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G J Thomas

Publications and source records attributed to G J Thomas.

At least 91 records · Page 5Linked to original sources
PubMed1996

Theory, design, and characterization of a microdialysis flow cell for Raman spectroscopy.

The theory, design, and application of a dialysis flow cell for Raman spectroscopy are described. The flow cell permits rapid collection of Raman spectra concurrent with the efflux of small solute molecules or ions into a solution of macromolecules and is well suited to acquisition of data during hydrogen-isotope exchange reactions of biological molecules. Kinetic parameters of the device are described by a diffusion model, which accounts satisfactorily for the observed rates of efflux of deuterium oxide (K2H = 0.30 min-1), calcium ions (KCa = 0.10 min-1) and EGTA (KEGTA = 0.07 min-1). Application to the kinetics of glutamate protonation in a peptide copolymer [poly(Glu, Lys, Tyr)] shows that pH-titration rates as high as 3.3 pH units/min can be monitored. It is also shown that one can extract first-order hydrogen-isotope exchange rate constants from measured second-order exchanges by taking into account the rate of entry of 2H2O effluent into the bulk H2O solution. Deuterium exchanges of the single-stranded polyribonucleotides poly(rA) and poly(rU) and of the double-stranded RNA genome from bacteriophage phi 6 have been investigated. The measured nucleotide base exchange rates are comparable with those determined previously by other methods. The results indicate that base exchanges as fast as approximately 2 min-1 can be determined reliably with the present design. Application of the Raman flow cell to hydrogen-isotope exchange of the basic pancreatic trypsin inhibitor confirms consistency with results obtained previously on this protein by tritiation and NMR techniques.

Calcium↗
PubMed1995

Solution conformation of the extracellular domain of the human tumor necrosis factor receptor probed by Raman and UV-resonance Raman spectroscopy: structural effects of an engineered PEG linker.

The solution structure of the Escherichia coli-expressed extracellular domain, residues 12-172, of the human 55 kDa type I tumor necrosis factor receptor (TNFR) has been probed by Raman (514.5 nm) and ultraviolet-resonance Raman (244 nm) excitations. The Raman spectra have been collected from both the free TNFR domain and an engineered "dumbbell-like" derivative, consisting of two mutant receptor moieties linked by a 20 kDa polyethylene glycol (PEG) tether. The results demonstrate a TNFR secondary structure which is rich in beta-sheet and deficient in alpha-helix, consistent with the reported X-ray crystal structure of baculovirus expressed receptor complexed with factor beta [Banner, D. W., D'Arcy, A., Janes, W., Gentz, R., Schoenfeld, H.-J., Broger, C., Loetscher, H., & Lesslauer, W. (1993) Cell 73, 431-445]. Conversely, the solution structure of TNFR differs from the crystal structure in its distribution of disulfide rotamers and in the orientation of its unique indole side chain (tryptophan-107). These differences are attributed, respectively, to N-terminal truncation and factor binding in the TNFR crystal structure. The tryptophan configuration, which is easily monitored in both Raman and UVRR spectra, is proposed as a potential signal of receptor/factor recognition and binding. Application of the Raman probes to the engineered TNFR dumbbell, which is of interest as a potential therapeutic, shows that TNFR moieties of the dumbbell exhibit secondary structures and side chain environments which are indistinguishable from those of the native, wild-type moiety. The results suggest that the PEGylated dumbbell may function as an effective TNFR drug delivery system without the consequence of a deleterious antigenic response.

Amino Acid Sequence↗
PubMed1995

Structure and dynamics of interstrand guanine association in quadruplex telomeric DNA.

