Photovoltaic Effects and Charge Transport Studies in Phycobiliproteins

Phycobiliproteins form highly efficient light absorbing systems in certain algae. We have investigated the charge-transport phenomena in these proteins by analyzing the dark current-voltage and photocurrent characteristics obtained across Au-phycobiliprotein-Au samples. A photovoltaic effect was observed for Au-phycoerythrin-Au sample. At low intensity levels, the photocurrent closely follows Onsager's law of geminate recombination in three dimensions.

A quartz crystal microbalance cell biosensor: detection of microtubule alterations in living cells at nM nocodazole concentrations

The quartz crystal microbalance (QCM) was used to create a piezoelectric biosensor utilizing living endothelial cells (ECs) as the biological signal transduction element. ECs adhere to the hydrophilically treated gold QCM surface under growth media containing serum. At 24 h following cell addition, calibration curves were constructed relating the steady state Deltaf and DeltaR shift values observed to the numbers of electronically counted cells requiring trypsinization to be removed from the surface. We then utilized this EC QCM biosensor for the detection of the effect of [nocodazole] on the steady state Deltaf and DeltaR shift values. Nocodazole, a known microtubule binding drug, alters the cytoskeletal properties of living cells. At the doses used in these studies (0.11-15 microM), nocodazole, in a dose dependent fashion, causes the depolymerization of microtubules in living cells. This leads a monolayer of well spread ECs to gradually occupy a smaller area, lose cell to cell contact, exhibit actin stress fibers at the cell periphery and acquire a rounded cell shape. We observed the negative Deltaf shift values and the positive DeltaR shift values to increase significantly in magnitude over a 4-h incubation period following nocodazole addition, in a dose dependent fashion, with a transition midpoint of 900 nM. Fluorescence microscopy of the ECs, fixed on the gold QCM surface and stained for actin, demonstrated that the shape and cytoskeleton of ECs were affected by as little as 330 nM nocodazole. These results indicate that the EC QCM biosensor can be used for the study of EC attachment and to detect EC cytoskeletal alterations. We suggest the potential of this cellular biosensor for the real time identification or screening of all classes of biologically active drugs or biological macromolecules that affect cellular attachment, regardless of their molecular mechanism of action.

Schistosoma mansoni: molecular characterization of a tegumental Ca-ATPase (SMA3)

A cDNA encoding a Ca-ATPase homologue, designated SMA3, was isolated from an adult cDNA library of Schistosoma mansoni. The full-length cloned DNA contains a 3105-bp open reading frame that potentially encodes a 1035-amino-acid protein with a M(r) of 113,729 and a pl of 6.48. Homology searches for SMA3 reveal high sequence identity with a variety of Ca-ATPases from evolutionarily diverse organisms. SMA3 is predicted to contain 10 transmembrane regions typical of this protein family as well as other conserved domains, such as the phosphorylation site and FITC binding domain. The greatest sequence identity (40-50%) is found to those Ca-ATPases belonging to the secretory pathway subclass. Identification of the 5' end of the SMA3 cDNA by RACE analysis reveals the presence of a 36-base spliced leader RNA, suggesting that the SMA3 pre-mRNA is processed by trans-splicing. Northern analysis reveals a single dominant transcript of 5 kb in adult RNA preparations. Antibodies raised against an amino terminal peptide detect the protein in the adult tegument, suggesting that SMA3 functions to help control Ca homeostasis within the tegument and may play a role in signal transduction at the host parasite interface.

The quartz crystal microbalance as a continuous monitoring tool for the study of endothelial cell surface attachment and growth

The quartz crystal microbalance (QCM) was used to monitor endothelial cell (EC) adhesion on the gold surface of an oscillating quartz crystal contained in a QCM device. A number of parameters were investigated. First, we observed differential QCM O-ring toxicities for ECs. Second, appropriate conditions for cell culture and QCM cell environment were identified that can eliminate large-scale frequency oscillations in the measurements. These artifacts are not due to added cells but originate in the time-dependent evaporation of water. Having eliminated these artifacts, we then demonstrated that the measured steady-state crystal frequency shift, Delta f, and motional resistance shift, DeltaR, were determined by the number of firmly attached ECs requiring trypsinization from the crystal surface. Last, following steady-state attachment of ECs, the EC growth stimulation by fibroblast growth factor was monitored in a continuous fashion by measuring f and R values over a 72 h. period. We observed the Delta f values to increase in a way that reflected the increase in EC number bound to the QCM surface. Following addition of ECs to the QCM, the time-dependent increase in DeltaR can be interpreted in terms of increase by the ECs of the energy dissipation properties of the solution at the solution-gold surface interface. This effect is due to their rapid surface attachment and the elaboration of their cytoskeletal properties. These results indicate that the QCM technique can be used for the study of EC attachment and growth and suggest its potential for the real time study of per unit surface area cell mass distribution dynamics and viscoelastic properties and the cells' responses to stresses or perturbations brought about using biologically active molecules.

Randomly amplified polymorphic DNA (RAPD) polymerase chain reaction assay for identification of Schistosoma mansoni strains sensitive or tolerant to anti-schistosomal drugs

The genetic differences between Schistosoma mansoni strains from different geographic areas that were reportedly resistant or sensitive to anti-schistosomal drugs were studied with randomly amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) polymerase chain reaction (PCR) assays. Of the 20 RAPD primers we chose, 19 showed the capacity to produce a medium to high level of amplification and 6 revealed difference PCR bands between drug-resistant and drug-sensitive strains. One particular primer, 5'-CAGCGACAAG-3', showed 2 major difference bands between praziquantel (PZQ)-resistant and PZQ-sensitive strains from the endemic area of Egypt. These results demonstrate that defined sequence primers could be applied as a useful tool for differentiating drug-resistant and -sensitive schistosome parasites in the field.

