maintenance.

Oxidation-Reduction↗
PubMed2000

Amlodipine bioequivalence achieved with a very sensitive liquid chromatography tandem mass spectrometric bioassay.

Amlodipine (CAS 88150-42-9) is a 1,4-dihydropyridine derivative, one of the most widely used drugs for the management of essential hypertension. In developing manidipine (CAS 120092-68-4), a new antihypertensive drug, amlodipine was selected as the reference comparator drug in a Phase III double blind clinical trial. However, manidipine is formulated in hard gelatin capsules, whereas amlodipine is presented as a tablet. In order to respect the double blind design of the study, it was necessary to insert the amlodipine tablet into hard gelatin capsules matching those of the new test product. This called for an amlodipine bioequivalence study on two halves of one tablet inserted into a capsule (test formulation) and two halves of one tablet ingested as such (reference formulation). The bioequivalence trial was carried out on 18 healthy volunteers (9 males and 9 females). Subjects were administered a single 10 mg dose of test and reference products according to a two-treatment, two-period, two-sequence crossover design, with a wash-out period of three weeks. Plasma concentrations of the parent compound were monitored over a period of 6 days, considering the long half-life of amlodipine. The drug was quantified with a very sensitive, robust bioassay, which was set up and validated in our laboratory. Peak concentration and area under the curve of plasma concentrations were log-transformed and analyzed to obtain 90% confidence intervals which proved to be 0.94-1.06, and thus within the acceptable bioequivalence range of 0.80-1.25. Time to peak, analyzed according to a non-parametric test, did not show any statistically significant difference between the test and reference. Both the test and reference products showed a similar and very good safety profile. The conclusion is that one amlodipine tablet broken into two halves and administered as such (reference formulation) is bioequivalent with one amlodipine tablet broken into two halves and encapsulated (test formulation).

Adult↗
PubMed2004

Modulation of plasma membrane calcium-ATPase activity by local calcium microdomains near CRAC channels in human T cells.

The spatial distribution of Ca(2+) signalling molecules is critical for establishing specific interactions that control Ca(2+) signal generation and transduction. In many cells, close physical coupling of Ca(2+) channels and their targets enables precise and robust activation of effector molecules through local [Ca(2+)](i) elevation in microdomains. In T cells, the plasma membrane Ca(2+)-ATPase (PMCA) is a major target of Ca(2+) influx through Ca(2+) release-activated Ca(2+) (CRAC) channels. Elevation of [Ca(2+)](i) slowly modulates pump activity to ensure the stability and enhance the dynamic nature of Ca(2+) signals. In this study we probed the functional organization of PMCA and CRAC channels in T cells by manipulating Ca(2+) microdomains near CRAC channels and measuring the resultant modulation of PMCAs. The amplitude and spatial extent of microdomains was increased by elevating the rate of Ca(2+) entry, either by raising extracellular [Ca(2+)], by increasing the activity of CRAC channels with 2-aminoethoxyborane (2-APB), or by hyperpolarizing the plasma membrane. Surprisingly, doubling the rate of Ca(2+) influx does not further increase global [Ca(2+)](i) in a substantial fraction of cells, due to a compensatory increase in PMCA activity. The enhancement of PMCA activity without changes in global [Ca(2+)](i) suggests that local [Ca(2+)](i) microdomains near CRAC channels effectively promote PMCA modulation. These results reveal an intimate functional association between CRAC channels and Ca(2+) pumps in the plasma membrane which may play an important role in governing the time course and magnitude of Ca(2+) signals in T cells.

Algorithms↗
PubMed2002

Accurate representation of B-DNA double helical structure with implicit solvent and counterions.

High-resolution nuclear magnetic resonance (NMR) and crystallographic data have been taken to refine the force field used in the torsion angle space nucleic acids molecular mechanics program DUPLEX. The population balance deduced from NMR studies of two carcinogen-modified DNA conformers in equilibrium was used to fine tune a sigmoidal, distance-dependent dielectric function so that reasonable relative energies could be obtained. In addition, the base-pair and backbone geometry from high-resolution crystal structures of the Dickerson-Drew dodecamer was used to re-evaluate the deoxyribose pseudorotation profile and the Lennard-Jones nonbonded energy terms. With a modified dielectric function that assumes a very steep distance-dependent form, a deoxyribose pseudorotation profile with reduced energy barriers between C2'- and C3'-endo minima, and a shift of the Lennard-Jones potential energy minimum to a distance approximately 0.4 A greater than the sum of the van der Waals' radii, the sequence-dependent conformational features of the Dickerson-Drew dodecamer in both the solid state and the aqueous liquid crystalline phase are well reproduced. The robust performance of the revised force field, in conjunction with its efficiency through implicit treatment of solvent and counterions, provides a valuable tool for elucidating conformations and structure-function relationships of DNA, including those of molecules modified by carcinogens and other ligands.

Biophysical Phenomena↗