Exchanges of the amino and imino protons in guanine quartets of telomeric DNA have been time-resolved by laser Raman spectroscopy. The Raman dynamic probe has been applied to parallel and antiparallel quadruplexes formed by the telomeric repeat of Oxytricha nova, d(T4G4)4, and to the highly thermostable parallel quadruplex formed by d(G12). Time-dependent Raman spectra of the d(G12) quadruplex reveal two characteristic exchange reactions for guanine N2 amino groups. At 10 degrees C, the pseudo-first-order exchange rates are kN2H(10 degrees C) = 5.7 x 10(-3) and k'N2H'(10 degrees C) = 1.2 x 10(-2) min-1, assignable to Hoogsteen-hydrogen-bonded and non-hydrogen-bonded N2 protons, respectively. These measurements provide the first quantitative determination of two kinetically distinct N2 amino proton exchange reactions in the guanine quartet and demonstrate that amino group rotation about the C2-N2 bond is highly restricted in the quadruplex. No exchange of guanine N1 imino sites occurs in d(G12) at 10 degrees C, and N1 exchange remains slow even at 95 degrees C [kN1H(95 degrees C) = 2.7 x 10(-2) min-1], indicating severe suppression of imino exchange in guanine quartets. For both parallel and antiparallel quadruplexes of d(T4G4)4, proton exchange rates decrease in the order thymine N3 imino > guanine N2 amino > guanine N1 imino. The rapid exchange of thymine N3 imino sites indicates that thymine quartets are not stabilized in Oxytricha quadruplexes. The protium-->deuterium exchange experiments also establish new guanine Raman band assignments. Importantly, the 1603 cm-1 band is due to in-plane bending of N1-H, while the 1644 cm-1 band involves scissoring of the N2 amino group. Accordingly, the 1603 and 1644 cm-1 bands are potentially valuable markers of hydrogen-bonding interactions specific to guanine imino and amino sites, respectively. The present findings also show that guanine hydrogen bonding and exchange dynamics are not interrelated in a simple manner. Despite extraordinary retardation of N1 imino proton exchange, Raman markers suggest that Hoogsteen-type guanine-guanine hydrogen bonding (N1-H...O=C6) is comparable in strength to hydrogen bonding of N1-H with water and, surprisingly, much weaker than hydrogen bonding between N1-H and the cytosine N3 acceptor of Watson-Crick B DNA.

Animals↗
PubMed1995

A phase diagram for sodium and potassium ion control of polymorphism in telomeric DNA.

Switching between antiparallel and parallel quadruplex structures of telomeric DNA under the control of intracellular Na+ and K+ has been implicated in the pairing of chromosomes during meiosis. Using Raman spectroscopy, we have determined the dependence of the interquadruplex equilibrium of the telomeric repeat of Oxytricha nova, upon solution concentrations of Na+ and K+. Both alkali cations facilitate the formation of an antiparallel foldback quadruplex at low concentration, and a parallel extended quadruplex at higher concentration. However, K+ is more effective than Na+ in inducing the parallel association. We propose a phase diagram relating d(T4G4)4 polymorphism to intracellular [Na+]/[K+] ratios. The phase diagram indicates that the interquadruplex equilibrium is highly sensitive to changes in the mole fraction of either cation when the total concentration falls within the interval 65 to 225 mM, a range which encompasses total of the Na+ and K+ concentrations occurring in a typical mammalian cell. These results support a role for the guanine-rich overhang of eukaryotic DNA in promoting chromosome association during meiotic synapsis.

Animals↗
PubMed1995

Raman spectroscopy of the filamentous virus Ff (fd, fl, M13): structural interpretation for coat protein aromatics.