The iso-competition point for counterion competition binding to DNA: calculated multivalent versus monovalent cation binding equivalence

In this paper we introduce an important parameter called the iso-competition point (ICP), to characterize the competition binding to DNA in a two-cation-species system. By imposing the condition of charge neutralization fraction equivalence theta1 = ZthetaZ upon the two simultaneous equations in Manning's counterion condensation theory, the ICPs can be calculated. Each ICP, which refers to a particular multivalent concentration where the charge fraction on DNA neutralized from monovalent cations equals that from the multivalent cations, corresponds to a specific ionic strength condition. At fixed ionic strength, the total DNA charge neutralization fractions thetaICP are equal, no matter whether the higher valence cation is divalent, trivalent, or tetravalent. The ionic strength effect on ICP can be expressed by a semiquantitative equation as ICPZa/ICPZb = (Ia/Ib)Z, where Ia, Ib refers to the instance of ionic strengths and Z indicates the valence. The ICP can be used to interpret and characterize the ionic strength, valence, and DNA length effects on the counterion competition binding in a two-species system. Data from our previous investigations involving binding of Mg2+, Ca2+, and Co(NH3)63+ to lambda-DNA-HindIII fragments ranging from 2.0 to 23.1 kbp was used to investigate the applicability of ICP to describe counterion binding. It will be shown that the ICP parameter presents a prospective picture of the counterion competition binding to polyelectrolyte DNA under a specific ion environment condition.

Quartz crystal microbalance measurement of self-assembled micellar tubules of the amphiphilic decyl ester of D-tyrosine and their enzymatic polymerization

Amphiphilic decyl derivatives of D-tyrosine self-assemble into long rodlike or tubular aggregate structures in aqueous buffered solution. In this report we demonstrate the novel use of the quartz crystal microbalance (QCM) to measure the presence in solution, and subequent enzymatic polymerization, of long rodlike monomer aggregates of the decyl ester of D-tyrosine (DEDT) as a function of their formation and increasing surface binding level as pH values increase from 3 to 7. From these data, using the Sauerbray equation to calculate the effective elastic mass surface binding of deprotonated DEDT aggregates, a pKapp of 8.3 is obtained for the DEDT alpha-NH2 group protonation-deprotonation and subsequent aggregation equilibrium. Furthermore, once aggregates are bound to the QCM surface, we initiate and subsequently monitor enzymatic polymerization of the DEDT monomers by horseradish peroxidase through the measurement of significant changes in the quartz crystal frequency and motional resistance. Following the onset of polymerization, the viscoelastic properties of the bound monomer aggregates change. A final polymerized state is achieved in which the altered physical properties of the polymerized rodlike aggregates make the solution immediately above the QCM surface-solution interface behave as a Newtonian fluid, producing a nearly pure viscosity-density energy dissipative effect on the measured crystal frequency and motional resistance values.

Statistical mechanical simulation of polymeric DNA melting with MELTSIM

MOTIVATION

MELTSIM is a windows-based statistical mechanical program for simulating melting curves of DNAs of known sequence and genomic dimensions under different conditions of ionic strength with great accuracy. The program is useful for mapping variations of base compositions of sequences, conducting studies of denaturation, establishing appropriate conditions for hybridization and renaturation, determinations of sequence complexity, and sequence divergence.

RESULTS

Good agreement is achieved between experimental and calculated melting curves of plasmid, bacterial, yeast and human DNAs. Denaturation maps that accompany the calculated curves indicate non-coding regions have a significantly lower (G+C) composition than coding regions in all species examined. Curves of partially sequenced human DNA suggest the current database may be heavily biased with coding regions, and excluding large (A+T)-rich elements.

AVAILABILITY

MELTSIM 1.0 is available at: //www.uml.edu/Dept/Chem/UMLBIC/Apps/MEL TSIM/MELTSIM-1.0-Win/meltsim. zip. Melting curve plots in this paper were made with GNUPLOT 3.5, available at: http://www.cs.dartmouth.edu/gnuplot_inf o.html Contact : blake@maine.maine.edu;

Comparison of experimental to MELTSIM calculated DNA melting of the (A+T) rich Dictyostelium discoideum genome: denaturation maps distinguish exons from introns

The slime mold, Dictyostelium discoideum, possesses an (A+T) rich eukaryotic genome that is being sequenced in the Human Genome Project. High resolution melting curves of isolated total and fractionated nuclear D. discoideum DNA(AX3 strain) were determined experimentally and are compared to melting curves calculated from GENBANK sequences (1.59% of genome) by the statistical thermodynamics program MELTSIM (1), parameterized for long DNA sequences (2,3). The lower and upper temperature limits of calculated melting agree well with the observed melting of total DNA. The experimental curve is unusual in that it contains a number of sharp peaks. MELTSIM allowed us to calculate positional denaturation maps of D. discoideum GENBANK sequence documents containing the 26S, 5.8S and 17S rDNA gene sequences, a major satellite DNA and repetitive sequence family present in 100-200 copies/nucleus. These denaturation maps contain subtransitions that correspond with a number of the experimentally observed peaks, some of which we show to correspond with rDNA gene enriched CsCl gradient fractions of D. discoideum DNA. MELTSIM calculated curves of coding, intron and flanking sequences indicate that both intron and flanking sequences are extremely (A+T) rich and account for most of the low temperature melting. There is no temperature overlap between thermal stabilities of these sequence domains and those of coding DNA. The latter must satisfy triplet codon constraints of higher (G+C) content. These large stability property differences enable a denaturation mapping feature of MELTSIM to clearly distinguish exon positions from those of introns and flanking DNA in long D. discoideum gene containing sequences.

