The native, denatured and renatured states of deoxyribonucleic acid

DNA Conformational Changes Induced by Its Interaction with Binuclear Platinum Complexes in Solution Indicate the Molecular Mechanism of Platinum Binding

Platinum anticancer drugs inhibit the division of cancer cells through a DNA binding mechanism. The bimetallic platinum compounds have a possibility for blocking DNA replication via the cross-linking of DNA functional groups at different distances. Many compounds with metals of the platinum group have been tested for possible antitumor activity. The main target of their biological action is a DNA molecule. A combined approach to the study of the interaction of DNA with biologically active compounds of this type is proposed. The capabilities of various methods (hydrodynamic, spectral, microscopy) in obtaining information on the type of binding of coordination compounds to DNA are compared. The analysis of DNA binding with platinum binuclear compounds containing pyrazine, tetrazole, 5- methyltetrazole, 3-propanediamine as bridging ligands in a solution was carried out with the methods of circular dichroism (CD), luminescent spectroscopy (LS), low gradient viscometry (LGV), flow birefringence (FB) and atomic force microscopy (AFM). The competitive binding of different platinum compounds to DNA and the analysis of platinum attachment to DNA after protonation of its nitrogen bases simply indicates the involvement of N7 guanine in binding. Fluorescent dye DAPI was also used to recognize the location of platinum compounds in DNA grooves. DNA conformational changes recorded by variations in persistent length, polyelectrolyte swelling, DNA secondary structure, and its stability clarify the molecular mechanism of the biological activity of platinum compounds.

DNA Integration with Silver and Gold Nanoparticles: Enhancement of DNA Optical Anisotropy

DNA integration with silver and gold nanoparticles was carried out by the chemical reduction of silver and gold ions after the formation of their complexes with high molecular DNA in solution. It is shown that, for a good association of DNA with nanoparticles, the ions of silver and gold should be linked with DNA bases rather strongly. The proposed model of gold interaction with DNA is the coordination of gold to N7 guanine in a major groove followed by the transformation of the GC pair to Hoogsteen's type pairing, in which the gold atom is located between the bases and is bonded simultaneously to N7 guanine and N3 cytosine. For gold and silver nanoparticles associated with DNA, the peak of plasmon resonance shifts relative to that of free nanoparticles in solution. AFM (atomic force microscopy) images of both free and associated with DNA nanoparticles were obtained. Binding of high molecular DNA to gold and silver nanoparticles leads to a decrease in the size of its molecular coil in solution, but the bending rigidity of DNA helix (persistent length) does not change. The almost 3-fold increase in the optical anisotropy of DNA was observed when DNA was associated with gold nanoparticles. This result was obtained with the flow birefringence method using a light source with a wavelength of 550 nm, which is close to the peak of the plasmon resonance of gold nanoparticles. For DNA associated with silver nanoparticles, a similar result was obtained when using a light source with a wavelength of about 410 nm.

DNA Complexes with Cobalt(II) Phthalocyanine Disodium Disulfonate

The interaction of cobalt phthalocyanine disodium disulfonate (CoPc) with calf thymus DNA in solutions was investigated by UV/vis spectrophotometry, circular dichroism (CD), and hydrodynamic methods (viscosity and flow birefringence). Two types of CoPc binding to DNA were observed. Fast CoPc interactions with DNA via external binding to phosphates were accompanied by the formation of stack-type phthalocyanine structures on the periphery of the DNA helix. The optical absorption spectra of such CoPc complexes with DNA were analyzed in order to obtain a binding constant K = (4.8 ± 0.4) × 10⁴ M^-1. CD spectra show the increasing optical activity of phthalocyanines bonded to DNA. DNA plays the role of a matrix, contributing to an increase in their stacking interactions. The CD spectrum of DNA varies slightly. The second type of cobalt-to-DNA binding manifests itself over a certain time. It can be associated with the reorganization of ligands in the cobalt coordination sphere by introducing DNA atoms. In our experiments, such binding was observed after storage of solutions for approximately 20 h at a temperature of 4 °C. It was shown that the minor groove of DNA remains free in CoPc-DNA complexes. CoPc does not bind with the most important group for metal coordinating to DNA in the major groove (N7 guanine). We completely excluded the intercalation binding model. The planes of phthalocyanines in CoPc-DNA complexes are oriented predominantly normal to the axis of the DNA helix. DNA rigidity (persistent length) does not change. This follows from the data on the measurement of the optical anisotropy and intrinsic viscosity of DNA in complexes.