Site-specific isotope substitutions in the coat protein (pVIII) of the filamentous bacterial virus Ff (fd, fl, M13) have been employed to advance vibrational band assignments and facilitate structural interpretation of the Raman spectrum. We report spectra of phage fd assembled in vivo from pVIII subunits incorporating either deuteriophenylalanine (Fd5), deuteriotryptophan (Wd5), or deuteriotyrosine (Yd4) residues with labeled ring sites. The deuterated aromatics were introduced into fd individually and in combination. On the basis of observed isotope shifts, definitive assignments have been developed for all prominent Raman bands diagnostic of the pVIII aromatic residues (F11, F42, F45, W26, Y21, Y24). The present study constitutes the first direct experimental determination of Raman fingerprints of tyrosine and phenylalanine side chains within hydrophobic alpha-helical domains and yields unexpected results. Importantly, neither Y21 nor Y24 of pVIII exhibits the "canonical" Fermi doublet expected in the 820-860 cm-1 interval of the Raman spectrum. Instead, each tyrosine exhibits a single band near 853 cm-1. Since the application of denaturing conditions is sufficient to generate in fd an apparent Fermi doublet, it is concluded that the anomalous singlet is intrinsic to tyrosine environments in the native virion assembly. In addition, the Raman results clearly demonstrate an interdependence of the environments of aromatic side chains in virion subunits. We show that the results on fd isotopomers are also confirmed by Raman spectroscopy of Ff virions incorporating the tyrosine mutations Y21M, Y24M, and Y21F/Y24S. The Raman marker bands identified for pVIII aromatics modify and extend Raman correlations proposed previously for proteins. The unusual environments detected for aromatic residues in the mature Ff assembly are discussed in relation to recently proposed models for filamentous virion architecture.

Amino Acid Sequence↗
PubMed1995

Raman spectroscopy of DNA-metal complexes. II. The thermal denaturation of DNA in the presence of Sr2+, Ba2+, Mg2+, Ca2+, Mn2+, Co2+, Ni2+, and Cd2+.

Differential scanning calorimetry, laser Raman spectroscopy, optical densitometry, and pH potentiometry have been used to investigate DNA melting profiles in the presence of the chloride salts of Ba2+, Sr2+, Mg2+, Ca2+, Mn2+, Co2+, Ni2+, and Cd2+. Metal-DNA interactions have been observed for the molar ratio [M2+]/[PO2-] = 0.6 in aqueous solutions containing 5% by weight of 160 bp mononucleosomal calf thymus DNA. All of the alkaline earth metals, plus Mn2+, elevate the melting temperature of DNA (Tm > 75.5 degrees C), whereas the transition metals Co2+, Ni2+, and Cd2+ lower Tm. Calorimetric (delta Hcal) and van't Hoff (delta HVH) enthalpies of melting range from 6.2-8.7 kcal/mol bp and 75.6-188.6 kcal/mol cooperative unit, respectively, and entropies from 17.5 to 24.7 cal/K mol bp. The average number of base pairs in a cooperative melting unit ( ) varied from 11.3 to 28.1. No dichotomy was observed between alkaline earth and transition DNA-metal complexes for any of the thermodynamic parameters other than their effects on Tm. These results complement Raman difference spectra, which reveal decreases in backbone order, base unstacking, distortion of glycosyl torsion angles, and rupture of hydrogen bonds, which occur after thermal denaturation. Raman difference spectroscopy shows that transition metals interact with the N7 atom of guanine in duplex DNA. A broader range of interaction sites with single-stranded DNA includes ionic phosphates, the N1 and N7 atoms of purines, and the N3 atom of pyrimidines. For alkaline earth metals, very little interaction was observed with duplex DNA, whereas spectra of single-stranded complexes are very similar to those of melted DNA without metal. However, difference spectra reveal some metal-specific perturbations at 1092 cm-1 (nPO2-), 1258 cm-1 (dC, dA), and 1668 cm-1 (nC==O, dNH2 dT, dG, dC). Increased spectral intensity could also be observed near 1335 cm-1 (dA, dG) for CaDNA. Optical densitometry, employed to detect DNA aggregation, reveals increased turbidity during the melting transition for all divalent DNA-metal complexes, except SrDNA and BaDNA. Turbidity was not observed for DNA in the absence of metal. A correlation was made between DNA melting, aggregation, and the ratio of Raman intensities I1335/I1374. At room temperature, DNA-metal interactions result in a pH drop of 1.2-2.2 units for alkaline earths and more than 2.5 units for transition metals. Sr2+, Ba2+, and Mg2+ cause protonated sites on the DNA to become thermally labile. These results lead to a model that describes DNA aggregation and denaturation during heating in the presence of divalent metal cations; 1) The cations initially interact with the DNA at phosphate and/or base sites, resulting in proton displacement. 2) A combination of metal-base interactions and heating disrupts the base pairing within the DNA duplex. This allows divalent metals and protons to bind to additional sites on the DNA bases during the aggregation/melting process. 3) Strands whose bases have swung open upon disruption are linked to neighboring strands by metal ion bridges. 4) Near the midpoint of the melting transition, thermal energy breaks up the aggregate. We have no evidence to indicate whether metal ion cross-bridges or direct base-base interactions rupture first. 5) Finally, all cross-links break, resulting in single-stranded DNA complexed with metal ions.