DNA bound to polypyrrole films: high-resolution imaging, DNA binding kinetics and internal migration

We have studied the time-dependent uptake of 35S radiolabeled DNA with electrochemically prepared polypyrrole films. The two distinct polypyrrole film surfaces, a rough (solution polymeric growth face, R) and a smooth surface (electrode face, S) were characterized by low-resolution AFM and high-resolution transmission electron microscopy (TEM). These studies showed the presence of steep contours and defects in the form of large and small surface holes and valleys on the rough surface of polypyrrole. The void dimensions ranged from the nanoscale to micron size. By contrast, the smooth surface was flatter and largely devoid of significant structural defects and exhibited closer packing of the polypyrrole chains over large areas. Both surfaces were comprised largely of chains whose average diameters were 1.0-1.2 +/- 0.3 nm. The surface characterization studies were complemented by time-dependent DNA uptake studies which showed a t1/2-dependent total uptake of 35S DNA at higher levels on the rough surface compared to the smooth surface. This is consistent with the apparent higher effective surface area of the rough surface compared to the smooth. Using a proportional counter the time-dependent ratio (R/S) of the 35S DNA detected from the rough surface of the polypyrrole disk to that detected from the smooth surface suggested that DNA was migrating into the disk interior from its uptake surface. The rough side defect dimensions measured by TEM were more than sufficient to allow for the penetration and migration of DNA into the disk interior. Both R/S ratios were extrapolated and found to intersect at an R/S value close to 1.0, suggesting a kinetic process leading ultimately towards a nearly uniform radiolabeled DNA distribution in the disk. These kinetic results were in agreement with the surface characterization studies and suggest a model in which sizeable internal pores exist throughout the electrochemically prepared polypyrrole, that could account for the DNA migration effect. This was confirmed by TEM of the interior of a polypyrrole disk produced by Argon ion milling.

A gel electrophoresis study of the competitive effects of monovalent counterion on the extent of divalent counterions binding to DNA

The behavior of alkaline earth metal cations (Mg2+ and Ca2+) and transition metal cations (Zn2+ and Cu2+) interacting with lambda-DNA-HindIII fragments ranging from 2,027 to 23,130 bp in Tris-borate-EDTA buffer solutions was investigated. The divalent counterions competed with Tris+ and Na+ for binding to polyion DNA, and the competition binding situations were investigated by measuring the reduction of the DNA mobility, by pulsed- or constant-field gel electrophoresis. The interaction of Mg2+ with DNA was intensively studied over a wide range of Mg2+ concentrations. In addition, we examined the competition binding as a function of ionic strength and DNA size. To compare valence effects, we studied Co(NH3)6(3+) interaction with DNA fragments under conditions similar to that of Mg2+. At relatively low Mg2+ concentration, the normalized titration curves of DNA mobility were well fit by Manning's two-variable counterion condensation (CC) theory. The agreement between the predicted value (total charge neutralization fraction theta) from Manning's CC theory and the data based on our measured DNA electrophoretic mobility reduction was consistent under our experimental conditions. In contrast to alkaline earth metal cations (Mg2+ and Ca2+), different binding behaviors were observed for the transition metal cations (Zn2+ and Cu2+). These differences highlight the usefulness of our reduced DNA electrophoretic mobility measurement approach to describing cation interactions with polyelectrolyte DNA.

Extracellular cysteines of the corticotropin-releasing factor receptor are critical for ligand interaction

The corticotropin-releasing factor receptor (CRF-R) contains six conserved cysteines in its amino-terminal domain (C30, C44, C54, C68, C87, and C102) and one cysteine in its first and second extracellular loops (C188 and C258, respectively). Additionally, several other cysteines are located in the transmembrane domains (C128, C211, C233, and C364) and first intracellular loop (C150). Reduction of disulfide bonds with DTT decreased CRF binding to detergent-solubilized membranes, suggesting an important role for disulfide bonds in ligand recognition. Therefore, site-directed mutagenesis was used to introduce single and paired Cys (C) to Ser (S) or Ala (A) mutations. A silent nine amino acid tag from c myc was introduced in the amino terminus of the mouse CRF-R. With the exception of C258S and C188S/C258S mutations, all C to S or to A receptor mutants had good surface expression that was at least 52.5% of control. C30S, C54S, and C30S/C54S mutations had good CRF binding and CRF-stimulated cAMP accumulation. No CRF binding was detected for the C44S, C68S, C87S, C102S, C188S, C258S, C30S/C44S, C30S/C68S, C54S/C68S, C87S/C102S, and C188S/C258S mutants, while CRF-stimulated cAMP accumulation occurred with high EC50 values. In particular, receptors carrying double mutations, C44S/C102S and C68S/C87S, had an improved signaling property as compared to receptors carrying the respective single cysteine mutations. These data, together with the effects of DTT on CRF binding, indicate that disulfide bridges are important for receptor functions. Functional data from single and paired cysteine mutations suggest potential pairings between C44 and C102, C68 and C87, and C188 and C258 that are critical for ligand-receptor interactions.

Two-photon-induced fluorescence from the phycoerythrin protein

Two-photon-induced fluorescence is observed from the photodynamic phycobiliprotein phycoerythrin. Temporal, spectral, and intensity-dependent properties of the two-photon-induced fluorescence emission from phycoerythrin excited by a 1.06-mum laser beam are reported. The measured two-photon absorption cross section of phycoerythrin is an order of magnitude larger than that of Rhodamine 6G. The potential applications of phycobiliproteins for two-photon-induced fluorescence for microscopy of three-dimensional biological samples and three-dimensional optical memory are discussed.

Trivalent counterion condensation on DNA measured by pulse gel electrophoresis

Pulse gel electrophoresis was used to measure the reduction of mobilities of lambda-DNA-Hind III fragments ranging from 23.130 to 2.027 kilobase pairs in Tris borate buffer solutions mixed with either hexammine cobalt(III), or spermidine3+ trivalent counterions that competed with Tris+ and Na+ for binding onto polyion DNA. The normalized titration curves of mobility were well fit by the two-variable counterion condensation theory. The agreement between measured charge fraction neutralized and counterion condensation prediction was good over a relatively wide range of trivalent cation concentrations at several solution conditions (pH, ionic strength). The effect of ionic strength, trivalent cation concentration, counterion structure, and DNA length on the binding were discussed based on the experimental measurements and the counterion condensation theory.

