Remote control of DNA-acting enzymes by varying the Brownian dynamics of a distant DNA end

Enzyme rates are usually considered to be dependent on local properties of the molecules involved in reactions. However, for large molecules, distant constraints might affect reaction rates by affecting dynamics leading to transition states. In single-molecule experiments we have found that enzymes that relax DNA torsional stress display rates that depend strongly on how the distant ends of the molecule are constrained; experiments with different-sized particles tethered to the end of 10-kb DNAs reveal enzyme rates inversely correlated with particle drag coefficients. This effect can be understood in terms of the coupling between molecule extension and local molecular stresses: The rate of bead thermal motion controls the rate at which transition states are visited in the middle of a long DNA. Importantly, we have also observed this effect for reactions on unsupercoiled DNA; other enzymes show rates unaffected by bead size. Our results reveal a unique mechanism through which enzyme rates can be controlled by constraints on macromolecular or supramolecular substrates.     

Direct electrical detection of DNA synthesis

Rapid, sequence-specific DNA detection is essential for applications in medical diagnostics and genetic screening. Electrical biosensors that use immobilized nucleic acids are especially promising in these applications because of their potential for miniaturization and automation. Current DNA detection methods based on sequencing by synthesis rely on optical readouts; however, a direct electrical detection method for this technique is not available. We report here an approach for direct electrical detection of enzymatically catalyzed DNA synthesis by induced surface charge perturbation. We discovered that incorporation of a complementary deoxynucleotide (dNTP) into a self-primed single-stranded DNA attached to the surface of a gold electrode evokes an electrode surface charge perturbation. This event can be detected as a transient current by a voltage-clamp amplifier. Based on current understanding of polarizable interfaces, we propose that the electrode detects proton removal from the 3'-hydroxyl group of the DNA molecule during phosphodiester bond formation.     

Molecular cardiology and genetics in the 21st century--a primer

The terminology and technology of molecular genetics and recombinant DNA have become an essential part of academic cardiology and will soon be applied at the bedside. The treatise includes a brief summary of the essentials of the DNA molecule, the more common techniques, and their application to genetics and molecular cardiology. It is written to be understood by physicians, scientists, and paramedical personnel who would not necessarily have a background in molecular biology. Inherent in the DNA molecule are three properties fundamental to all of the diagnostic and therapeutic applications, namely, the ability of DNA to separate into single strands, recombine (annealment or hybridization), and the presence of the negative charge enables DNA fragments to be separated easily by electrophoresis. Genetic linkage analysis of a family with an inherited disease enables one to identify the gene without knowing its protein product. Over 50 diseases in cardiology due to single-gene disorders have been identified and multiple mutations have been detected. The new therapeutic frontier will be stem cells and nuclear transfer. Identification of genes responsible for coronary artery disease made possible by genome-wide single nucleotide polymorphism (SNP) mapping techniques paves the way for personalized medicine.     

Low molecular weight iron from guinea pig reticulocytes isolated by Sephadex G-25 chromatography

As part of a continuing study of the low MW iron pool, guinea pig reticulocytes were incubated with 59Fe-labeled transferrin, and the reticulocyte hemolysate was chromatographed on Sephadex G-25. 59Fe, in amounts corresponding to that which was in a low MW peak eluting from an Ultrogel column and to that not precipitated by ammonium sulfate, adsorbed to the Sephadex column. The adsorbing 59Fe, on elution from the Sephadex with dilute formic acid, coeluted with phosphate and pentose. When EDTA was added to disrupt the putative iron complex, neither iron nor P adsorbed to the column, supporting the argument that they exist as a compound in the cytosol and adsorb and elute together for that reason. These observations provide additional evidence that P-containing compounds, probably originating as nucleotides, are important components of the low MW iron pool of cells.     

RNA-directed DNA synthesis by the DNA polymerase of Rous sarcoma virus: structural and functional identification of 4S primer RNA in uninfected cells.