DNA Interaction with Head-to-Tail Associates of Cationic Surfactants Prevents Formation of Compact Particles

Cationic azobenzene-containing surfactants are capable of condensing DNA in solution with formation of nanosized particles that can be employed in gene delivery. The ratio of surfactant/DNA concentration and solution ionic strength determines the result of DNA-surfactant interaction: Complexes with a micelle-like surfactant associates on DNA, which induces DNA shrinkage, DNA precipitation or DNA condensation with the emergence of nanosized particles. UV and fluorescence spectroscopy, low gradient viscometry and flow birefringence methods were employed to investigate DNA-surfactant and surfactant-surfactant interaction at different NaCl concentrations, [NaCl]. It was observed that [NaCl] (or the Debye screening radius) determines the surfactant-surfactant interaction in solutions without DNA. Monomers, micelles and non-micellar associates of azobenzene-containing surfactants with head-to-tail orientation of molecules were distinguished due to the features of their absorption spectra. The novel data enabled us to conclude that exactly the type of associates (together with the concentration of components) determines the result of DNA-surfactant interaction. Predomination of head-to-tail associates at 0.01 M < [NaCl] < 0.5 M induces DNA aggregation and in some cases DNA precipitation. High NaCl concentration (higher than 0.8 M) prevents electrostatic attraction of surfactants to DNA phosphates for complex formation. DAPI dye luminescence in solutions with DNA-surfactant complexes shows that surfactant tails overlap the DNA minor groove. The addition of di- and trivalent metal ions before and after the surfactant binding to DNA indicate that the bound surfactant molecules are located on DNA in islets.

Interactions of tetracationic porphyrins with DNA and their effects on DNA cleavage

The interaction of tetracationic porphyrins with DNA was studied using UV-Vis absorption, fluorescence spectroscopy and viscometry, and the particle sizes were determined. Аs cationic porphyrins, two isomer porphyrins, 3,3',3″,3‴-(5,10,15,20-Porphyrintetrayl)tetrakis(1-methylpyridinium) (TMPyP3) and 4,4',4″,4‴-(5,10,15,20-Porphyrintetrayl)tetrakis(1-methylpyridinium) (TMPyP4), were studied. They differ in the position of NCH₃⁺ group in phenyl ring of the porphyrins and hence, in degree of freedom of rotation of the phenyl rings about the central macrocycle. It was found that intercalated complexes are formed at DNA/porphyrin molar ratios (R) of 2.2 and 3.9 for TMPyP3 и TMPyP4, respectively. Decreasing R up to 0.4 and 0.8 for TMPyP3 и TMPyP4, respectively, leads mainly to formation of outside complexes due to π-π stacking between the porphyrin chromophores interacting electrostatically with phosphate framework of DNA. Each type of the obtained complexes was characterized using Scatchard approach. It was ascertained that the affinity of TMPyP4 to DNA is stronger than TMPyP3, meanwhile the wedge effect of the latter is higher. The differences between the porphyrin isomers become more evident at irradiation of their complexes with DNA. It was established that irradiation of the intercalated complexes results in DNA fragmentation. In the case of TMPyP4, DNA fragments of different size are formed. The irradiation of the outside DNA/porphyrin complexes leads to cleavage of DNA (TMPyP3 and TMPyP4) and partial destruction of the complex due to photolysis of the porphyrin (TMPyP3).

DNA Binding with Acetate Bis(1,10-phenanthroline)silver(I) Monohydrate in a Solution and Metallization of Formed Structures

The study of DNA interaction with the acetate bis(1,10-phenanthroline)silver(I) monohydrate in a solution is of interest both for understanding the mechanism of biological activity of silver compound and for forming ordered structures (DNA fibrils) that can be used to solve various problems in the field of nanotechnology. The analysis of changing the DNA conformation (secondary structure, persistent length and volume effects) during the interaction by the methods of UV spectroscopy with the analysis of DNA melting, circular dichroism, viscosity, flow birefringence, AFM (atomic force microscopy) and SEM (scanning electron microscopy) was performed. The formation of two types of complexes was observed. At lower concentration of compound in DNA solution, silver atoms form the coordination bonds with a macromolecule, while the released phenanthroline ligands intercalate between DNA bases. When the concentration of the compound increases, the phenanthroline ligands form an ordered "layer" around the helix. The excess of silver compounds in the DNA solution (with more than five silver atoms per base pair), DNA precipitation is observed with the formation of long fibrils. It was shown that the binding of silver to DNA during the formation of complexes provides further metallization of the resulting structures with the aid of reducing agents; phenanthroline ligands influence the result of such metallization.