Animals↗
PubMed1995

Polarized Raman spectra of oriented fibers of A DNA and B DNA: anisotropic and isotropic local Raman tensors of base and backbone vibrations.

Polarized Raman spectra of oriented fibers of calf thymus DNA in the A and B conformations have been obtained by use of a Raman microscope operating in the 180 degrees back-scattering geometry. The following polarized Raman intensities in the spectral interval 200-1800 cm-1 were measured with both 514.5 and 488.0 nm laser excitations: (1) Icc, in which the incident and scattered light are polarized parallel to the DNA helical axis (c axis); (2) Ibb, in which the incident and scattered light are polarized perpendicular to c; and (3) Ibc and Icb, in which the incident and scattered light are polarized in mutually perpendicular directions. High degrees of structural homogeneity and unidirectional orientation were confirmed for both the A and B form fibers, as judged by comparison of the observed Raman markers and intensity anisotropies with measurements reported previously for oligonucleotide single crystals of known three-dimensional structures. The fiber Raman anisotropies have been combined with solution Raman depolarization ratios to evaluate the local tensors corresponding to key conformation-sensitive Raman bands of the DNA bases and sugar-phosphate backbone. The present study yields novel vibrational assignments for both A DNA and BDNA conformers and also confirms many previously proposed Raman vibrational assignments. Among the significant new findings are the demonstration of complex patterns of A form and B form indicator bands in the spectral intervals 750-900 and 1050-1100 cm-1, the identification of highly anisotropic tensors corresponding to vibrations of base, deoxyribose, and phosphate moieties, and the determination of relatively isotropic Raman tensors for the symmetrical stretching mode of phosphodioxy groups in A and B DNA. The present fiber results provide a basis for exploitation of polarized Raman spectroscopy to determine DNA helix orientation as well as to probe specific nucleotide residue orientations in nucleoproteins, viruses, and other complex biological assemblies.

Animals↗
PubMed1995

Design and performance of an ultraviolet resonance Raman spectrometer for proteins and nucleic acids.

We describe an ultraviolet resonance Raman (UVRR) spectrometer appropriate for structural studies of biological macromolecules and their assemblies. Instrument design includes the following features: a continuous wave, intracavity doubled, ultraviolet laser source for excitation of the Raman spectrum; a rotating cell (or jet source) for presentation of the sample to the laser beam; a Cassegrain optic with f/1.0 aperture for collection of the Raman scattering; a quartz prism dispersing element for rejection of stray light and Rayleigh scattering; a 0.75-m single grating monochromator for dispersion of the Raman scattering; and a liquid-nitrogen-cooled, charge-coupled device for detection of the Raman photons. The performance of this instrument, assessed on the basis of the observed signal-to-noise ratios, the apparent resolution of closely spaced spectral bands, and the wide spectrometer bandpass of 2200 cm-1, is believed superior to previously described UVRR spectrometers of similar design. Performance characteristics of the instrument are demonstrated in UVRR spectra obtained from standard solvents, p-ethylphenol, which serves as a model for the tyrosine side chain, the DNA nucleotide deoxyguanosine-5'-monophosphate, and the human tumor necrosis factor binding protein, which is considered representative of soluble globular proteins.