The RNA-directed DNA polymerase of Rous sarcoma virus requires a 4S RNA molecule as primer for the initiation of DNA synthesis on the viral 70S RNA genome. We have now functionally identified primer activity in uninfected cells on the basis of the capacity of cellular 4S RNA to actively participate in the initiation of DNA synthesis by the RNA-directed DNA polymerase of Rous sarcoma virus in vitro. This was accomplished by reconstitution experiments in which 4S RNA from uninfected avian cells was tested for its ability to restore template activity to the viral RNA genome from which all primer had been removed. Similar reconstitution experiments were employed to demonstrate a primer activity in the 4S RNA population of duck, mouse, and human cells. Primer activity appears to be absent in lower eukaryotic or prokaryotic cells. Unambiguous identification of the Rous sarcoma virus primer molecule in uninfected cells was accomplished by directly purifying a 4S RNA molecule from the bulk of host cell transfer RNA and establishing structural similarities between this cellular 4S RNA species and the Rous sarcoma virus primer by two-dimensional paper electrophoresis of oligonucleotides obtained from a T1 ribonuclease digest of the RNA species. We conclude that the Rous sarcoma virus DNA polymerase can utilize a host cell molecule as primer for the initiation of RNA-directed DNA synthesis in vitro.     

An RNA topoisomerase.

A synthetic strand of RNA has been designed so that it can adopt two different topological states (a circle and a trefoil knot) when ligated into a cyclic molecule. The RNA knot and circle have been characterized by their behavior in gel electrophoresis and sedimentation experiments. This system allows one to assay for the existence of an RNA topoisomerase, because the two RNA molecules can be inter-converted only by a strand passage event. We find that the interconversion of these two species can be catalyzed by Escherichia coli DNA topoisomerase III, indicating that this enzyme can act as an RNA topoisomerase. The conversion of circles to knots is accompanied by a small amount of RNA catenane generation. These findings suggest that strand passage must be considered a potential component of the folding and modification of RNA structures.     

Multiple events on single molecules: unbiased estimation in single-molecule biophysics

Most analyses of single-molecule experiments consist of binning experimental outcomes into a histogram and finding the parameters that optimize the fit of this histogram to a given data model. Here we show that such an approach can introduce biases in the estimation of the parameters, thus great care must be taken in the estimation of model parameters from the experimental data. The bias can be particularly large when the observations themselves are not statistically independent and are subjected to global constraints, as, for example, when the iterated steps of a motor protein acting on a single molecule must not exceed the total molecule length. We have developed a maximum-likelihood analysis, respecting the experimental constraints, which allows for a robust and unbiased estimation of the parameters, even when the bias well exceeds 100%. We demonstrate the potential of the method for a number of single-molecule experiments, focusing on the removal of DNA supercoils by topoisomerase IB, and validate the method by numerical simulation of the experiment.     

Charge equilibration between two distinct sites in double helical DNA

DNA assemblies containing a pendant dipyridophenazine complex of Ru(II) along with two oxidative traps, a site containing the nucleoside analog methylindole (5'-GMG-3') and a 5'-GGG-3' site, have been constructed to explore long-range charge transport through the base pair stack. With these chemically well defined assemblies, in combination with the flash/quench technique, formation of the methylindole cation radical and the neutral guanine radical is monitored directly by using transient absorption spectroscopy, and yields of oxidative damage are quantitated biochemically by gel electrophoresis. In these assemblies the base radicals form with a rate of > or =10(7) s(-1). The rate of base radical formation does not change upon the addition of a second radical trap, the 5'-GGG-3' site; however, the yield of methylindole oxidation is significantly lower. This observation indicates that the 5'-GGG-3' site is effective in competing for the migrating charge and provides a second trapping site. Switching the orientation of the two trapping sites does not affect the yield of oxidized products at either site. Therefore, in DNA both forward and reverse charge transport occur so as to provide equilibration across the duplex on a timescale that is fast compared with trapping at a particular site. Further evidence of charge equilibration results from incorporating an intervening base-stacking perturbation and monitoring the fate of the injected charge. These experiments underscore the dynamic nature of DNA charge transport and reveal the importance of considering radical propagation in both directions along the DNA duplex.     

