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NASA NTRS2011

Z-Pinch Magneto-Inertial Fusion Propulsion Engine Design Concept

Fusion-based nuclear propulsion has the potential to enable fast interplanetary transportation. Due to the great distances between the planets of our solar system and the harmful radiation environment of interplanetary space, high specific impulse (Isp) propulsion in vehicles with high payload mass fractions must be developed to provide practical and safe vehicles for human spaceflight missions. Magneto-Inertial Fusion (MIF) is an approach which has been shown to potentially lead to a low cost, small fusion reactor/engine assembly (1). The Z-Pinch dense plasma focus method is an MIF concept in which a column of gas is compressed to thermonuclear conditions by an estimated axial current of approximately 100 MA. Recent advancements in experiments and the theoretical understanding of this concept suggest favorable scaling of fusion power output yield as I(sup 4) (2). The magnetic field resulting from the large current compresses the plasma to fusion conditions, and this is repeated over short timescales (10(exp -6) sec). This plasma formation is widely used in the field of Nuclear Weapons Effects (NWE) testing in the defense industry, as well as in fusion energy research. There is a wealth of literature characterizing Z-Pinch physics and existing models (3-5). In order to be useful in engineering analysis, a simplified Z-Pinch fusion thermodynamic model was developed to determine the quantity of plasma, plasma temperature, rate of expansion, energy production, etc. to calculate the parameters that characterize a propulsion system. The amount of nuclear fuel per pulse, mixture ratio of the D-T and nozzle liner propellant, and assumptions about the efficiency of the engine, enabled the sizing of the propulsion system and resulted in an estimate of the thrust and Isp of a Z-Pinch fusion propulsion system for the concept vehicle. MIF requires a magnetic nozzle to contain and direct the nuclear pulses, as well as a robust structure and radiation shielding. The structure, configuration, and materials of the nozzle must meet many severe requirements. The configuration would focus, in a conical manner, the Deuterium-Tritium (D-T) fuel and Lithium-6/7 liner fluid to meet at a specific point that acts as a cathode so the Li-6 can serve as a current return path to complete the circuit. In addition to serving as a current return path, the Li liner also serves as a radiation shield. The advantage to this configuration is the reaction between neutrons and Li-6 results in the production of additional Tritium, thus adding further fuel to the fusion reaction and boosting the energy output. To understand the applicability of Z-Pinch propulsion to interplanetary travel, it is necessary to design a concept vehicle that uses it. The propulsion system significantly impacts the design of the electrical, thermal control, avionics, radiation shielding, and structural subsystems of a vehicle. The design reference mission is the transport of crew and cargo to Mars and back, with the intention that the vehicle be reused for other missions. Several aspects of this vehicle are based on a previous crewed fusion vehicle study called Human Outer Planet Exploration (HOPE), which employed a Magnetized Target Fusion (MTF) propulsion concept. Analysis of this propulsion system concludes that a 40-fold increase of Isp over chemical propulsion is predicted. This along with a greater than 30% predicted payload mass fraction certainly warrants further development of enabling technologies. The vehicle is designed for multiple interplanetary missions and conceivably may be suited for an automated one-way interstellar voyage.

Miernik, Janie H.↗

NASA NTRS2015

Investigation of HZETRN 2010 as a Tool for Single Event Effect Qualification of Avionics Systems - Part II

An accurate prediction of spacecraft avionics single event effect (SEE) radiation susceptibility is key to ensuring a safe and reliable vehicle. This is particularly important for long-duration deep space missions for human exploration where there is little or no chance for a quick emergency return to Earth. Monte Carlo nuclear reaction and transport codes such as FLUKA can be used to generate very accurate models of the expected in-flight radiation environment for SEE analyses. A major downside to using a Monte Carlo-based code is that the run times can be very long (on the order of days). A more popular choice for SEE calculations is the CREME96 deterministic code, which offers significantly shorter run times (on the order of seconds). However, CREME96, though fast and easy to use, has not been updated in several years and underestimates secondary particle shower effects in spacecraft structural shielding mass. Another modeling option to consider is the deterministic code HZETRN 20104, which includes updates to address secondary particle shower effects more accurately. This paper builds on previous work by Rojdev, et al. to compare the use of HZETRN 2010 against CREME96 as a tool to verify spacecraft avionics system reliability in a space flight SEE environment. This paper will discuss modifications made to HZETRN 2010 to improve its performance for calculating SEE rates and compare results with both in-flight SEE rates and other calculation methods.