Acetonitriles↗
PubMed1995

Rat mesangial cells in vitro synthesize a spectrum of proteoglycan species including those of the basement membrane and interstitium.

Accumulation of extracellular matrix within the mesangium is an important event in the development of glomerular disease. In this report we have used indirect immunofluorescence to positively identify a number of constituents of the mesangial matrix synthesized by rat mesangial cells (RMC) in vitro including laminin, fibronectin, type IV collagen and the basement membrane heparan sulphate proteoglycan (BM-HSPG) known as perlecan. In addition, using Mab 2B5 we demonstrate that RMC synthesize a specific basement membrane chondroitin sulfate (BM-CSPG), a matrix component that in normal animals is localized in the mesangium but is not found in the pericapillary glomerular basement membrane (GBM). Further characterization of the proteoglycans synthesized by RMC in vitro revealed: (i) a second large CSPG, identified as versican; (ii) two small dermatan sulphate proteoglycans identified as biglycan and decorin, which together account for the majority of the proteoglycans; (iii) a large HSPG-I, probably related to perlecan; and (iv) a small HSPG-II. The cell layer proteoglycans can be sub-divided into a class that are probably free in the membrane, and a class of anchored molecules of the extracellular matrix or stabilized by cytoskeletal elements.

Animals↗
PubMed1995

Source of peritoneal proteoglycans. Human peritoneal mesothelial cells synthesize and secrete mainly small dermatan sulfate proteoglycans.

This study describes experiments that compare the proteoglycans (PGs) extracted from the dialysate from patients receiving continuous peritoneal ambulatory dialysis (CAPD) with those secreted by metabolically labeled human peritoneal mesothelial cells in vitro. The PGs isolated from both sources were predominantly small chondroitin sulfate/dermatan sulfate PGs. Western blot of the core proteins obtained after chondroitin ABC lyase treatment with specific antibodies identified decorin and biglycan. With [35S]sulfate and [35S]methionine as labeling precursors it was shown that dermatan sulfate rather than chondroitin sulfate were the major glycosaminoglycan chains and that decorin was the predominant species. These data provide the first evidence that human peritoneal mesothelial cells may be the principal source of PGs in the peritoneum. Given the proposed functions of decorin and biglycan, the results suggest that these PGs may be involved in the control of transforming growth factor-beta activity and collagen fibril formation in the peritoneum.

Ascitic Fluid↗
PubMed1994

Secondary structure and interaction of phage D108 Ner repressor with a 61-base-pair operator: evidence for altered protein and DNA structures in the complex.

Ner repressors of the transposable phages Mu and D108 play a central role in regulating the expression of the early (transposase) operon and in ensuring that phage growth proceeds along a lytic pathway. The latter function is analogous to that performed by the Cro protein of phage lambda. Unlike lambda Cro, however, the structural basis of operator recognition is not known for the Ner repressors. In order to elucidate the structural features underlying operator recognition by Ner repressors, we have employed Raman spectroscopy as a probe of the solution secondary structures of both D108 Ner and Mu Ner. Additionally, we have obtained Raman spectra of the D108 Ner repressor when bound to a 61-base-pair oligodeoxynucleotide containing the 55-base-pair D108 ner binding site. Conformation-sensitive Raman bands show that both D108 and Mu Ner contain similar, highly alpha-helical (approximately 45%) secondary structures. The Raman markers also show that the substantial nonhelical secondary structure of both D108 Ner and Mu Ner is largely beta-stranded. The protein-free 61-bp D108 ner operator exhibits Raman marker bands diagnostic of an uninterrupted B DNA duplex. In the D108 Ner:DNA complex, we find the following: (i) B DNA stereochemistry is fully conserved, although with significant perturbations to the B form backbone geometry, particularly in AT-rich regions of the bound operator. (ii) The specific interactions that occur between Ner repressor and operator involve B DNA major groove sites. (iii) A small (8 +/- 3%) increase in alpha-helix content of the Ner repressor is detected upon operator binding. (iv) Finally, the local environments of many aromatic amino acids are substantially altered in the D108 Ner:DNA complex. We propose a molecular model for binding of D108 Ner to its operator that is consistent with both the present spectroscopic findings and the results of recent biochemical studies. Essential features of this model are bending of the DNA double helix and contact of operator sites with repressor domains bearing sequence homologies with the helix-turn-helix (HTH) motifs of other DNA-binding proteins. The Raman fingerprint of the Ner:DNA complex is shown to be clearly distinguishable from that of the lambda cI:DNA complex, even though both gene regulatory complexes are presumed to employ HTH recognition motifs. The unique Raman signatures observed for these repressor complexes suggest that the Raman methodology may be useful in discriminating different modes of operator recognition by the HTH motifs of regulatory proteins.

