The accuracy of DNA replication

Role of thermal fluctuations in biological copying mechanisms

During transcription, translation, or self-replication of DNA or RNA, information is transferred to the newly formed species from its predecessor. These processes can be interpreted as (generalized) biological copying mechanism as the new biological entities like DNA, RNA, or proteins are representing the information of their parent bodies uniquely. The accuracy of these copying processes is essential, since errors in the copied code can reduce the functionality of the next generation. Such errors might result from perturbations on these processes. Most important in this context is the temperature of the medium, i.e., thermal noise. Although a reasonable amount of experimental studies have been carried out on this important issue, theoretical understanding is truly sparse. In the present work, we illustrate a model study which is able to focus on the effect of the temperature on the process of biological copying mechanisms, as well as on mutation. We find for our paradigmatic models that, in a quite general scenario, the copying processes are most accurate at an intermediate temperature range; i.e., there exists an optimum temperature where mutation is most unlikely. This allows us to interpret the observations for some biological species with the aid of our model study.

Thermodynamic framework for information in nanoscale systems with memory

Information is represented by linear strings of symbols with memory that carry errors as a result of their stochastic nature. Proofreading and edition are assumed to improve certainty although such processes may not be effective. Here, we develop a thermodynamic theory for material chains made up of nanoscopic subunits with symbolic meaning in the presence of memory. This framework is based on the characterization of single sequences of symbols constructed under a protocol and is used to derive the behavior of ensembles of sequences similarly constructed. We then analyze the role of proofreading and edition in the presence of memory finding conditions to make revision an effective process, namely, to decrease the entropy of the chain. Finally, we apply our formalism to DNA replication and RNA transcription finding that Watson and Crick hybridization energies with which nucleotides are branched to the template strand during the copying process are optimal to regulate the fidelity in proofreading. These results are important in applications of information theory to a variety of solid-state physical systems and other biomolecular processes.

Models for the evolution of GC content in asexual fungi Candida albicans and C. dubliniensis

Although guanine–cytosine (GC)-biased gene conversion (gBGC) following meiotic recombination seems the most probable mechanism accounting for large-scale variations in GC content for many eukaryotes, it cannot explain such variations for organisms belonging to ancient asexual lineages, such as the pathogenic fungi Candida albicans and C. dubliniensis. Analysis of the substitution patterns for these two species reveals a strong anticorrelation between the synonymous transition rates at third codon positions. I propose two models that can account for this observation. According to the first model, the evolution of GC content is driven by gBGC linked to mitotic recombination, either associated with parasexuality or with damage repair. Variations in the GC content thus reflect variations in the strength of gBGC, presumably variations in the mitotic recombination rate. According to the second model, the evolution of GC content is driven by misincorporation errors during the process of DNA replication in S phase. This model proposes that variations in GC content are due to variations in the proportions of dCTPs and dGTPs at the time when sequences are replicated. Experimental data regarding mitotic recombination rates or the variations of dCTPs and dGTPs during S phase are required to validate definitively one of the two models, but in any case, the fit of the models to the data suggests that C. albicans and C. dubliniensis constitute so far unique examples of GC content evolution driven either by mitotic recombination or replicative errors.

Three subsets of sequence complexity and their relevance to biopolymeric information

Genetic algorithms instruct sophisticated biological organization. Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC). FSC alone provides algorithmic instruction. Random and Ordered Sequence Complexities lie at opposite ends of the same bi-directional sequence complexity vector. Randomness in sequence space is defined by a lack of Kolmogorov algorithmic compressibility. A sequence is compressible because it contains redundant order and patterns. Law-like cause-and-effect determinism produces highly compressible order. Such forced ordering precludes both information retention and freedom of selection so critical to algorithmic programming and control. Functional Sequence Complexity requires this added programming dimension of uncoerced selection at successive decision nodes in the string. Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).

Mammalian DNA replication: mutation biases and the mutation rate

Experimental studies have shown that the fidelity of DNA replication can be affected by the concentrations of free deoxyribonucleotides present in the cell. Replication of mammalian chromosomes is achieved using pools of newly-synthesized deoxyribonucleotides which fluctuate during the cell cycle. Since regions of mammalian chromosomes are replicated sequentially, there is the potential for differences among mammalian loci in both the relative and absolute frequencies of the various transitional and transversional mutations which may occur. Where these mutations are effectively neutral, at silent sites in genes and in non-coding sequences, this may result in different rates of evolution and in different base compositions, as have been observed in data from mammalian genes. A simple model of the DNA replication process is developed to describe how the mutation rate could be affected by the G + C contents of the deoxyribonucleotide pools and of the replicating DNA. Mutation rates are predicted to vary from locus to locus; only in the particular case of identical G + C contents in the DNA locus and the deoxyribonucleotide pools, and no proofreading, will the mutation rate be uniform over all loci.