The intrinsic viscosity of linear DNA

We measured the intrinsic viscosity of very small synthetic DNA molecules, of 20-395 base pairs, and incorporated them in a nearly complete picture for the whole span of molecular weights reported in the literature to date. A major transition is observed at M approximately 2 × 10(6) . It is found that in the range of approximately 7 × 10(3) ≤ M ≤ 2 × 10(6) , the intrinsic viscosity scales as [η] approximately M(1.05) , suggesting that short DNA chains are not as rigid as generally thought. The corresponding scaling for the range of 2 × 10(6) ≤ M ≤ 8 × 10(10) is [η] approximately M(0.69) . A comparison of our results with existing equations, for much narrower data distributions, is made, and the agreement is very satisfactory considering the huge range of data analyzed here. Experimental concerns such as the effect of ionic strength, polydispersity, temperature, and shear rate are discussed in detail. Some issues concerning the Huggins coefficient, polymer chain stiffness, and the relationship between the Mark-Houwink constants K, α are also presented; it is found that log K = 1.156 - 6.19α.

Sequence-selective binding of phenazinium dyes phenosafranin and safranin O to guanine-cytosine deoxyribopolynucleotides: spectroscopic and thermodynamic studies

The sequence selectivity of the DNA binding of the phenazinium dyes phenosafranin and safranin O have been investigated with four sequence-specific deoxyribopolynucleotides from spectroscopic and calorimetric studies. The alternating guanine-cytosine sequence selectivity of the dyes has been revealed from binding affinity values, circular dichroism, thermal melting, competition dialysis, and calorimetric results. The binding affinities of both the dyes to the polynucleotides were of the order of 10(5) M(-1), but the values were higher for the guanine-cytosine polynucleotides over adenine-thymine ones. Phenosafranin had a higher binding affinity compared to safranin O. Isothermal titration calorimetric studies revealed that the binding reactions were exothermic and favored by negative enthalpy and predominantly large positive entropy contributions in all cases except poly(dA)·poly(dT) where the profile was anomalous. Although charged, nonpolyelectrolytic contribution was revealed to be dominant to the free energy of binding. The negative heat capacity values obtained from the temperature dependence of enthalpy changes, which were higher for phenosafranin compared to safranin O, suggested significant hydrophobic contribution to the binding process. In aggregate, the data presents evidence for the alternating guanine-cytosine base pair selectivity of these phenazinium dyes and a stronger binding of phenosafranin over safranin O.

Intrinsic viscosity of native and single-stranded T7 DNA and its relationship to sedimentation coefficient

The intrinsic viscosity and sedimentation coefficient of native and single-stranded T7 DNA have been determined at 25⁰C as a function of ionic strength in neutral and alkaline NaCl. The relationship between [η] and S⁰(20,w), is well represented by the Mandelkern-Flory equation over the entire range of conditions between 0.0013 and 1M Na+. An apparent discrepancy between the two methods at moderate to high ionic strengths is probably due to a change in V with ionic strength. It appears that [η] is a more sensitive and reliable measure of molecular expansion for native DNA,but S⁰(20,w) is a better index of conformational change in single strands, since [η] becomes too small to measure conveniently at high ionic strengths. At moderate to high ionic strengths, denaturation leads to a decrease in [η], although unfolded single strands retain considerable viscosity. At sufficiently low ionic strength, the intrinsic viscosity of the single strands becomes higher than that of native DNA, and the effective volume of a single strand approaches that of the native molecule.