Rojdev, Kristina↗

NASA NTRS2007

Analysis and Down Select of Flow Passages for Thermal Hydraulic Testing of a SNAP Derived Reactor

As past of the Vision for Space Exploration, man will return to the moon. To enable safe and productive time on the lunar surface will require adequate power resources. To provide the needed power and to give mission planners all landing site possibilities, including a permanently dark crater, a nuclear reactor provides the most options. Designed to be l00kWt providing approx. 25kWe this power plants would be very effective in delivering dependable, site non-specific power to crews or robotic missions on the lunar surface. An affordable reference reactor based upon the successful SNAP program of the 1960's and early 1970's has been designed by Los Alamos National Laboratory that will meet such a requirement. Considering current funding, environmental, and schedule limitations this lunar surface power reactor will be tested using non-nuclear simulators to simulate the heat from fission reactions. Currently a 25kWe surface power SNAP derivative reactor is in the early process of design and testing with collaboration between Los Alamos National Laboratory, Idaho National Laboratory, Glenn Research Center, Marshall Space Flight Center, and Sandia National Laboratory to ensure that this new design is affordable and can be tested using non-nuclear methods as have proven so effective in the past. This paper will discuss the study and down selection of a flow passage concept for a approx. 25kWe lunar surface power reactor. Several different flow passages designs were evaluated using computational fluid dynamics to determine pressure drop and a structural assessment to consider thermal and stress of the passage walls. The reactor design basis conditions are discussed followed by passage problem setup and results for each concept. A recommendation for passage design is made with rationale for selection.

Godfroy, T. J.↗

NASA NTRS1994

Ion Chemistry in Atmospheric and Astrophysical Plasmas

There are many differences and also remarkable similarities between the ion chemistry and physics of planetary ionospheres and the ion chemistry and physics of astronomical environments beyond the solar system. In the early Universe, an expanded cooling gas of hydrogen and helium was embedded in the cosmic background radiation field and ionized by it. As the Universe cooled by adiabatic expansion, recombination occurred and molecular formation was driven by catalytic reactions involving the relict electrons and protons. Similar chemical processes are effective in the ionized zones of gaseous and planetary nebulae and in stellar winds where the ionization is due to radiation from the central stars, in the envelopes of supernovae where the ionization is initiated by the deposition of gamma-rays, in dissociative shocks where the ionization arises from electron impacts in a hot gas and in quasar broad-line region clouds where the quasar is responsible for the ionization. At high altitudes in the atmospheres of the Jovian planets, the main constituents are hydrogen and helium and the ion chemistry and physics is determined by the same processes, the source of the ionization being solar ultraviolet radiation and cosmic rays. After the collapse of the first distinct astronomical entities to emerge from the uniform flow, heavy elements were created by nuclear burning in the cores of the collapsed objects and distributed throughout the Universe by winds and explosions. The chemistry and physics became more complicated. Over 90 distinct molecular species have been identified in interstellar clouds where they are ionized globally by cosmic ray impacts and locally by radiation and shocks associated with star formation and evolution. Complex molecules have also been found in circumstellar shells of evolved stars. At intermediate and low altitudes in the Jovian atmospheres, the ion chemistry is complicated by the increasing abundance of heavy elements such as carbon, and an extensive array of complex molecules has been predicted. Reactions involving heavy elements dominate the structure of the ionspheres of the terrestrial planets and the satellites Titan and Triton.

Dalgarno, A.↗

NASA NTRS1989

Surface structure of neutron stars with high magnetic fields

The equation of state of cold dense matter in strong magnetic fields is calculated in the Thomas-Fermi and Thomas-Fermi-Dirac approximations. For use in the latter calculation, a new expression is derived for the exchange energy of the uniform electron gas in a strong magnetic field. Detailed calculations of the density profile in the surface region of a neutron star are described for a variety of equations of state, and these show that the surface density profile is strongly affected by the magnetic field, irrespective of whether or not matter in a magnetic field has a condensed state bound with respect to isolated atoms. It is also shown that, as a consequence of the field dependence of the screening potential, magnetic fields can significantly increase nuclear reaction rates.

Fushiki, I.↗

NASA NTRS2008

Thermonuclear Burning as a Probe of Neutron Star

Thermonuclear fusion is a fundamental process taking place in the matter transferred onto neutron stars in accreting binary systems. The heat deposited by nuclear reactions becomes readily visible in the X-ray band when the burning is either unstable or marginally stable, and results in the rich phenomenology of X-ray bursts, superbursts, and mHz quasiperiodic oscillations. Fast X-ray timing observations with NASA's Rossi X-ray Timing Explorer (RXTE) over the past decade have revealed a wealth of new phenomena associated with thermonuclear burning on neutron stars, including the discovery of nuclear powered pulsations during X-ray bursts and superbursts. I will briefly review our current observational and theoretical understanding of these new phenomena, with an emphasis on recent findings, and discuss what they are telling us about the structure of neutron stars.