A biotinylated undecylthiophene copolymer bioconjugate for surface immobilization: creating an alkaline phosphatase chemiluminescence-based biosensor

Methodology is described for the creation of a molecular assembly consisting of the enzyme alkaline phosphatase immobilized onto a glass surface using a biotinylated conjugated copolymer, poly(3-undecylthiophene-co-3-thiophenecarboxaldehyde) 6-biotinamidohexanohydrazone. The biotinylated polymer is attached to the inside walls of a silanized glass capillary via hydrophobic interactions, and a streptavidin-conjugated alkaline phosphatase is interfaced with the polymer through the classical biotin-streptavidin interaction. Utilizing a simple optical setup, we can detect the activity of as little as approximately 0.1 fmol of alkaline phosphatase with this molecular assembly. The assembly is mechanically robust and retains the majority of bound enzyme activity for up to 30 days. We have utilized this molecular assembly for the detection of organophosphorus-based pesticides. Both paraoxon and methyl parathion inhibit the enzyme-mediated generation of chemiluminescence signal. We are able to detect paraoxon and methyl parathion concentrations down to 500-700 ppb.

Chemiluminescence-based inhibition kinetics of alkaline phosphatase in the development of a pesticide biosensor

The use and application of the enzyme alkaline phosphatase in a chemiluminescence assay are discussed. The enzyme catalyzes the hydrolysis of a macrocyclic phosphate compound generating a chemiluminescence signal. On the basis of inhibition of this signal, a methodology for the detection and quantitation of organophosphorus-based pesticides has been developed. The methodology is studied with alkaline phosphatase in the bulk aqueous phase, and detection of the signal is accomplished by a simple optical setup. Parts per billion level detection of paraoxon and methyl parathion in bulk solutions is achieved. The technique is rapid and sensitive and is applicable to the detection of most organophosphorus-based pesticides. The results from kinetic studies indicate a mixed type of inhibition of the enzyme by paraoxon and methyl parathion. The detection methodology forms an integral part of a biosensor under development and is adaptable to incorporating optical fibers for remote detection of pesticides.

Involvement of the Na,K-ATPase in the induction of ion channels by palytoxin

The effects of ouabain, ATP, and vanadate on palytoxin induction of ion channels were examined with the aim of elucidating the role of Na,K-ATPase in palytoxin action. Palytoxin-induced membrane depolarization of crayfish giant axons and single channel currents of frog erythrocytes and mouse neuroblastoma N1E-115 cells were examined using the intracellular microelectrode and patch-clamp techniques. External application of palytoxin in nanomolar concentrations induced depolarization in the crayfish giant axons, and the depolarization was inhibited by pretreatment of the axon with ouabain (10 microM). Internally perfused axons were less sensitive to palytoxin unless ATP (6 mM) was added internally. In patch-clamp experiments, picomolar palytoxin in the patch electrode induced single channels in both cell-attached and inside-out patches of erythrocytes and neuroblastoma cells. The induced channels had a conductance of about 10 pS, reversed near 0 mV in physiological saline solution, and was permeable to Na+, K+, Cs+, and NH4+, but not to choline. Single channel activities induced by palytoxin were inhibited by ouabain (10 microM) and vanadate (1 mM), but promoted by ATP (1 mM). The modulating effects of ouabain, vanadate, and ATP on palytoxin action suggest that the Na,K-ATPase is involved in the induction of single channels by palytoxin. Palytoxin-induced and ouabain-inhibitable single channels were observed in planar lipid bilayer incorporated with purified Na,K-ATPase. The results indicate that an interaction between palytoxin and Na,K-ATPase leads to opening of a 10-pS ion channel. They further raise the possibility that a channel structure may exist in the sodium pump which is uncovered by the action of palytoxin.

Uptake, intracellular distribution, and stability of oligodeoxynucleotide phosphorothioate by Schistosoma mansoni

The in vitro uptake, cellular distribution, efflux, stability, and toxicity levels of an oligodeoxynucleotide phosphorothioate (PS-oligonucleotide) have been studied in mature Schistosoma mansoni worms. The intracellular accumulation of 35S-labeled PS-oligonucleotide occurred roughly in proportion to the worm body mass over a wide concentration range, whether the worms were exposed singly or in mating pairs. Cellular uptake was dependent on the extracellular concentration. A minor fraction (13%) of the PS-oligonucleotide taken up by the worm accumulated in the surface tegumental coat. Most of the PS-oligonucleotide taken up localized in the cytosol (54%) and the nuclei-enriched (33%) fractions. In a time course study on adult worms in culture, oligonucleotide uptake was observed within the first 2 h and peaked at about 36 h. A decrease in the intracellular concentration of the PS-oligonucleotide was observed by 42 h. Analysis of the extracted oligonucleotides showed that PS-oligonucleotide was digested slowly. Efflux of the oligonucleotide was time and temperature dependent. Significant toxicity to the cultured worms did not occur until the PS-oligonucleotide concentration was over 8 mg/ml (1 mM).

Alignment of (dA).(dT) homopolymer tracts in gene flanking sequences suggests nucleosomal periodicity in D. discoideum DNA

It has been shown that the frequency versus size distribution of A and T overlapping and non-overlapping homopolymer tracts of N > 5 in D. discoideum gene flanking and intron regions are significantly greater than in coding regions(1). In the present report, we demonstrate, that a spatial periodicity exists in long A and T tracts (N > 10) in long flanking sequences by scored alignments of those tracts (N > 10) with the nucleosomal repeat. A tract spacing was found at 185-190 bp that corresponds to a maximum alignment score. This is exactly the average spacing of D. discoideum nucleosomes determined experimentally. A majority of A and T tracts in flanking sequences are often spaced by short DNA stretches and the total length of adjacent A and T tracts plus the interrupting short DNA stretch corresponds closely to the average experimentally measured nucleosomal linker DNA size in D. discoideum-42 bp. These data suggest a model which has A and T runs of N > 10 bp in flanking DNA of D. discoideum organized in a regular phase with nonhomopolymer sequences along the DNA. This model has functional implications for A and T tracts, suggesting that they are found in nucleosomal linker DNA regions of chromatin during some necessary portion(s) of the life of the cell.