Compositional patterns in vertebrate genomes: conservation and change in evolution

The evolution of vertebrate genomes can be investigated by analyzing their regional compositional patterns, namely the compositional distributions of large DNA fragments (in the 30-100-kb size range), of coding sequences, and of their different codon positions. This approach has shown the existence of two evolutionary modes. In the conservative mode, compositional patterns are maintained over long times (many million years), in spite of the accumulation of enormous numbers of base substitutions. In the transitional, or shifting, mode, compositional patterns change into new ones over much shorter times. The conservation of compositional patterns, which has been investigated in mammalian genomes, appears to be due in part to some measure of compositional conservation in the base substitution process, and in part to negative selection acting at regional (isochore) levels in the genome and eliminating deviations from a narrow range of values, presumably corresponding to optimal functional properties. On the other hand, shifts of compositional patterns, such as those that occurred between cold-blooded and warm-blooded vertebrates, appear to be due essentially to both negative and positive selection again operating at the isochore level, largely under the influence of changes in environmental conditions, and possibly taking advantage of mutational biases in the replication/repair enzymes and/or in the enzyme make-up of nucleotide precursor pools. Other events (like translocations and changes in chromosomal structure) also play a role in the transitional mode of genome evolution. The present findings (1) indicate that isochores, which correspond to the DNA segments of individual or contiguous chromatin domains, represent selection units in the vertebrate genome; and (2) shed new light on the selectionist-neutralist controversy.

Mnemonic aspects of Escherichia coli DNA polymerase I. Interaction with one template influences the next interaction with another template

When Escherichia coli DNA polymerase I (Pol I) replicates a homopolymer, the excision/polymerization (exo/pol) ratio varies with enzyme and initiator concentration. The study of this effect in the case of poly(dA).oligo(dT) replication led us to propose a mnemonic model for Pol I, in which the 3' to 5' excision activity warms up when the enzyme is actively polymerizing, and cools down when it dissociates from the template. The model predicts that the exo/pol ratio must increase with processivity length and initiator concentration and decrease with enzyme concentration. It predicts also that contact of the enzyme with one template alters its excision efficiency towards another template. The exo/pol ratio and processivities of Pol I and its Klenow fragment were studied on four templates: poly(dA).(dT)10, poly(dT).(dA)10, poly(dC).(dG)10 and poly(dI).(dC)10. We show that the Klenow fragment is usually much less processive than Pol I and when this is the case it has a much lower exo/pol ratio. At equal processivity, the exo/pol ratios are nearly equal. Furthermore, many factors that influence processivity length (e.g. manganese versus magnesium, inorganic pyrophosphate, ionic strength) influence the exo/pol ratio in the same direction. The study of deaminated poly(dC) replication, where we followed incorporation and excision of both G and A residues, allowed us to assign the origin of the dNMP variations to changes in the 3' to 5' proof-reading activity of Pol I. Similarly, the lower dNMP turnover of the Klenow fragment observed with deaminated poly(dC) was specifically assigned to a decreased 3' to 5' exonuclease activity. The exo/pol ratio generally increased with initiator and decreased with enzyme concentration, in agreement with the model, except for poly(dI).oligo(dC), where it decreased with initiator concentration. However, by terminating chain elongation with dideoxy CTP, we showed directly that, even in this system, excision is relatively inefficient at the beginning of synthesis. Interaction of Pol I with poly(dA).(dT) or with poly(dC).(dG) modifies its exo/pol characteristics in the replication of poly(dI).(dC) and poly(dA).(dT), respectively. The Klenow enzyme is not sensitive to such influences and this correlates with its reduced processivity on the influencing templates. Our results reveal the existence of differences between Pol I and its Klenow fragment that are more profound than has been thought previously.(ABSTRACT TRUNCATED AT 400 WORDS)

Alteration of the DNA double helix conformation upon incorporation of mispairs as revealed by energy computations and pathways of point mutations

To explain biochemical and genetic data on spontaneous nucleotide replacements in nucleic acid biosynthesis all the 8 mispairs in normal tautomeric forms have been considered. Possible B-conformations of DNA fragments containing each of such mispairs incorporated between Watson-Crick pairs have been found using computations of the energy of non-bonded interactions via classical potential functions. These conformations have no reduced interatomic contacts. The values of each dihedral angle of the sugar-phosphate backbone fall within the limits of those of double-helical fragments of B-DNA in crystals. These values differ from those of the corresponding angles for the low-energy polynucleotide conformations consisting of canonical pairs by no more than 30 degrees (except for the fragment with the U:U pair for which the C4'-C3'-O-P angle differs by about 50 degrees). The difference in experimentally observed frequencies of various nucleotide replacements in DNA biosynthesis correlates with the difference in the energy of non-bonded interactions and with the extent of the sugar-phosphate backbone distortion for the fragments containing the mispairs which serve as intermediates for the replacements.