Amides↗
PubMed1994

Glomerular mesangial cells in vitro synthesize an aggregating proteoglycan immunologically related to versican.

Recent studies have shown that mesangial cells derived from human adult glomeruli synthesize a number of 35S-labelled proteoglycans including a large chondroitin sulphate proteoglycan (CSPG), two dermatan sulphate proteoglycans (biglycan and decorin) and two heparan sulphate proteoglycans [Thomas, Mason and Davies (1991) Biochem. J. 277, 81-88]. In the present study we have examined the interaction of these proteoglycans with hyaluronan (HA) using associative gel chromatography. Only the large CSPG bound to HA, with 60% of those molecules in the medium and 80% of those in the cell layer being able to interact. Reduction and alkylation, or treatment of the monomer CSPG with proteinases, prevented the formation of aggregates, suggesting that the core protein was involved. The aggregates formed between purified CSPG and HA could be dissociated in the presence of HA-oligosaccharides of at least 10 monosaccharides in length. The inclusion of link protein with CSPG and HA promoted the formation of aggregates. Experiments with 3H-labelled mesangial-cell proteoglycans confirmed that only the large CSPG, with core protein molecular masses of 400 kDa and 500 kDa, interacted with HA. After chondroitin ABC lyase treatment of CSPG isolated from conditioned culture medium, several bands similar to those observed with 3H-labelled core proteins were identified using a polyclonal antiserum that recognizes versican. A monoclonal antibody recognizing the 1-C-6 epitope in the G1 and G2 globular regions of aggrecan did not recognize either mesangial-cell CSPG or bovine aortic versican. Northern-blot analysis confirmed that human mesangial cells express versican. Thus human mesangial large CSPG is a member of the versican family of proteoglycans. The interaction of CSPG and HA within the glomerulus may be important in glomerular cell migration and proliferation.

Adult↗
PubMed1994

Hydrogen exchange dynamics of the P22 virion determined by time-resolved Raman spectroscopy. Effects of chromosome packaging on the kinetics of nucleotide exchanges.