Characteristics of the large (dA).(dT) homopolymer tracts in D. discoideum gene flanking and intron sequences

D. discoideum, the slime mold, is one of the most AT rich eukaryotic genomes known. In this paper we examine this organism's database for overlapping N-tuples of high frequency and find A and T tracts possess among the highest frequencies in flanking sequences but not in coding sequences. We examined both overlapping and non-overlapping frequencies of the A, T, G and C homopolymer tracts of 2 < N < 6. Overlapping (dG).(dC) and (dA).(dT) tracts occur at greater frequencies than expected, based on random occurrence. Long (dA).(dT) tracts of N > 10 occur at well above expected frequencies in flanking and intron regions, while (dG).(dC) tracts above N = 5 are rarely found. Some of the implications of these findings for tract origins in slip-strand replication and for chromatin structure are discussed.

High affinity DNA-microtubule interactions: evidence for a conserved DNA-MAP interaction involving unusual high CsCl density repetitious DNA families

We have examined high affinity interactions of chick brain microtubule proteins with 35S labelled tracer DNAs from chick, mouse and D. melanogaster under equilibrium conditions by the nitrocellulose filter binding technique. Ternary reaction mixtures of the above two components and a third component, an excess of unlabelled competitor DNA from either E. coli., mouse, D. melanogaster or chick, were used to measure small fractions of DNA in each case (1-4%) bound to microtubule protein under high stringency- large competitor DNA concentration and 0.5 M NaCl. As seen in part previously (Marx, K.A. and Denial, T. (1985) in The Molecular Basis of Cancer, 172B, 65-75 (Rein, ed), A. Liss, N.Y.) the measured order of competitor DNA strengths was identical for all three tracer DNAs. That is: chick > mouse > D. melanogaster > E. coli competitor DNA. Since the homologous interaction, chick competitor DNA with chick brain microtubule protein, is always the strongest interaction measured, we interpret this as evidence for a conserved protein-DNA sequence interaction. 35S chick DNA tracer sequences, isolated from nitrocellulose filters following the stringent binding in the presence of 0.9 mM-1 E. coli. competitor DNA, was used in driven reassociation reactions with total chick driver DNA. This fraction was found to be significantly enriched in repetitive chick DNA sequences. Since we have observed a similar phenomenon in mouse, we then compared the stringent binding mouse sequences and showed that the bulk of these sequences did not cross-hybridize with total chick DNA. Finally, all three 35S tracer DNAs binding to nitrocellulose were isolated and sedimented to equilibrium on CsCl density gradients. The CsCl density distributions from all three DNAs showed significant (100-fold) enrichment in classical satellite DNAs as well as higher enrichment in two very unusual high CsCl density families of DNA (1.720-1.740 g/cm3; 1.750-1.765 g/cm3). These families are never observed as distinct bands in total DNA CsCl gradients, nor could we isolate them in purified tubulin control binding experiments. This apparently general phenomena may be identifying some of the sequence families involved in the high affinity microtubule interaction, which appears to be conserved in evolution.

High affinity DNA-microtubule associated protein interaction

We have isolated the MAP/tau proteins from twice-cycled chick brain microtubule preparations and demonstrated that they are responsible for the nitrocellulose DNA binding activity we and others have measured. Using the isolated MAP/tau proteins we then measured the apparent affinity constant K(app) for the homologous chick DNA interaction and found evidence for two equilibrium affinity classes-a K(app) = 6 x 10(7) M-1, responsible for the bulk of the DNA binding activity and a small (less than 10%) higher affinity K(app) = 10(8) - 10(9) M-1, likely due to sequence specific binding protein species. Using the same chick brain MAP-tau protein, a heterologous interaction with D. melanogaster DNA, was found to possess just the lower affinity class-K(app) = 2 x 10(7) M-1. Under stringent binding conditions we carried out equilibrium nitrocellulose filter binding experiments in a ternary reaction mixture at constant MAP/tau protein and 35S radiolabelled chick DNA concentration using increasing and excess concentrations of competitor DNAs of different sources. The order of competitor strengths found was-chick DNA greater than mouse DNA greater than D. melanogaster = E. coli. DNA. These data and specifically the homologous DNA: protein case being the strongest competitor corroborate our previous studies using total microtubule protein and provide new evidence for a conserved interaction of a small DNA sequence class with MAP/tau protein species. Moreover, these data allow us to conclude that the conserved DNA sequence: MAP/tau protein interactions do not critically depend upon any energetic feature co-involving tubulin for their properties since tubulin is absent from these preparations.

The affinity of DNA-microtubule protein complexes and their disruption by tubulin binding drugs

Using the gel shift assay system, we have measured the apparent affinity constant for the interaction of two different DNAs with MAP proteins found in both total calf brain microtubules and heat stable brain preparations. Both DNAs studied contained centromere/kinetochore sequences- one was enriched in the calf satellite DNA; the other was a large restriction fragment containing the yeast CEN11 DNA sequence. Complexes formed using both DNAs had similar Kapp values in the range of 2.1 x 10(7) M-1 to 2.0 x 10(8) M-1. CEN11 DNA-MTP complexes had by far the highest Kapp value of 2.0 x 10(8) M-1. The CEN11 DNA sequence is where the yeast kinetochore of chromosome 11 is formed and where the single yeast microtubule is bound in vivo. The CEN11 conserved region II known binding sites-(dA/dT)n runs- for mammalian MAP2 protein, are in good agreement with this higher Kapp value. The effects of the classical tubulin binding drugs colchicine, podophyllotoxin and vinblastine on the DNA-MAP protein complex stability were investigated by determining the drug concentrations where the complexes were destabilized. Only the complexes formed from total microtubule protein (tubulin containing) were destabilized over a wide drug concentration range. Heat stable brain protein complexes (no tubulin) were largely unaffected. Furthermore, it took 10-100 fold higher drug concentrations to disrupt the CEN11 DNA complexes compared to the calf thymus satellite DNA enriched complexes. These data support our previous results suggesting that there is a DNA sequence dependent interaction with MAP proteins that appears to be conserved in evolution (Marx et. al., Biochim. Biophys. Acta. 783, 383-392, 1984; Marx and Denial, Molecular Basis of Cancer 172B, 65-75 1985). In addition, these results imply that the classical tubulin binding drugs may exert their biological effects in cells at least in part by disrupting DNA-Protein complexes of the type we have studied here.