Sequence information can be obtained from single DNA molecules

The completion of the human genome draft has taken several years and is only the beginning of a period in which large amounts of DNA and RNA sequence information will be required from many individuals and species. Conventional sequencing technology has limitations in cost, speed, and sensitivity, with the result that the demand for sequence information far outstrips current capacity. There have been several proposals to address these issues by developing the ability to sequence single DNA molecules, but none have been experimentally demonstrated. Here we report the use of DNA polymerase to obtain sequence information from single DNA molecules by using fluorescence microscopy. We monitored repeated incorporation of fluorescently labeled nucleotides into individual DNA strands with single base resolution, allowing the determination of sequence fingerprints up to 5 bp in length. These experiments show that one can study the activity of DNA polymerase at the single molecule level with single base resolution and a high degree of parallelization, thus providing the foundation for a practical single molecule sequencing technology.     

A novel dysfunctional protein C (Protein C Padua 2) associated with a thrombotic tendency: substitution of Cys for Arg-1 results in a strongly reduced affinity for binding of Ca++

Summary. A dysfunctional protein C (PC) molecule (Protein C Padua 2) was found in a 40-year-old man presenting with recurrent deep vein thrombosis/pulmonary embolism and a family history of thrombotic disease. The patient exhibited a normal PC antigen level, normal chromogenic activity (using Protac as PC activator) but markedly reduced coagulometric activity. After adsorption of patient plasma onto AI(OH), between 30% and 45% PC antigen/chromogenic activity but no coagulometric activity was detectable in the supernatant. The dysfunctional molecule exhibited reduced affinity for a Ca⁺⁺ dependent anti-protein C monoclonal antibody as detected by specific ELISA assay. Immunoblotting experiments showed that PC Padua 2 had an increased MW (95 kD v 65 kD for normal PC).
The lesion responsible was determined by PCR/direct sequencing to be a heterozygous CGT/TGT transition in exon 3 of the protein C gene resulting in the substitution of Arg by Cys at residue — 1 in the pro-peptide leader sequence.
The presence of a high MW PC was consistent with the fact that (part of) the propeptide (at least Cys-1) still was attached to the protein C molecule. This finding could also explain the strongly reduced affinity of PC Padua 2 for the Ca⁺⁺ dependent anti-protein C monoclonals.     

The Nature of Renin Precursor and Inactive Renin

The biosynthesis of renin in the mouse submaxillary gland was defined using both cell-free translation and pulse-labelling methods. Renin is synthesized as a preproform and cleaved by microsomes to the proform. Prorenin (MW = 46 kilodaltons, pI 6.35) is processed intracellulary into an intermediate form (MW = 41 kilodaltons). The latter is converted by a slow intracellular process to the final major storage form (MW = 37 kilodaltons). Both the intermediate and the 37 KD forms are secreted. The biosynthetic precursor does not bind to pepstatin-aminohexyl sepharose. in parallel experiments, using rapid tissue extraction with buffers containing protease inhibitors and fractionation with affinity chromatography, we have also identified in the mouse submaxillary gland an inactive form of renin which has a MW of 48 2 KD and pI of 6.4. Mouse submaxillary gland inactive renin binds to affigel-blue and not to pepstatin-sepharose. The similarity in the properties of inactive renin and the biosynthetic renin precursor lends further support to the suggestion that tissue inactive renin may be the renin precursor.     

X-ray Absorption (XRA): A New Technique for the Characterization of Granular Activated Carbons

The X-ray absorption (XRA) method using digital image processing techniques is a reliable technique to determine the exhaustion degree of granular activated carbons (GACs). Using an innovative digital image processing technique, the identification of individual adsorbed molecules or ions in a GAC was possible. Adsorption isotherm models (Langmuir and Freundlich) were used to simulate the adsorption equilibrium data of Methylene Blue (MB), nickel, cobalt and iodine. Freundlich equation was found to have the highest value of R² compared with Langmuir. The identification of distinctive patterns applying XRA for different adsorbed ions and molecules onto GAC was explored. It is demonstrated that unique XRA configurations for each adsorbed ion or molecule are found, as well as a proportional relationship between its incident energy (needed to achieve maximum photon attenuation) and the (effective) atomic number, the adsorbate mass and the molar or atomic mass of adsorbed molecule or ion. XRA method in combination with image histogram modifications was used to obtain a digital signature of adsorbed ions/molecules, giving distinct GSI values for each one in the used energy range. Probabilistic models prove that XRA results are within relationships between effective atomic number and photonic interaction probability, reinforcing the potentialities of XRA for monitoring (multi-)ion and/or molecule combinations on GAC using advanced digital image processing techniques. It was proved that the proposed approach could assess different adsorbed ions/molecules onto GACs in water purification systems.     