We describe the application of laser Raman spectroscopy to probe hydrogen isotope exchange dynamics of nucleic acid and protein constituents in a double-stranded DNA virus, the icosahedral bacteriophage P22. The Raman dynamic method employs a dialysis flow cell to control D2O efflux into an H2O solution of the virus sample while the rates of deuterium exchange of protons in the viral nucleic acid and protein molecules are measured spectrophotometrically in real time. The method provides structural and kinetic information about three different and distinct classes of exchangeable protons of the native virion: (1) labile imino (NH) and amino (NH2) protons of the bases which participate in Watson-Crick hydrogen bonding in the packaged genome; (2) pseudolabile purinic (8CH) protons that line the major groove of packaged P22 DNA; and (3) main-chain amide (NH) protons of viral subunits comprising the shell that encapsidates the DNA. The results obtained on P22 demonstrate that interchange of aqueous solvent with the virion interior is rapid and complete. We find that while labile protons of packaged DNA exchange rapidly, most amide protons in capsid subunits are resistant to solvent-catalyzed exchange. Further, stereospecific retardation of exchange is observed for major-groove protons of the packaged P22 genome. The quantitative measurements can be summarized and interpreted as follows. (1) Imino and amino protons of all bases in packaged P22 DNA exchange more rapidly (approximately 2-fold faster) than the corresponding protons in unpackaged P22 DNA. Remarkably, packaging actually accelerates labile imino and amino hydrogen exchanges of the viral DNA, an effect which can be attributed to selective stabilization in the packaged chromosome of a base-pair open state (breathing model). (2) Conversely, purine 8CH exchange rates in packaged P22 DNA are significantly retarded in comparison to those of unpackaged P22 DNA. The observed 8CH exchange retardation effects are similar for both adenine and guanine residues, indicating that they do not originate from purine-specific interactions but probably reflect steric shielding of the major groove of packaged DNA from free access to solvent. This effect is likely distributed throughout the 43,400 base-pair genome. (3) Only a small population (approximately 15 to 20%) of subunit amide protons exchanges within the time frame of complete exchange of all protons of packaged P22 DNA. Complete exchange of the capsid is not achieved even after several months of incubation at 40 degrees C.(ABSTRACT TRUNCATED AT 400 WORDS)

Bacteriophage P22↗
PubMed1994

Structural polymorphism of telomere DNA: interquadruplex and duplex-quadruplex conversions probed by Raman spectroscopy.

The solution secondary structures and nucleotide conformations in the telomeric DNA of Oxytricha nova have been determined by Raman spectroscopy. Structural polymorphism is demonstrated for both single-stranded [d(T4G4)4] and double-stranded [d(G4T4G4).d(C4A4C4)] telomere models. In the case of d(T4G4)4, which is a prototype for the single-stranded telomeric tail, an interquadruplex equilibrium involving parallel and antiparallel strand configurations is shown to be governed by the solution concentrations of both Na+ and K+. In both the parallel and antiparallel quadruplexes of d(T4G4)4, the local geometry of the phosphodiester backbone is similar to that of canonical B DNA, and associations between bases of the guanine quartet involve Hoogsteen hydrogen bonding. However, the deoxyguanosine (dG) sugar conformations are significantly different in the two quadruplexes. In the extended parallel form, dG residues assume only the C2'-endo/anti conformation with respect to deoxyribose pucker and glycosyl orientation. In the foldback antiparallel form, dG residues are distributed equally between C2'-endo/anti and C2'-endo/syn conformations. In the case of d(G4T4G4).d(C4A4C4), which serves as a model for the double-stranded B DNA regions of Oxytricha telomeres, we show that disproportionation of the B form duplex to yield stable parallel quadruplexes of the guanine-rich strand occurs reversibly at high solution concentrations of either Na+ or K+. The present study reveals that both interquadruplex and duplex-quadruplex conversions of Oxytricha telomeric DNA are under the control of an alkali cation switch.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1994

Purification of viruses and macromolecular assemblies for structural investigations using a novel ion exchange method.

We describe a novel ion exchange chromatographic technique suitable for large-scale preparation of viruses and other biomacromolecular assemblies in highly purified form. The method, which utilizes anion exchange on either of two commercially available cellulose cartridges, is applied to the Escherichia coli bacteriophage PRD1. Viral particles eluted from both QMA and DEAE cartridges retain infectivity and exhibit greater homogeneity of composition, as judged by gel electrophoresis and electron microscopy, than particles purified by rate zonal sucrose gradient centrifugation. The ion exchange protocols are rapid, requiring less than 15 min elution time, and permit retrieval of the purified viral particles at high concentration in aqueous media without centrifugal pelleting. The present method is particularly well suited to the preparation of milligram to decigram quantities of virus, sufficient for many biophysical structural analyses, including investigations by solution spectroscopic and crystal diffraction techniques. The feasibility and advantages of the ion exchange chromatographic procedure are demonstrated by application of laser Raman spectroscopy to ion exchange purified PRD1 virions and subviral assemblies.

Centrifugation, Zonal↗