Solution structure of bacteriophage T4D and icosahedral capsid geometry visualized in freeze-fractured, deep-etched replicas

The prolate icosahedral capsid geometry of wild type bacteriophage T4D has been determined by direct visualization of the triangular faces in stereoimages of transmission electron micrographs of phage particles. Bacteriophage T4 was prepared for transmission electron microscopy (TEM) following a protocol of freeze-fracturing, deep-etching (FDET) and replication by vertical deposition (80 degrees angle) of a thin platinum-carbon (Pt-C) metal layer of 1.01 nm. From direct statistical measurements of the ratio of the head length to width and of stereometric angles on T4 heads, we have estimated a Q number of 21. This confirms previous indirect studies on T4 and agrees with determinations on bacteriophage T2. Many of the structural features of T4 observed in FDET preparations differ significantly from those observed by classical negative staining methods for TEM imaging. Most important among the differences are the conformation of the baseplate (a closed rosebud) and the positioning of the tail fibers (retracted). The retracted position of the tail fibers in the FDET preparations has been confirmed by negatively staining phage previously fixed suspended in solution with 2% glutaraldehyde. The FDET protocols appear to reveal important structural features not seen in negative stained preparations. These have implications for bacteriophage T4 conformation in solution, viral assembly and phage conformation states prior to tail contraction and DNA ejection.

Reduced RNA synthesis levels in isolated mouse liver nuclei following reaction with [(H2O)(NH3)5Ru(II)]2+

The goal of this study is to establish the effect of [(H2O)(NH3)5Ru(II)]2+ reaction of nuclei on their RNA transcription levels. This question is important because ammineruthenium compounds share chemical and biological properties with the chemotherapeutic agent cis-dichlorodiammineplatinum(II) or cisplatin. First we demonstrate that mouse liver nuclei are active in RNA transcription in vitro and characterize the optimum conditions for in vitro transcription. Synthetic rates in the presence of inhibitors actinomycin D and alpha-Amanitin and measurements of oligo(dT)-cellulose RNA binding levels suggest that all three RNA Polymerases are active in synthesis at about the following percentages-RNA Polymerase I(30%), II(50%) and III(20%). Mouse liver nuclei reacted with [(H2O)(NH3)5Ru(II)]2+ and then oxidized had (NH3)5 Ru(III)3+n-DNA adduct levels inversely related to total RNA synthetic rates. Oligo(dT) cellulose RNA binding levels did not vary with DNA adduct density. These data suggest that direct DNA lesions rather than [(NH3)5Ru(III)]3+ effects on other aspects of the transcription system are responsible for the diminished RNA synthesis levels. Ammineruthenium complexes remain desirable candidates for chemotherapeutic agents that may be safely administered in the unreactive ruthenium(III) state and be activated toward DNA binding by reduction in the hypoxic environment of many tumour cells.

Micrococcal nuclease digestion study of spermidine-condensed DNA

Spermidine-condensed lambda DNA tertiary structures have been studied by micrococcal nuclease digestion. Broad but discrete DNA bands were observed in gel electrophoresis experiments of digests at sizes of: 1003 +/- 115 bp, 1972 +/- 190 bp and 3100 +/- 350 bp. These bands comprise an arithmetic series, similar to, but larger than, arithmetic DNA band series sizes we have observed previously in calf thymus and phi x-174 DNA condensates. The 1003bp monomer lambda DNA band size corresponds to wrapping B DNA once circumferentially about the toroidal-shaped tertiary structures, the predominant condensed structures present in these preparations, and is consistent with the measured electron microscopic dimensions for hydrated lambda DNA toruses previously presented. DNA fragment length stability was determined by release from the digested condensates. Fragments of 80-85bp and sizes below are thermodynamically unstable in the lambda DNA condensates. This fragment size agrees well with a recent determination of the cooperativity size in DNA condensates.

Binding of the transition metal ion [(H2O)(NH3)5Ru(II)]2+ to nucleosomal core and internucleosomal DNA

The goal of this study is to establish the nature of pentammineruthenium(III) binding to DNA in intact mouse liver nuclei. Also, we wish to determine whether the nucleosomal organization of mouse chromatin has a substantial effect on the relative Ru(III) binding levels of internucleosomal and nucleosomal core DNA. These questions are important because ammineruthenium compounds share chemical and biological properties with the cis-dichlorodiammineplatinum(II) or cisplatin chemotherapeutic agent. Therefore, they represent a potential class of new chemotherapeutic agents. We find that in intact nuclei the predominant DNA binding site for pentammineruthenium(II), followed by air oxidation to pentammineruthenium(III), is N-7 guanine, as is the case with cisplatin. Also, the Ru(III) distribution between internucleosomal and nucleosomal core DNA was found to be nearly identical as probed with three non-specific deoxyribonucleases.