Strohmayer, Tod↗

NASA NTRS1993

The evolution of massive stars including mass loss - Presupernova models and explosion

The evolution of massive stars of 35, 40, 60, and 85 solar masses is followed through all stages of nuclear burning to the point of Fe core collapse. Critical nuclear reaction and mass-loss rates are varied. Efficient mass loss during the Wolf-Rayet (WR) stage is likely to lead to final masses as small as 4 solar masses. For a reasonable parameterization of the mass loss, there may be convergence of all WR stars, both single and in binaries, to a narrow band of small final masses. Our representative model, a 4.25 solar-mass WR presupernova derived from a 60 solar mass star, is followed through a simulated explosion, and its explosive nucleosynthesis and light curve are determined. Its properties are similar to those observed in Type Ib supernovae. The effects of the initial mass and mass loss on the presupernova structure of small mass WR models is also explored. Important properties of the presupernova star and its explosion can only be obtained by following the complete evolution starting on the main sequence.

Woosley, S. E.↗

NASA NTRS1988

Interactions of silicate glasses with aqueous environments under conditions of prolonged contact and flow

This paper discusses mechanisms involving saturation and reactions that lead to the formation of altered phases in silicate glasses considered for use in geologic repositories for nuclear waste. It is shown that the rate of dissolution of silicate glasses exposed to a broad range of contact times, leachant compositions, and surface-to-volume ratios is strongly affected by the presence of reactive species such as Al, Mg, and Fe. The reactive materials may originate in the leachant or, under conditions of high surface-to-volume ratio, in the glass itself. The effects of glass composition on the course of the corrosion process can be viewed in terms of the formation of a surface layer on the leached glass; the type, composition, and structure of this layer control the dissolution behavior of the glass.

Barkatt, Aaron↗

NASA NTRS1993

CCD imaging of Comet Wilson (1987VII) - A quantitative coma analysis

Distinctive cometary components (dust, ions, and radicals) are studied on the basis of 2D, narrow-band CCD images of Comet Wilson (1987VII). The fact that Comet Wilson showed no significant structures in the neutral coma during its first perihelion passage is additional evidence for the hypothesis that dynamically new comets do not show a heterogeneous nucleus, but still have a relatively uniform surface. The deviations from the 1/rho law for the decrease of surface brightness as a function of nuclear distance are explained by a combination of short-term variations in the dust production and the effects of solar radiation pressure. The C2 production rate remains basically constant during the whole observational period, while the CN production rate decreases with increasing heliocentric distance. It is inferred that the formation of C2 might be due both to photolytic destruction of some parent molecules as well as to chemical reactions between other species.

Schulz, Rita↗

NASA NTRS1999

Dark Matter in the Universe and in the Galaxy

During the past four years, Prof. Kamionkowski and collaborators have made progress in research on the nature and distribution of dark-matter in the Universe and in the Galaxy, and on related topics in astrophysics and cosmology. We have made progress on research on the cosmic microwave background, large-scale structure, issues related to particle dark matter, and the gamma-ray-burst enigma. A significant fraction of the research supported by this ATP has been on the cosmic microwave background (CMB). Prof. Kamionkowski and collaborators showed how the polarization of the CMB could be used to detect long-wavelength gravitational waves, such as those produced by inflation. With Kosowsky, Prof. Kamionkowski calculated the amplitude of a stochastic gravitational-wave background that could be detected for a satellite experiment of a given sensitivity and angular resolution. They showed that polarization should improve the sensitivity oa MAP to these gravity waves, and that the Planck Surveyor should do even better. Prof. Kamionkowski, Caldwell, and a student calculated and illustrated the CMB temperature/polarization pattern produced by a single plane-wave gravitational wave. They calculated the amplitude of such a wave that would be detectable with MAP and Planck, and compared that with the sensitivity of traditional gravitational-wave detectors like LIGO and LISA. With Lue and Wang, the PI showed how parity violation from new high-energy physics could conceivably give rise to an observable signature in the CMB polarization. With Loeb, Prof. Kamionkowski showed how measurement of the polarization of CMB photons scattered by hot gas in a cluster could be used to determine the quadrupole moment of the CMB incident on that cluster. Prof. Kamionkowski and Jaffe calculated the amplitude of secondary anisotropies produced by scattering of CMB photons from reionized regions. Research has also been carried out on probing the large-scale distribution of mass in the Universe today, and on structure-formation theories. They investigated the possibility of determining the large-scale distribution of mass in the Universe via measurement of ellipticity-ellipticity correlations in the FIRST radio survey induced by weak gravitational lensing due to mass inhomogeneities along the line of sight. Dr. Summers, Prof. Kamionkowski, and a student investigated the distribution of protogalactic masses and angular momenta in an effort to understand how the luminosity function and angular-momentum distribution of disk galaxies arises from an initial power spectrum of density perturbations. Several projects related to the distribution and possible detection of dark matter in our Galactic halo were studied. The PI was involved in several projects involving the calculation of nuclear-reaction rates needed for stellar evolution and for predictions of solar-neutrino fluxes.