Unusual conformational effect exerted by Z-DNA upon its neighboring sequences.

Supercoiled plasmid DNA harboring an insert of (dG-dC)16, a sequence known to form Z-DNA upon negative supercoiling, was reacted with chloroacetaldehyde. Chloroacetaldehyde, like bromoacetaldehyde, was found to be a specific probe for detecting unpaired DNA bases in supercoiled plasmid DNA. Under torsional stress (at bacterial superhelical density), chloroacetaldehyde reacted at multiple discrete regions within the neighboring sequences of the (dG-dC)16 insert. When the plasmid population was considered as a whole, the distribution of the chemically reactive bases exhibited a pattern of inversion symmetry with the center of inversion in the middle of the (dG-dC)16 insert. However, when a single supercoiled plasmid molecule was considered, chloroacetaldehyde reacted with only one of the neighboring sequences, either 5' or 3' of the (dG-dC)16 insert, but not with both. The possibility that the supercoiled plasmid DNA is in equilibrium with these two structural forms is discussed.     

Epstein-Barr virus genomes with properties of circular DNA molecules in carrier cells.

A high-density fraction of high-molecular-weight DNA was isolated from the human lymphoid cell line Raji. This cell line contains 50 to 60 virus genome equivalents of Epstein-Barr virus DNA per cell, and the high-density DNA fraction was 10-fold enriched in such viral sequences. Sedimentation analysis on neutral glycerol gradients, followed by hybridization experiments with viral complementary RNA, showed that most of the intracellular viral DNA sequences in this material did not cosediment with the cellular DNA, but were recovered as two distinct species with sedimentation coefficients of 100 S and 65 S. These two forms sediment 1.70-1.75 and 1.10-1.12 times as fast as the linear Epstein-Barr virus DNA from virus particles, and thus have the hydrodynamic properties of a covalently closed circular form and a nicked (containing single-strand breaks) circular form of the virus genome. The 100S form also behaved as a covalently closed circular EBV DNA molecule on gradient centrifugation in CsC1/propidium diiodide, It would appear that latent Epstein-Barr virus DNA has the properties of a mammalian episome, and that both nonintegrated and integrated viral DNA sequences can be isolated from carrier cells.     

Molecular level stochastic model for competence cycles in Bacillus subtilis

The role of stochasticity and noise in controlling genetic circuits is investigated in the context of transitions into and from competence in Bacillus subtilis. Recent experiments have demonstrated that bistability is not necessary for this function, but that the existence of one stable fixed point (vegetation) and an excitable unstable one (competence) is sufficient. Stochasticity therefore plays a crucial role in this excitation. Noise can be generated by discrete events such as RNA and protein synthesis and their degradation. We consider an alternative noise source connected with the protein binding/unbinding to the DNA. A theoretical model that includes this "nonadiabatic" mechanism appears to produce a better agreement with experiments than models where only the adiabatic limit is considered, suggesting that this nonconventional stochasticity source may be important for biological functions.     

A recombinase from Drosophila melanogaster embryos.