A study of phi X-174 DNA torus and lambda DNA torus tertiary structure and the implications for DNA self-assembly

Hydrated torus shaped complexes were examined by transmission electron microscopy in both spermidine-condensed linear and nicked circular phi X-174 DNA and lambda DNA preparations. Freeze-etch replicas of both these torus samples, produced with very low Pt metal deposition levels (9APt/C), were found to have circumferentially wound single DNA double helix size surface fibers in the range of 30A width. Measurements of torus inner and outer circumference as well as ring thickness were performed. Observed differences in the torus dimension distributions from circular phi X-174 DNA and linear phi X-174 DNA may be related to the different topological constraints on DNA folding in these two samples (1). On the basis of annulus thickness measurements phi X-174 DNA toruses, in contrast to lambda DNA toruses, were observed to fall into two classes identified as being formed from monomer DNA condensation and multimer DNA condensation. All of the torus substructure and population dimensions observed here are consistent with the continuous circumferential DNA winding model of torus organization proposed by Marx and Reynolds (1) to explain the micrococcal nuclease cleavage properties of the toruses. End-on view measurements of the torus thickness were made from micrographs obtained by extensive tilting of the object replica. These direct measurements confirmed quaternary structure interpretations made from simple strand packing models. We compared the measured torus properties in this linear DNA size series (5386-48000 bp). With increasing DNA length the pattern of DNA strand self-assembly was found to be more varied producing lambda DNA toruses of varying shape. The relevance of our study to the problem of lambda bacteriophage DNA head packaging was discussed.

High-affinity microtubule protein-higher organism DNA complexes. Many-fold enrichment in repetitive mouse DNA sequences comprised of satellite DNAs

We have examined aspects of the interaction of cycled microtubule protein preparations with 35S-labeled mouse DNA tracer in a competition system with unlabelled competitor E. coli or mouse DNA. The nitrocellulose filter binding assay was used to measure interaction by scintillation counting. DNA molecular weight affected the levels of filter retained 35S-labelled mouse tracer DNA. Filter retention levels increased if 35S-labelled mouse DNA tracer size was increased, and the filter binding level decreased if competitor DNA size was increased. There was a sizeable, reproducible difference in the 35S-labelled mouse DNA tracer binding level of about 1% when E. coli or mouse DNA competitors were compared. Mouse DNA more effectively competed with 35S-labelled mouse DNA for microtubule protein binding than did E. coli DNA, suggesting that a small class of higher-organism DNA sequences interacts very strongly with microtubule protein. From other studies we know this to be the MAP fraction (Marx, K.A. and Denial, T. (1984) in The Molecular Basis of Cancer (Rein, R., ed.), Alan R. Liss, New York, in the press; and Villasante, E., Corces, V.G., Manso-Martinez, R. and Avila, J. (1981) Nucleic Acids Res. 9, 895-908). We find that this difference in competitor DNA strength is qualitatively similar under high-stringency conditions (0.5 M NaCl, high competitor [DNA]) we developed for examining high-affinity complexes. Under high-stringency conditions we isolated 1.2% and 0.6% of 35S-labelled mouse DNA at 4200 and 350 bp respective sizes as nitrocellulose filter bound DNA-protein complexes. At both molecular weights these high-affinity DNA sequences, isolated from the filters, were shown to be significantly enriched in repetitive DNA sequences by S1 nuclease solution reassociation kinetics. The kinetics are consistent with about a 4-fold mouse satellite DNA enrichment as well as enrichment in other repetitious DNA sequence classes. The high molecular weight filter-bound DNA samples were sedimented to equilibrium in CsCl buoyant density gradients and found to contain primarily mouse satellite DNA density sequences (1.691 g/cm3) with some minor fractions at other density positions (1.670, 1.682, 1.705, 1.740, 1.760 g/cm3) similar to those observed by our laboratory in previous investigations of micrococcal nuclease-resistant chromatin (Marx, K.A. (1977) Biochem. Biophys. Res. Commun. 78, 777-784). That the high-affinity microtubule-bound DNA was some 3-5-fold enriched in mouse satellite sequences was demonstrated by its characteristic BstNI restriction enzyme cleavage pattern.

Studies of DNA organization in hydrated spermidine-condensed DNA toruses and spermidine-DNA fibres

We have investigated in vitro spermidine-condensed DNA preparations by both biochemical and freeze-etch electron microscopic approaches. These studies lead us to the conclusion that the reversibly condensed preparations, qualitatively described by Manning's counterion condensation theory, contain disk-like torus structures largely comprised of unidirectional, circumferentially wrapped DNA. Stereoscopic measurements on stereomicrographs of DNA torus and fibre objects have demonstrated the feasibility of directly measuring DNA writhe or, for that matter, mapping any secondary, tertiary or quaternary structure features of a hydrated macromolecular array in which the features can be differentially highlighted by low replica metal shadow levels.

Ion competition and micrococcal nuclease digestion studies of spermidine-condensed calf thymus DNA. Evidence for torus organization by circumferential DNA wrapping

Spermidine-condensed calf thymus DNA structures have been studied by ion competition using a sedimentation assay and by micrococcal nuclease digestion. Competitor ions Mg2+, Ca2+ and putrescine2+ show specific ion effects; but all three appear to affect the DNA condensation-decondensation equilibrium caused by spermidine3+ in a qualitatively similar manner, suggesting the spermidine3+-DNA interaction is largely electrostatic. Our data show a hysteresis in condensation and decondensation transition directions. We interpret this in terms of a kinetic block in the condensation direction with decondensation representing the equilibrium state of the system. These results agree with results obtained from related systems using different measurement techniques. Micrococcal nuclease digestion of spermidine-condensed calf thymus DNA produces broad but discrete bands in gel electrophoresis experiments. At least two bands determined to be 760 +/- 87 bp and 1355 +/- 135 bp, possess the size ratio 1:1.8 +/- 0.4 consistent with their forming the monomer and dimer fragments of an arithmetic band series. We rationalize this result in terms of a localized micrococcal nuclease cleavage model of circumferentially-wrapped DNA toruses proposed previously by Marx, K.A. and Reynolds, T.C. (Proc. Natl. Acad. Sci. (1982) 79, 6484-6488). The arithmetic series monomer band (760 +/- 87 bp), corresponding to wrapping B DNA once circumferentially about the torus, is in agreement with the electron microscopic measurements of hydrated calf thymus DNA torus circumferences presented by Marx, K.A. and Ruben, G.C. (Nucleic Acids Res. (1983) 11, 1839-1853).