Mechanism of thermal renaturation and hybridization of nucleic acids: Kramers' process and universality in Watson-Crick base pairing

Renaturation and hybridization reactions lead to the pairing of complementary single-stranded nucleic acids. We present here a theoretical investigation of the mechanism of these reactions in vitro under thermal conditions (dilute solutions of single-stranded chains, in the presence of molar concentrations of monovalent salts and at elevated temperatures). The mechanism follows a Kramers' process, whereby the complementary chains overcome a potential barrier through Brownian motion. The barrier originates from a single rate-limiting nucleation event in which the first complementary base pairs are formed. The reaction then proceeds through a fast growth of the double helix. For the DNA of bacteriophages T7, T4, and phiX174, as well as for Escherichia coli DNA, the bimolecular rate k2 of the reaction increases as a power law of the average degree of polymerization <N> of the reacting single-strands: k2 is proportional to <N> alpha. This relationship holds for 100 < or = <N> < or = 50,000 with an experimentally determined exponent alpha = 0.51 +/- 0.01. The length dependence results from a thermodynamic excluded-volume effect. The reacting single-stranded chains are predicted to be in universal good solvent conditions, and the scaling law is determined by the relevant equilibrium monomer contact probability. The value theoretically predicted for the exponent is alpha = 1 - nutheta2, where nu is Flory's swelling exponent (nu approximately equal 0.588), and theta2 is a critical exponent introduced by des Cloizeaux (theta2 approximately equal 0.82), yielding alpha = 0.52 +/- 0.01, in agreement with the experimental results.

Size and average density spectra of macromolecules obtained from hydrodynamic data

It is proposed to normalize the Mark-Kuhn-Houwink-Sakurada type of equation relating the hydrodynamic characteristics, such as intrinsic viscosity, velocity sedimentation coefficient and translational diffusion coefficient of linear macromolecules to their molecular masses for the values of linear density M(L) and the statistical segment length A. When the set of data covering virtually all known experimental information is normalized for M(L), it is presented as a size spectrum of linear polymer molecules. Further normalization for the A value reduces all data to two regions: namely the region exhibiting volume interactions and that showing hydrodynamic draining. For chains without intachain excluded volume effects these results may be reproduced using the Yamakawa-Fujii theory of wormlike cylinders. Data analyzed here cover a range of contour lengths of linear chains varying by three orders of magnitude, with the range of statistical segment lengths varying approximately 500 times. The plot of the dependence of [eta]M on M represents the spectrum of average specific volumes occupied by linear and branched macromolecules. Dendrimers and globular proteins for which the volume occupied by the molecule in solution is directly proportional to M have the lowest specific volume. The homologous series of macromolecules in these plots are arranged following their fractal dimensionality.

4-Anilinopyrimido[4',5':4,5]selenolo(2,3-b)quinoline and 4-piperazino pyrimido[4',5':4,5]selenolo(2,3-b)quinoline: new DNA intercalating chromophores with antiproliferative activity

We have used circular dichroism, hydrodynamic methods, absorbance, and fluorescence titration to study the interaction of 4-anilinopyrimido[4',5':4,5] selenolo (2,3-b)quinoline (APSQ) and 4-piperazinopyrimido[4',5':4,5] selenolo(2,3-b)quinoline (PPSQ) with DNA. The association constants of APSQ and PPSQ were of the order of 10(4)M(-1). The fluorescence properties at ionic strength 0.01M are best fit by the neighbor exclusion model, with K=0.58-9.2 x 10(4)M(-1) and an exclusion parameter of 0.9-6.4 bp. Binding to the GC-rich DNA of Micrococcus lysodeikticus was stronger than the binding to calf thymus DNA, suggest that drug binds preferentially to G+C pairs at low r. CD spectra indicate that stacking of these compounds with DNA induces a strong helicity in the usually disordered structure of this double strand. Viscosity experiments show with sonicated calf thymus DNA with PPSQ an twice increase in slope (m) as that with APSQ. PPSQ increases the T(m) for calf thymus DNA melting by approximately 10 degrees C as binding approaches saturation, with biphasic melting. The cytotoxicities of these compounds on leukemia HL-60, K-562, B16F10 melanoma and Colo-205 are quite similar and inhibition (IC(50)) was in the range of 0.39-9.80 microM. The anticancer efficacy against B16F10 melanoma has provided evidence of major anticancer activity for PPSQ. Single or multiple intraperitonial (i.p.) doses of drug proved high level activity against the subcutaneous (s.c.) grafted B16 melanoma, significantly increase in life span (ILS 139% and 170%). The aim of this study was to analyze the physiochemical properties of these compounds in an attempt to understand its superior biological activity.

