Saturation mutagenesis of a DNA region of bend. Base steps other than ApA influence the bend

Intrinsic curvature in the VP1 gene of SV40: comparison of solution and gel results

DNA restriction fragments that are stably curved are usually identified by polyacrylamide gel electrophoresis because curved fragments migrate more slowly than normal fragments containing the same number of basepairs. In free solution, curved DNA molecules can be identified by transient electric birefringence (TEB) because they exhibit rotational relaxation times that are faster than those of normal fragments of the same size. In this article, the results observed in free solution and in polyacrylamide gels are compared for a highly curved 199-basepair (bp) restriction fragment taken from the VP1 gene in Simian Virus 40 (SV40) and various sequence mutants and insertion derivatives. The TEB method of overlapping fragments was used to show that the 199-bp fragment has an apparent bend angle of 46 +/- 2 degrees centered at sequence position 1922 +/- 2 bp. Four unphased A- and T-tracts and a mixed A3T4-tract occur within a span of approximately 60 bp surrounding the apparent bend center; for brevity, this 60-bp sequence element is called a curvature module. Modifying any of the A- or T-tracts in the curvature module by site-directed mutagenesis decreases the curvature of the fragment; replacing all five A- and T-tracts by random-sequence DNA causes the 199-bp mutant to adopt a normal conformation, with normal electrophoretic mobilities and birefringence relaxation times. Hence, stable curvature in this region of the VP1 gene is due to the five unphased A- and T- tracts surrounding the apparent bend center. Discordant solution and gel results are observed when long inverted repeats are inserted within the curvature module. These insertion derivatives migrate anomalously slowly in polyacrylamide gels but have normal, highly flexible conformations in free solution. Discordant solution and gel results are not observed if the insert does not contain a long inverted repeat or if the long inverted repeat is added to the 199-bp fragment outside the curvature module. The results suggest that long inverted repeats can form hairpins or cruciforms when they are located within a region of the helix backbone that is intrinsically curved, leading to large mobility anomalies in polyacrylamide gels. Hairpin/cruciform formation is not observed in free solution, presumably because of rapid conformational exchange. Hence, DNA restriction fragments that migrate anomalously slowly in polyacrylamide gels are not necessarily stably curved in free solution.

A possible role of DNA superstructures in genome evolution

The concept of DNA as a simple repository of the gene information has changed in that of a polymorphic macromolecule, which plays a relevant part in the management of the complex biochemical transformations in living matter. As a consequence of the slight stereochemical differences between base pairs, the direction of the DNA double helix axis undergoes deterministic writhing. A useful representation of such sequence-dependent structural distortions is the curvature diagram. Here, it is reported as an evolution simulation obtained by extensive point mutations along a biologically important DNA tract. The curvature changes, consequence of the point mutations. were compared to the related experimental gel electrophoresis mobility. The curvature of most mutants decreases and the mobility increases accordingly, suggesting the curvature of that tract is genetically selected. Moreover, DNA images by scanning force microscopy, show evidence of a sequence-dependent adhesion of curved DNA tracts to inorganic crystal surfaces. In particular, mica shows a large affinity towards the TT-rich dinucleotide sequences. This suggests a possible mechanism of selection of curved DNA regions, characterized by AA.TT dinucleotides in phase with double-helical periodicity, in the very early evolution steps.

From the sequence to the superstructural properties of DNAs

A theoretical model for predicting intrinsic and induced DNA superstructures as well as their thermodynamic properties is presented. Intrinsic sequence-dependent superstructures are evaluated by integrating local deviations from the canonical B-DNA of the different dinucleotide steps. Induced superstructures are obtained by adopting the principle of minimum deformation free energy, evaluated in the Fourier space, in the framework of first-order elasticity. Finally dinucleotide stacking energies and melting temperatures are considered to account for local flexibility. In fact the two scales are strongly correlated. The model works very satisfactorily in predicting the sequence-dependent effects on the DNA experimental behavior, such as the gel electrophoresis retardation, the writhe transitions in topologically constrained domains, the thermodynamic constants of circularization reactions as well as the nucleosome thermodynamic stability constants.