Evidence for hydrated spermidine-calf thymus DNA toruses organized by circumferential DNA wrapping

In spermidine-condensed calf thymus DNA preparations, torus-shaped condensates were shown by transmission electron microscopy to exist under the hydrated conditions of the freeze fracture experiment. Using extremely low Pt metal deposition levels (9 A Pt/C) high-contrast replicas of the spermidine-DNA toruses were obtained that showed circumferential wrapping of single DNA double helix-size surface fibres. Stereoscopic analysis of high magnification stereomicrographs established some details of the three-dimensional organization of two DNA double helix sections winding circumferentially on the inner surface of one such torus. These measurements demonstrate the usefulness of stereoscopic analysis of these high macromolecular organization magnification. Measurements on a number of torus-shaped complexes (n = 16) yielded these average dimensions: inner circumference (1840 +/- 204 A) outer circumference (2800 +/- 222 A), torus ring thickness (143 +/- 18 A). These data support a continuous circumferential DNA-winding model of torus organization proposed by Marx & Reynolds.

Spermidine-condensed phi X174 DNA cleavage by micrococcal nuclease: torus cleavage model and evidence for unidirectional circumferential DNA wrapping

Spermidine-condensed phi X174 replicative form (RF) II DNA was digested with micrococcal nuclease to yield seven identifiable DNA bands forming an arithmetic fragment-length series. The DNA monomer unit length was found to be 780 +/- 80 base pairs. This result is most consistent with a proposed model for micrococcal nuclease cleavage of a DNA torus organized by the unidirectional, circumferential wrapping of B-geometry DNA. By a topological consideration, the blunt-end-rod-fusion model for torus formation [Eickbush, T. H. & Moudrianakis, E. N. (1978) Cell 13, 295-306] is shown to be inconsistent with our empirical solution results. We propose a continuous, circumferential DNA wrapping model in which a significant fraction of the collapsed circular phi X174 RFII DNA molecules form regular toruses comprised of seven complete, unidirectional double-helical wraps.

Non-satellite repetitive human DNA families. Sequence properties and evidence for occurrence in chimpanzee DNA

Repetitive human DNA, fractionated on CsCl gradients following hydroxyapatite isolation, contains two complex DNA fractions, the 1.703 and 1.714 DNA families (Marx, K.A., Allen, J.R. and Hearst, J.E. (1976) Biochim. Biophys. Acta 425, 129-147). Biphasic Topt profiles, obtained in DNA excess hybridizations with cRNA tracers from each DNA family, have been shown to be the likely result of a fast kinetic component hybridizing at higher temperatures (67 degrees C peak) and this fast plus a slow kinetic component both hybridizing at lower temperatures (47 degrees C peak). Equilibrium CsCl gradient DNA-cRNA hybrid distributions support previous interpretations of the sequence composition of both DNA families. That is, the fast component is a relatively undiverged repetitive sequence of recent origin, while the slow component is a highly diverged, less thermally stabile, old primate sequence. This interpretation is further strengthened by cRNA tracer hybridization experiments in chimpanzee DNA excess where the fast component appears to be absent and the slow component present.

Primate repetitive DNAs: evidence for new satellite DNAs and similarities in non-satellite repetitive DNA sequence properties

Repetitious DNA sequences have been isolated from a number of the primates in in both Suborders Anthropoidea and Prosimii by hydroxy-apatite chromatography at a Cot of 10. In addition to finding previously unreported possible AT-rich satellite DNAs in Orangutan, Gibbon, Rhesus and Slow Loris a clear similarity to human DNA was found in the nonsatellite repetitious DNA sequence properties of the primates in the Suborder Anthropoidea. This is based on the presence of the hydroxyapatitie isolated 1.703 and 1.714 g/cm3 DNA families in CsCl gradients in the analytical ultracentrifuge following renaturation and extensive DNA hyperpolymer network formation. Within the superfamily Hominoidea the amount of the 1.714 g/cm3 DNA family was greater than that of the 1.703 g/cm3 DNA family while the reverse situation was true within the Superfamily Cercopithecoidea. The orangutan 1.703 and 1.714 g/cm3 DNA families were shown to exhibit the same differential reassociation behavior demonstrated previously in human DNA (Marx et al., 1976a). These data are interpreted as preliminary evidence for a similar sequence organization in the Order Primates Suborder Anthropoidea.

Chromosomal localizations by in situ hybridization of the repetitious human DNA families and evidence of their satellite DNA equivalents

Four of the five major repetitious human DNA families have been mapped by the in situ hybridization technique at their TOPT values. Two of the lighter density DNA families have autoradiographic grain patterns over heterochromatic chromosomal regions that resemble those of known satellite DNAs. The two heaviest density DNA families have autoradiographic grain patterns of middle repetitious DNAs, with all chromosomes showing labelling. Some evidence suggests that one of these DNA families is concentrated in certain chromosomal regions. Both DNA families exhibit biphasic TOPT curves. The presence of two thermal stability classes of hybrids suggests sequence interspersion. By co-enrichment studies in Ag+-CS2SO4 gradients, evidence suggests the origin of the three lightest density renaturated human DNA families to be satellites I, II and III.

Characterization of the repetitious human DNA families

Human DNA isolated from HeLa cells or human placental tissue has been fractionated on hydroxyapatite at COt 1.0. The 25% of total DNA isolated at COt 1.0 is composed of 3% foldback DNA and 22% which renatures by second-order kinetics and can be resolved into five renatured DNA families banding at distinct densities in CsC1 gradients. The individual renatured DNA families were isolated and their physical properties including reassociation kinetics determined. A two-component kinetic analysis was used to resolve kinetic heterogeneity. The three lightest density DNA families possess satellite DNA-like properties. The two heaviest density DNA families were shown to contain reassociated highly repetitious DNA as well as single-stranded, middle-repetitious DNA sequences, suggesting interspersion. The middle repetitious DNA sequences are thought to be related in these two DNA families.