Kamionkowski, Marc↗

NASA NTRS2004

Update on the Status of the FLUKA Monte Carlo Transport Code

The FLUKA Monte Carlo transport code is a well-known simulation tool in High Energy Physics. FLUKA is a dynamic tool in the sense that it is being continually updated and improved by the authors. Here we review the progresses achieved in the last year on the physics models. From the point of view of hadronic physics, most of the effort is still in the field of nucleus--nucleus interactions. The currently available version of FLUKA already includes the internal capability to simulate inelastic nuclear interactions beginning with lab kinetic energies of 100 MeV/A up the the highest accessible energies by means of the DPMJET-II.5 event generator to handle the interactions for greater than 5 GeV/A and rQMD for energies below that. The new developments concern, at high energy, the embedding of the DPMJET-III generator, which represent a major change with respect to the DPMJET-II structure. This will also allow to achieve a better consistency between the nucleus-nucleus section with the original FLUKA model for hadron-nucleus collisions. Work is also in progress to implement a third event generator model based on the Master Boltzmann Equation approach, in order to extend the energy capability from 100 MeV/A down to the threshold for these reactions. In addition to these extended physics capabilities, structural changes to the programs input and scoring capabilities are continually being upgraded. In particular we want to mention the upgrades in the geometry packages, now capable of reaching higher levels of abstraction. Work is also proceeding to provide direct import into ROOT of the FLUKA output files for analysis and to deploy a user-friendly GUI input interface.

Pinsky, L.↗

NASA NTRS1998

Spectroscopy of Chlorosyl Fluoride, FClO

FClO has been proposed as an intermediate in reactions involving ClF, Cl2O, and ClF3O, and it has been suggested as a molecule of atmospheric interest. It has been prepared in situ by the hydrolysis of ClF3. The pure rotational spectrum of FClO has been studied by conventional millimeter wave techniques and by microwave Fourier transform spectroscopy. Selected transitions were searched for using predictions based on an analysis of the nu(sub 1) band. FClO is an asymmetric prolate top, kappa = -0.8950 for F(35)ClO, with a rather small dipole component of 0.093 (4) D along the a-axis and a larger one of 1.93 (5) D along the b-axis. Transitions with 0 <= J <= 54 and 0 <= K(sub a) <= 18 were observed. Cl hyperfine splitting was generally observable throughout the spectrum with F-19 spin-rotation splitting observable as well in the microwave region. Structural parameters, harmonic force constants, and nuclear magnetic shielding parameters were derived and will be compared with data of related molecules, such as ClF3, ClF, FClO2, and FClO3. High resolution infrared spectra were taken in the regions of the FCl stretching mode and bending mode around 600 and 310/cm, respectively. A preliminary analysis indicates that the FCl stretch, near 596.86/cm for F(35)ClO, is in resonance with the dark overtone of delta near 617/cm. A brief progress report will be given.