Synthesis, Biological Activity, and Quantitative Structure−Activity Relationship Study of Azanaphthalimide and Arylnaphthalimide Derivatives

A series of quinoline derivatives as aza analogues of the naphthalene chromophore and a series of "nonfused" tricyclic aromatic systems, in particular 5-arylquinolines and 5- or 6-aryl and heteroaryl naphthalene systems, were synthesized and evaluated for growth-inhibitory properties in several human cell lines. The analysis of quantitative structure-antitumor activity relationships for the growth-inhibitory properties is also reported. Findings suggest that these compounds may not express their cytotoxicity via interaction on DNA.

New Analogues of Amonafide and Elinafide, Containing Aromatic Heterocycles: Synthesis, Antitumor Activity, Molecular Modeling, and DNA Binding Properties

Amonafide- and elinafide-related mono and bisintercalators, modified by the introduction of a pi-excedent furan or thiophene ring fused to the naphthalimide moiety, have been synthesized. These compounds have shown an interesting antitumor profile. The best compound, 9, was 2.5-fold more potent than elinafide against human colon carcinoma cells (HT-29). Molecular dynamic simulations and physicochemical experiments have demonstrated that these compounds are capable of forming stable DNA complexes. These results, together with those previously reported by us for imidazo- and pyrazinonaphthalimide analogues, have prompted us to propose that the DNA binding process does not depend on the electronic nature of the fused heterocycle.

Thermal stability and DNA binding activity of a variant form of the Sso7d protein from the archeon Sulfolobus solfataricus truncated at leucine 54

Sso7d is a 62-residue, basic protein from the hyperthermophilic archaeon Sulfolobus solfataricus. Around neutral pH, it exhibits a denaturation temperature close to 100 degrees C and a non-sequence-specific DNA binding activity. Here, we report the characterization by circular dichroism and fluorescence measurements of a variant form of Sso7d truncated at leucine 54 (L54Delta). It is shown that L54Delta has a folded conformation at neutral pH and that its thermal unfolding is a reversible process, represented well by the two-state N <=> D transition model, with a denaturation temperature of 53 degrees C. Fluorescence titration experiments indicate that L54Delta binds tightly to calf thymus DNA, even though the binding parameters are smaller than those of the wild-type protein. Therefore, the truncation of eight residues at the C-terminus of Sso7d markedly affects the thermal stability of the protein, which nevertheless retains a folded structure and DNA binding activity.

The 100 most-cited articles from JMB

Over the last 40 years, JMB has published many thousands of articles, all of which have been important in some way. Compiling a list of the 'most important' however, is an invidious task. Friendships can falter on such an undertaking, but the Institute of Scientific Information has provided us with an objective methodology for 'ranking' articles, according to the number of times any paper is cited in other publications. This evaluation can of course be criticised for its bias towards papers describing novel techniques or methods. Often, the true intellectual milestones may be found in the reference list of the most cited papers. With increasing age, each paper also has more time in which to have been cited, and so the group of highest scoring articles is also dominated by some of the oldest. On the other hand, with increasing time, papers have an increasing chance of being forgotten, and the citation rates of these are therefore also a measure of their persisting importance. On balance, it does represent a value in some way related to how often that paper has been used. With many caveats, we present the list of the 100 most cited papers in JMB over the past 40 years. Many of these papers have helped or influenced both a great many people, and a great many subsequent advances in molecular biology.

Complex Formation of E. coli RNA Polymerase with Bacteriophage T2 DNA: Long-Range Effects in DNA

Conformation behavior of phase T2 DNA in the process of its interaction with it E. coli RNA polymerase was studied using spin labeling technique. T2 DNA was modified by the spin-labeled imidazole at OH-groups of glucosylated cytidine residues. It was shown that the binding of RNA polymerase under the conditions favoring the formation of open promoter complexes induces specific conformational changes in the spin-labeled DNA. The observed conformational changes encompass not only the promoter regions of DNA which are involved in direct contacts with RNA polymerase molecules but extend over remote DNA sites (long-range effect). In relation to this effect, current theoretical models of DNA dynamics are discussed.

A review of dsb induction data for varying quality radiations

PURPOSE

This short review summarizes the data obtained with various techniques for measuring the yields of double strand breaks (dsb) produced by particle radiations of differing linear energy transfer (LET) in order to obtain relative biological effectiveness (RBE) values.