Coding strategy differences between constant and variable segments of immunoglobulin genes

Vertebrate immunoglobulin (Ig) mRNAs reveal intraspecies variation in codon usage distinct from that seen with yeast or bacterial genes. Comparison of all available Ig gene sequences shows that %(G + C) in codon position III is consistently lower in variable (V) segments than in constant (C) segments. I find an even lower %(G + C) in the hypervariable domains of V segments. This analysis suggests that base substitution in Ig genes correlates positively with local A + T content.

Enzymic editing mechanisms and the origin of biological information transfer

Current knowledge of enzymic editing mechanisms in DNA replication, transcription and translation can be used to predict error rates in the absence of editing. Primitive enzymes which possessed synthetic activity but not yet editing mechanisms would have had extremely high error rates resulting in heterogeneous proteins. Based on present knowledge of molecular biology and biochemistry, it is concluded that the evolution of contemporary information transfer systems from primitive systems lacking such editing mechanisms remains an unsolved problem in theoretical biology.

A memory effect in DNA replication

A study of the polymerization/excision ratio in the replication of poly(dA), primed with oligo(dT), was carried out with E. coli DNA polymerase I, at various primer and enzyme concentrations. The variations in this ratio suggest that 1) the DNA polymerase is able to switch between two states of low and high exonuclease activities and 2) after dissociating from the template, the DNA polymerase drifts towards the low exonuclease state. The recovery of the high exonuclease state would require several successive incorporations.

Selective inactivation of the 3' to 5' exonuclease activity of Escherichia coli DNA polymerase I by heat

Heat selectively inactivates the 3' to 5' exonuclease activity of E. coli DNA polymerase I, resulting in reduced dNTP turnover and lower fidelity of replication of homopolymer and natural DNA templates.

Free energy cost and accuracy in branched selection processes of biosynthesis

Selection in biochemical synthesis processes is a very important task: processes as protein or nucleic acid synthesis must be very accurate although the cell abounds with closely related molecules which, intuitively, should be difficult to distinguish. The mechanisms of selection and the underlying processes have been extensively studied in the last years, and the ideas have been developed into mathematical models to visualize the potentials of recognition and error correction. There are several aspects on this, the main aspect of the present work being the important fact that the cell must pay for the increased accuracy in terms of available free energy: processes are driven from equilibrium, and do away with appreciable dissipation.

Contribution of 3' leads to 5' exonuclease activity of DNA polymerase III holoenzyme from Escherichia coli to specificity

The effects of deoxynucleoside monophosphates on the 3' leads to 5' exonuclease activity of DNA polymerase III holoenzyme have been correlated with their effects on the fidelity of DNA replication. In particular, dGMP inhibits the proofreading activity of the enzyme and decreases the fidelity in those cases where a "following nucleotide effect" is also noted. This is strong evidence for proofreading. However, the absence of the effects of proofreading inhibitors or following nucleotides need not be evidence against the occurrence of proofreading: a theoretical analysis shows that these effects may not be observed even though there is active proofreading. This is suggested to be the case with the phage T4 enzyme system. The proofreading activity of Pol III appears to be directed primarily towards removing purine x pyrimidine-mediated rather than purine x purine-mediated misincorporations. recA protein inhibits the proofreading activity of Pol III on synthetic templates containing mismatched 3' termini. This is paralleled by a decrease in the fidelity of DNA replication in vitro. The inhibition is increased in the presence of dGMP or dAMP but there is no further increase in the infidelity of replication. The presence of both dNMPs and recA protein does not enable Pol III to copy past pyrimidine photodimers.

Polymerization/excision kinetics of Escherichia coli DNA polymerase I. Stability in kinetic behaviour and variations of the rate constants with temperature and pH