Mueller, Holger S. P.↗

NASA NTRS2016

Collisional Dissociation of CO: ab initio Potential Energy Surfaces and Quasiclassical Trajectory Rate Coefficients

We have generated accurate global potential energy surfaces for CO+Ar and CO+O that correlate with atom-diatom pairs in their ground electronic states based on extensive ab initio electronic structure calculations and used these potentials in quasi-classical trajectory nuclear dynamics calculations to predict the thermal dissociation rate coefficients over 5000- 35000 K. Our results are not compatible with the 20-45 year old experimental results. For CO + Ar we obtain fairly good agreement with the experimental rate coefficients of Appleton et al. (1970) and Mick and Roth (1993), but our computed rate coefficients exhibit a stronger temperature dependence. For CO + O our dissociation rate coefficient is in close agreement with the value from the Park model, which is an empirical adjustment of older experimental results. However, we find the rate coefficient for CO + O is only 1.5 to 3.3 times larger than CO + Ar over the temperature range of the shock tube experiments (8000-15,000 K). The previously accepted value for this rate coefficient ratio is 15, independent of temperature. We also computed the rate coefficient for the CO + O ex- change reaction which forms C + O2. We find this reaction is much faster than previously believed and is the dominant process in the removal of CO at temperatures up to 16,000 K. As a result, the dissociation of CO is accomplished in two steps (react to form C+O2 and then O2 dissociates) that are endothermic by 6.1 and 5.1 eV, instead of one step that requires 11.2 eV to break the CO bond.

exchange rate coefficient↗

NASA NTRS2004

Nuclear Physics in Space: What We Can Learn From Cosmic Rays

Studies and discoveries in cosmic-ray physics and generally in Astrophysics provide a fertile ground for research in many areas of Particle Physics and Cosmology, such as the search for dark matter, antimatter, new particles, and exotic physics, studies of the nucleosynthesis, origin of Galactic and extragalactic gamma-ray diffuse emission, formation of the large scale structure of the universe etc. In several years new missions are planned for cosmic-ray experiments, which will tremendously increase the quality and accuracy of cosmic-ray data. On the other hand, direct measurements of cosmic rays are possible in only one location on the outskirts of the Milky Way galaxy and present only a snapshot of very dynamic processes. It has been recently realized that direct information about the fluxes and spectra of cosmic rays in distant locations is provided by the Galactic diffuse gamma-rays, therefore, complementing the local cosmic-ray studies. A wealth of information is also contained in the isotopic abundances of cosmic rays, therefore, accurate evaluation of the isotopic production cross sections is of primary importance for Astrophysics of cosmic rays, studies of the galactic chemical evolution, and Cosmology. In this talk, I will show new results obtained with GALPROP, the most advanced numerical model for cosmic-ray propagation, which includes in a self-consistent way all cosmic-ray species (stable and long-lived radioactive isotopes from H to Ni, antiprotons, positrons and electrons, gamma rays and synchrotron radiation), and all relevant processes and reactions.

Moskalenko, Igor V.↗

NASA NTRS2012

Effects of Dietary Iron and Gamma Radiation on the Rat Retina

A health risk of concern for NASA relates to radiation exposure and its synergistic effects with other space environmental factors, includi ng nutritional status of the crew. Astronauts consume almost three times the recommended daily allowance of iron due to the use of fortifie d foods aboard the International Space Station, with iron intake occa sionally exceeding six times the recommended values. Recently, NASA has become concerned with visual changes associated with spaceflight, a nd research is being conducted to elucidate the etiology of eye structure alterations in the spaceflight environment. Terrestrially, iron o verload is also associated with certain optic neuropathies. In additi on, due to its role in Fenton reactions, iron can potentiate oxidative stress, which is a recognized cause of cataract formation. As part o f a study investigating the combined effects of radiation exposure an d iron overload on multiple physiological systems, we focused on defining the effects of both treatments on eye biology. In this study, 12- week-old Sprague-Dawley rats were assigned to one of four experimental groups: normal iron/no radiation (Control/Sham), high iron/no radiat ion (Fe/Sham), normal iron/gamma radiation (3 Gy cumulative dose, fra ctionated at 0.375 Gy/d every other day for 16 d) (Control/Rad), and high iron/gamma radiation (Fe/Rad). Oxidative stress-induced DNA damag e, measured as concentration of the marker 8-hydroxy-2'-deoxyguanosine (8OHdG) in eye retinal tissue by enzyme-immunoanalysis did not show significant changes among treatments. However, there was an overall i ncrease in 8OHdG immunostaining density in retina sections due to radiation exposure (P = 0.05). Increased dietary iron and radiation expos ure had an interactive effect (P = 0.02) on 8OHdG immunostaining of t he retinal ganglion cell layer with iron diet increasing the signal in the group not exposed to radiation (P = 0.05). qPCR gene expression profiling of relevant target genes indicated upregulation of ferritin light chain (P = 0.09) as a result of dietary iron but no change in e xpression of the gene for ferritin heavy chain. Immunolocalization of light chain and heavy chain of the iron storage protein ferritin showed the expected distribution in the choroid, photoreceptor layer, inn er nuclear layer and in the inner plexiform layer that corresponded t o the synaptic terminals of bipolar cells. Evidence of stress and damage in the retina was also suggested by a decrease in expression of th e survival marker Bcl2 (P = 0.01) and the protective proteins clusterin (P = 0.04) and heat shock factor 1 (Hsf1, P < 0.001), as a result o f increased dietary iron. The effect of increased iron on expression of the antioxidant enzyme heme oxygenase 1 (Hmox1) had a significant interaction with the effect of radiation (P < 0.001). In summary, the results of this study indicate that both gamma radiation exposure and a moderate increase in dietary iron can contribute to deleterious cha nges in retinal health and physiology.