RESULTS AND CONCLUSIONS

Studies aimed at understanding the interactions of different types of radiation with cellular DNA have monitored the yields of DNA dsb versus radiation quality. Several techniques have been used to measure dsb yields in mammalian cells, and these include: neutral sedimentation gradients, filter elution and more recently pulsed field gel electrophoresis techniques (PFGE). Recent developments in PFGE have allowed the measurement of both the yields and the distribution of breaks within the genome, which go part of the way to explaining the RBE values close to 1.0 previously measured using other approaches with various radiation qualities. It is clear that future studies to determine the effectiveness of radiations of differing LET must use techniques that determine both yields and distributions of dsb, and assays need to be developed to allow these measurements at biologically relevant doses.

Dielectric studies of chain melting and denaturation in native DNA

Dielectric methods, based on time domain reflectometry (TDR), have been employed to characterise DNA chain melting and denaturation. A dielectric dispersion has been identified, centred in the low megahertz region, which has been attributed to the fluctuation of counterions along short segments of the DNA chain. Chain melting studies have shown that the magnitude of this dispersion is dependent not only on the relative proportions of single to double stranded DNA but also on the intermolecular interactions between the DNA chains.

Interaction of sanguinarine iminium and alkanolamine form with calf thymus DNA

The interaction of sanguinarine iminium form (structure I) and sanguinarine alkanolamine form (structure II) with calf thymus DNA has been studied in buffer of pH 5.2 and pH 10.5, respectively, where the physicochemical properties of DNA remain unchanged. The binding of sanguinarine iminium form to DNA is characterized by hypochromism and bathochromism in the absorption band, quenching of fluorescence intensity, increase in fluorescence polarization anisotropy, increase in positive and negative ellipticity of DNA, sign and magnitude of the thermodynamic parameters and increase in contour length of sonicated rodlike duplex DNA indicating that it binds to DNA by a mechanism of intercalation. In contrast, sanguinarine alkanolamine form does not show (i) any significant change in fluorescence polarization anisotropy, (ii) alteration of B form structure of DNA and (iii) increase in contour length of DNA indicating that it does not bind to DNA. But at a very high concentration of DNA, the alkanolamine form is influenced to form an iminium-DNA complex.

Conformational changes in oligo-nucleotides upon binding to a peptide representing the N-terminal region of a viral coat protein. An optical spectroscopy study

Conformational changes of the oligonucleotides r(A)12, d(GC)5, and d(AT)5 upon binding to a pentacosapeptide representing the RNA-binding N-terminus of the coat protein of cowpea chlorotic mottle virus (CCMV) were studied by using absorption and circular dichroism spectroscopy. The peptide destabilizes the single-stranded structure of r(A)12 at pH 7.2, but disrupts the double-stranded structure of r(A)12 at pH 5.0. However, at pH 4.0, the peptide is not able to disrupt this double-stranded structure. The double-stranded structures of d(GC)5 and d(AT)5 with Watson-Crick base-pairing are stabilized upon binding to the peptide.

Effect of gamma-irradiation on the conformation of the native DNA molecule

Extensive investigation of gamma-irradiated DNA solutions with the application of several informative physical methods suggested that at doses of 10-30 Gy the observed change in the size of the DNA molecule is due to a decrease in long-range interactions in the macromolecule. The comparison of the results of investigations of non-irradiated and irradiated DNA and its complexes with low molecular weight ligands over a wide range of ionic strengths showed that these interactions are electrostatic in nature and are due to a decrease in the charge density on the DNA molecule when its solutions are irradiated. In the irradiation dose range discussed here, the persistent length of the DNA molecule determined by short-range interactions in the chain does not undergo pronounced changes. It is shown that the free ligand in the irradiated solution can protect the DNA molecule against radiation damage. In contrast, the ligand bonded by intercalation does not exhibit this ability.