1. The incorporation and excision kinetics of Escherichia coli DNA polymerase I in the replication of (dA)n with dUTP and (dI)n with dCTP was studied at various temperatures and pH. When the incorporation/excision ratio (dy/dx) is plotted against the concentration of deoxynucleoside triphosphate [S] two kinds of curves are obtained. With (dI)n, dy/dx increases with [S], then reaches an asymptotic value. This behaviour, consistent with a kinetic amplification or kinetic proofreading mechanism, is observed at all temperatures and pH. With (dA)n, dy/dx increases with [S] but in a convex, instead of a concave manner. In this case, we approximated the curves by straight lines at the origin, in conformity with the prediction of the frayed-unfrayed model. Again a single behaviour is consistently observed at all temperatures and pH. 2. The data were analyzed in terms of ratios or products of three kinetic constants: ki for incorporation, ke for excision and, in the (dI)n system, theta for the processing of the incoming dNTP. The dNMP production in the (dI)n system is dominated by the ke theta term which increases with temperature and pH. Temperature influences excision more than incorporation, the net result being a linear decrease of ki/ke with temperature. The effect is more pronounced with (dI)n than with (dA)n and is probably related to the stability of the template-primer complex. The ki/ke term shows a bell-shaped dependency with pH in the (dI)n system. With (dA)n it remains constant between pH 7.5 and 8.5 then decreases with a transition midpoint at pH 9.0. We suggest that the pH profiles may reflect the ionization of the template in the first case, and of the substrate in the second.

Inhibitor studies of phage T4 wild-type and mutant DNA polymerases. V. A. summary of kinetic and inhibitor data

The DNA polymerases of phage T4 wild-type, the mutator mutant L98 and the antimutator mutant CB121 were purified about 100-fold free of foreign enzyme activities interfering with the polymerase assay. The enzymes were characterized as to thermostability, exonuclease activity and kinetic data with DNA template primer, deoxythymidine 5' -triphosphate, and a mixture of all four deoxynucleoside 5' -triphosphates. The effects of eight inhibitors of DNA synthesis on the three enzymes were determined (Schroeder and Jantschak 1978 and 1980, Jantschak and Schroeder 1980) and are compared here. The most selective inhibitor, pyridoxal 5' -phosphate, interacts with the active site of the polymerases while the two least discriminating drugs, distamycin A and actinomycin D, do not directly interact with the polymerases at all. The study was intended to test whether specific enzyme inhibitors elicit a differential response in temperature-sensitive structural variants of this enzyme and whether, in principle, structural variants of virus enzymes or the respective ts- mutants in vivo are suitable as a screening system for selective antiviral agents.

Prediction of pairing schemes in RNA molecules-loop contributions and energy of wobble and non-wobble pairs

Previously published models for predicting pairing schemes in RNA molecules, when applied to tRNA, give the clover leaf structure in only half the cases. We made a systematic investigation of the predictability of the clover leaf structure under various assumptions concerning the energetic contributions of single and double-stranded regions. We tested 21 different models and variants on a set of 100 tRNA sequences and many other variants on a smaller set of sequences. In our models we allowed not only G.C, A.U and G.U pairing, but also every other pair. Under conditions which are much less restrictive than those of previous attempts, we can nevertheless reach 90 per cent predictability for the clover leaf structure of tRNA. A most surprising and far-reaching result is that we can assign to C.G and C.C pairs binding energies quite close to the energies of G.U pairs, and still predict the clover leaf. The following ranking for non-complementary pairs was obtained : G.U, G.G and C.C, U.U, C.A, A.A and G.A, U.C. The main practical innovation which made possible the improvements in predictability are: i) not counting the stacking of base pairs separated by a bulge loop; ii) making the terminal C.C's in stems more stable than the terminal A.U's by merely -- 0.7 kcal; iii) replacing the distinction between G.C and A.U-closed loops by a distinction based on the presence of loop-favoring residues; iv) carefully adjusting the energetic balance between the various kinds of loops; v) narrowing the gap between the GC/GC and the GC/AU contributions; vi) using observations on nearest-neighbours in tRNA sequences to refine the contributions of G.U pairs.

Mutagenic DNA repair: insertion of nucleotides opposite non-coding template structures by a reversed 3'-5' exonuclease reaction? A hypothesis

1. The enzymatic mechanism of mutagenic DNA repair is unknown. None of the characterized DNA polymerases is capable of polymerization past non-coding template structures. 2. A hypothesis is proposed according to which polymerization opposite non-coding template structures is catalyzed by the DNA-polymerase-associated 3'-5' exonuclease under conditions which shift the equilibrium of the 3'-5' exonuclease reaction DNAn + H2O in equilibrium DNAn-1 + dNMP to the left, i.e. to the incorporation of deoxynucleoside monophosphates. 3. Conditions which favor the incorporation of dNMP by the reversed 3'-5' exonuclease reaction include a high dNMP concentration, a coupled H2O-consuming reaction and a hydrophobic enzyme environment. 4. The statements of the hypothesis are supported by published work on the biochemistry of DNA polymerases and their associated 3'-5' exonucleases, the genetics of mutagenic DNA repair and the involvement of Escherichia coli DNA polymerase III in this process. 5. The hypothesis offers an explanation of the mutator and antimutator properties of certain genes, in particular of DNA polymerase genes, and also explains how some drugs act mutagenically during DNA replication and antimutagenically against mutagenic DNA repair.