We have partially purified a DNA strand-exchange activity (recombinase) from nuclear extracts of Drosophila melanogaster embryos. The protein fraction forms a joint molecule between a circular single-strand DNA and a homologous linear duplex DNA that is resolved from the substrates by agarose gel electrophoresis. A strand-exchange activity can be obtained from nuclear extracts from embryos as old as 24 hr. The activity is similar to that partially purified from human cells [Hsieh, P., Meyn, S.M. & Camerini-Otero, R.D. (1986) Cell 44, 885-894]. It is homology-dependent, requires Mg2+, appears to be directional in that it prefers to displace the 3' end of the noncomplementary strand, and does not require exogenous ATP. Forty nanograms of protein in the partially purified DNA strand-exchange fraction from D. melanogaster embryos can completely convert 50 ng of substrate single-strand DNA into joint molecules in 10 min. In the electron microscope, joint molecules are seen to consist of a circular single-strand DNA molecule attached to only one end of a linear duplex DNA molecule; a displaced strand is also seen. The region of heteroduplex formation can be as long as 600 base pairs. The demonstration of a strand-exchange activity from wild-type D. melanogaster embryos invites analysis of recombination-defective mutants to explore the role of DNA strand exchange in homologous recombination.     

DNA molecule provides a computing machine with both data and fuel

The unique properties of DNA make it a fundamental building block in the fields of supramolecular chemistry, nanotechnology, nano-circuits, molecular switches, molecular devices, and molecular computing. In our recently introduced autonomous molecular automaton, DNA molecules serve as input, output, and software, and the hardware consists of DNA restriction and ligation enzymes using ATP as fuel. In addition to information, DNA stores energy, available on hybridization of complementary strands or hydrolysis of its phosphodiester backbone. Here we show that a single DNA molecule can provide both the input data and all of the necessary fuel for a molecular automaton. Each computational step of the automaton consists of a reversible software molecule input molecule hybridization followed by an irreversible software-directed cleavage of the input molecule, which drives the computation forward by increasing entropy and releasing heat. The cleavage uses a hitherto unknown capability of the restriction enzyme FokI, which serves as the hardware, to operate on a noncovalent software input hybrid. In the previous automaton, software input ligation consumed one software molecule and two ATP molecules per step. As ligation is not performed in this automaton, a fixed amount of software and hardware molecules can, in principle, process any input molecule of any length without external energy supply. Our experiments demonstrate 3 x 10(12) automata per microl performing 6.6 x 10(10) transitions per second per microl with transition fidelity of 99.9%, dissipating about 5 x 10(-9) W microl as heat at ambient temperature.     

Requirement for two DNA polymerases in the replication of simian virus 40 DNA in vitro.

DNA polymerase alpha-primase has long been considered the primary, if not sole, replicative DNA polymerase in eukaryotic cells. However, recent experiments have provided indirect evidence that a second DNA polymerase may play a role in DNA replication. To identify cellular proteins necessary for DNA synthesis in mammalian cells, we have been studying the cell-free system developed for the replication of simian virus 40 DNA. In this report, we present direct evidence that a second DNA polymerase is required in addition to DNA polymerase alpha-primase complex to obtain efficient replication of simian virus 40 origin-containing DNA. This DNA polymerase activity is not affected by monoclonal antibodies that inhibit the activity of DNA polymerase alpha and is relatively resistant to the inhibitor [N2-(p-n-butylphenyl)-9-(2-deoxy-beta-D-ribofuranosyl)guanine 5'-triphosphate]. Moreover, the activity of the polymerase is highly dependent upon the accessory protein, proliferating-cell nuclear antigen. These characteristics are consistent with the hypothesis that this second DNA polymerase is DNA polymerase delta.     

Solubilization of insulin binding and degrading activity from guinea pig kidneys

Summary Insulin binding and degrading activities were solubilized by a nonionic detergent. Triton X100, from guinea pig kidney particulate fractions (100,000 × g pellet). The solubilized insulin binding activity appeared as a single peak on Sepharose 6B gel filtration with a Stokes radius of 73 A. The pI of the solubilized insulin binding activity determined by flat-bed isoelectric focusing was 5.6. On the other hand, the Stokes radius of the solubilized molecule with insulin degrading activity was 54 Å by the same column with a pI of 5.2. More than 98% of the insulin binding activity could be adsorbed to a column of concanavalin A-agarose, while about 94% of the insulin degrading activity could not be adsorbed to this column. These results strongly suggest that the macromolecule for the insulin binding activity is not identical to that for the insulin degrading activity.