Compositional patterns in the nuclear genome of cold-blooded vertebrates

DNA preparations obtained from 122 species of fishes, 5 species of amphibians, and 13 species of reptiles were investigated in their compositional properties by analytical equilibrium centrifugation in CsCl density gradients. These species represented 21 orders of Osteichthyes, 3 orders of Chondrichthyes, 2 orders of amphibians, and 3 orders of reptiles. Modal buoyant densities of fish DNAs ranged from 1.696 to 1.707 g/cm3, the vast majority of values falling, however, between 1.699 and 1.704 g/cm3, which is the range covered by the DNAs of amphibians and reptiles. In all cases, DNA bands in CsCl were only weakly asymmetrical and only very rarely were accompanied by separate satellite bands (mostly on the GC-rich side). Intermolecular compositional heterogeneities were low in the vast majority of cases, and, like CsCl band asymmetries, at least partially due to cryptic or poorly resolved satellites. The present findings indicate, therefore, that DNAs from cold-blooded vertebrates are characterized by a number of common properties, namely a very wide spectrum of modal buoyant densities, low intermolecular compositional heterogeneities, low CsCl band asymmetries, and, in most cases, small amounts of satellite DNAs. In the case of fish DNAs a negative correlation was found between the GC level and the haploid size (c value) of the genome. If polyploidization is neglected, this phenomenon appears to be mainly due to the fact that increases and decreases in GC are associated with contraction and expansion phenomena, respectively, of intergenic noncoding sequences, which are GC poor relative to coding sequences.

Single-stranded RNA molecular weight and shape determination by differential pressure capillary viscometry, sedimentation velocity, and gel electrophoresis

Determination of the size of a population of nucleic acids can be achieved by several distinct methods. Most of these methods are cumbersome and require complicated equipment or techniques. We demonstrate here the use of a differential pressure capillary viscometer for the rapid and simple determination of RNA molecular weight. This highly sensitive viscometer allowed single viscosity determinations on dilute solutions of RNA, providing a direct measure of the intrinsic viscosity without the need to extrapolate from several concentrations. The molecular weights and conformations of the linear single-stranded RNA homopolymer poly(inosinic acid) (poly(I] and the single-stranded RNA (ssRNA) copolymer poly(cytidylic acid:uridylic acid, 12:1) (poly(C12,U], were determined. The ssRNAs were synthesized in a range of sizes (100 to 100,000 bases). They were widely polydisperse. The Mandelkern-Flory equation (1952, J. Chem. Phys. 20, 212-214), which requires both the intrinsic viscosity and sedimentation coefficient of a macromolecule, was used to calculate the molecular weights. The molecular weights determined by agarose gel electrophoresis were compared to those determined by intrinsic viscosity plus sedimentation coefficient. The correlation between the molecular weights determined by these two methods was good, at R2 greater than or equal to 0.92. The conformations of the RNAs were determined by application of the Mark-Houwink equation. The Mark-Houwink exponents for poly(I) and poly(C12,U) intrinsic viscosities were 0.90 and 0.84, respectively. When compared to other nucleic acid polymers, for which the conformations have been established by several methods, poly(I) and poly(C12,U) are rigid, extended random coils, in a low-salt buffer (15 mM).(ABSTRACT TRUNCATED AT 250 WORDS)

Low angle light scattering studies on whole, half, and quarter molecules of T2 bacteriophage DNA

Static light scattering measurements have been made at angles as low as 8 degrees on whole, half, and quarter molecules of native, T2 bacteriophage DNA in 0.195 M Na+. The fragments were obtained by high-speed stirring of the native DNA, and fractionated on methylated-albumin-kieselguhr columns. Accompanying measurements of sedimentation coefficients and intrinsic viscosities were made. Because linear extrapolations of light scattering data above 8 degrees for these samples were suspect, the measurements were analyzed by fitting curves calculated from the theory of wormlike coils to experimental curves at c = 0. Results showed that the excluded volume parameter, epsilon, must be used in analyzing the scattering curves; a reasonable value of epsilon was 0.08, in agreement with that found for T7 DNA (Harpst, J. A. 1980. Biophys. Chem. 11:295-302). The persistence length of all three DNAs in this paper was 50 +/- 5 nm, showed no dependence on molecular weight, but was somewhat below that reported previously for T7 DNA (60 nm). Theoretical curves calculated with the preceding parameters had a clear upward curvature in scattering envelopes below 8 degrees for quarter and half molecules, but such curvature was minimal for whole T2 DNA, so that linear extrapolations of experimental data above 8 degrees gave a molecular weight and root-mean-square radius which were nearly the same as those from theory. The molecular weight and radius for whole T2, derived from the comparison of theory and experiment, were 115 X 10(6) and 1,224 nm, respectively. The measurements on T2 DNA were clearly at the upper limit of current techniques.