Morgan, Jennifer↗

NASA NTRS2019

The Afterglow and Kilonova of the Short GRB 160821B

GRB 160821B is a short duration gamma-ray burst (GRB) detected and localized by the Neil Gehrels Swift Observatory in the outskirts of a spiral galaxy at z = 0.1613, at a projected physical offset of 16 kpc from the galaxy’s center. We present X-ray, optical/nIR, and radio observations of its counterpart and model them with two distinct components of emission: a standard afterglow, arising from the interaction of the relativistic jet with the surrounding medium, and a kilonova, powered by the radioactive decay of the sub-relativistic ejecta. Broadband modelling of the afterglow data reveals a weak reverse shock propagating backward into the jet, and a likely jet-break at 3.5 d. This is consistent with a structured jet seen slightly off-axis (θview ∼ θcore) while expanding into a low-density medium (n ≈ 10−3 cm−3). Analysis of the kilonova properties suggests a rapid evolution towards red colours, similar toAT2017gfo, and a low-nIR luminosity, possibly due to the presence of a long-lived neutron star. The global properties of the environment, the inferred low mass (Mej <~ 0.006 Msun) and velocities (vej >~ 0.05c) of lanthanide-rich ejecta are consistent with a binary neutron star merger progenitor.

Gravitational waves↗

NASA NTRS1997

Structure of an anti-HIV-1 hammerhead ribozyme complex with a 17-mer DNA substrate analog of HIV-1 gag RNA and a mechanism for the cleavage reaction: 750 MHz NMR and computer experiments

The structure of an anti-HIV-1 ribozyme-DNA abortive substrate complex was investigated by 750 MHz NMR and computer modeling experiments. The ribozyme was a chimeric molecule with 30 residues-18 DNA nucleotides, and 12 RNA residues in the conserved core. The DNA substrate analog had 17 residues. The chimeric ribozyme and the DNA substrate formed a shortened ribozyme-abortive substrate complex of 47 nucleotides with two DNA stems (stems I and III) and a loop consisting of the conserved core residues. Circular dichroism spectra showed that the DNA stems assume A-family conformation at the NMR concentration and a temperature of 15 degrees C, contrary to the conventional wisdom that DNA duplexes in aqueous solution populate entirely in the B-form. It is proposed that the A-family RNA residues at the core expand the A-family initiated at the core into the DNA stems because of the large free energy requirement for the formation of A/B junctions. Assignments of the base H8/H6 protons and H1' of the 47 residues were made by a NOESY walk. In addition to the methyl groups of all T's, the imino resonances of stems I and III and AH2's were assigned from appropriate NOESY walks. The extracted NMR data along with available crystallographic data, were used to derive a structural model of the complex. Stems I and III of the final model displayed a remarkable similarity to the A form of DNA; in stem III, a GC base pair was found to be moving into the floor of the minor groove defined by flanking AT pairs; data suggest the formation of a buckled rhombic structure with the adjacent pair; in addition, the base pair at the interface of stem III and the loop region displayed deformed geometry. The loop with the catalytic core, and the immediate region of the stems displayed conformational multiplicity within the NMR time scale. A catalytic mechanism for ribozyme action based on the derived structure, and consistent with biochemical data in the literature, is proposed. The complex between the anti HIV-1 gag ribozyme and its abortive DNA substrate manifests in the detection of a continuous track of A.T base pairs; this suggests that the interaction between the ribozyme and its DNA substrate is stronger than the one observed in the case of the free ribozyme where the bases in stem I and stem III regions interact strongly with the ribozyme core region (Sarma, R. H., et al. FEBS Letters 375, 317-23, 1995). The complex formation provides certain guidelines in the design of suitable therapeutic ribozymes. If the residues in the ribozyme stem regions interact with the conserved core, it may either prevent or interfere with the formation of a catalytically active tertiary structure.

NASA Discipline Exobiology↗