Sequence determinants of the intrinsic bend in the cyclic AMP response element

The cyclic AMP response element (CRE site, ATGACGTCAT) is the DNA target for transcription factors whose activities are regulated by cyclic AMP (1). Recently, we discovered that the CRE site is bent by 10-13 degrees toward the major groove (2). Little or no bend is detected in the related AP-1 site (ATGACTCAT), which differs from the CRE site by loss of a single, central, C.G base pair (2, 3). Here we describe experiments designed to identify which base pairs within the CRE site induce the bent structure in an attempt to understand the origins of the dramatically different conformations of the CRE and AP-1 sites. Our data indicate that the intrinsic CRE bend results from distortion within the TGA sequence found in each CRE half site (ATGAC). These two TGA sequences are located in phase with one another in the CRE sequence but are not (completely) in phase in the AP-1 sequence. This difference in phasing leads to the overall difference in bend as detected by gel (2) and cyclization methods (S. C. Hockings, J. D. Kahn, and D. M. Crothers, unpublished results; M. A. Fabian and A. Schepartz, unpublished results). Our results confirm earlier predictions of altered structure within TG steps, provide insight into the structural reorganizations induced in DNA by bZIP proteins, and lead to a revision of the relationship between the structures of the free and bZIP-bound forms of the CRE and AP-1 sites.

DNA mobility anomalies are determined primarily by polyacrylamide gel concentration, not gel pore size

The dependence of DNA mobility anomalies on gel pore size has been studied in polyacrylamide gels with a wide variety of compositions, using molecular weight ladders containing multiple copies of normal (12B) and anomalously slowly migrating (12A) 147-base pair restriction fragments from plasmid pBR322 as the migrating probe molecules. If the gel pore size is increased by decreasing the total acrylamide concentration (%T) at constant cross-linker ratio (%C), the usual method of increasing gel pore size, the mobility anomalies decrease with increasing gel pore radius as though the 12A multimers were retarded by a sieving mechanism. However, the decrease in the mobility anomalies is independent of whether the apparent gel pore radius is larger or smaller than the DNA radius of gyration, suggesting that gel pore size is not the controlling variable. If the acrylamide concentration is held constant and the gel pore size is increased by decreasing %C at constant %T, the mobility anomalies of the largest 12A multimers (6 mers and higher) decrease with increasing gel pore radius, because of sieving effects, until the effective gel pore radius becomes approximately equal to the DNA radius of gyration, after which the mobility anomalies level off and become independent of gel pore size. The mobility anomalies exhibited by 5-mers and smaller multimers of fragment 12A are independent of gel pore radius in all gels with constant %T. Similar results are observed with a molecular weight ladder containing phased A-tracts from the kinetoplast bending locus. Since the anomalous electrophoretic mobilities depend primarily on the total acrylamide concentration in the gel, and not on the apparent gel pore radius, increases in the magnitude of the mobility anomalies with increasing gel concentration (and decreasing gel pore radius) cannot be taken as evidence for DNA curvature.

Influence of dynamic fluctuations on DNA curvature

The effect of dynamic fluctuations on physical manifestations of DNA curvature such as electrophoretic retardation, circularization of DNA tracts and nucleosomes positioning is examined. It is shown that in all cases the main features of the processes can be satisfactorily explained by a static curvature model, which appears to be a good representation of time and ensemble averaged superstructures of DNA chains. The dynamic fluctuations around the average curvature appear to influence only the kinetics of these processes. In the case of polyacrylamide gel electrophoretic retardation it is demonstrated that the approximation of the static model holds on the assumption that dynamic fluctuations are independent from intrinsic curvature. The actual validity of the static model we proposed several years ago is satisfactorily demonstrated by the explanation and prediction of different experiments, such as cyclic permutation gel electrophoresis, differential DNAase I cleavage of cyclic versus linear DNA tracts and nucleosome positioning.

Differential binding of RNA polymerase to the wild type Mu mom promoter and its C independent mutant: a theoretical analysis

Using the theoretical model for DNA bending we have analyzed the Mu mom promoter wild type and its mutant tin7 which showed differential binding to the RNA polymerase. We have demonstrated here the structural change as a result of the point mutation which may be responsible for the altered binding of RNA polymerase. Analysis using both sets of parameters essentially gives the same result.

On the consensus structure within the E. coli promoters

Using the theoretical model of DNA curvature, we have studied about 112 different E. coli promoters with a view to obtain some common super structures associated with them. Out of the 112 promoters analyzed by theoretical gel electrophoresis permutation about 66 of them have their minima lying between the -10 and the -35 region. The analysis of the bases at the minima reveals strong structural similarities. The differences can account for the varying strengths of the promoters as well as for different degree with which the RNA polymerase binds to these regions. The effects of mutation in each of these 112 promoters and their changes in curvature dispersion have also been evaluated.

A simple physical model for the gel electrophoretic manifestations of sequence-dependent DNA superstructures

A simple physical model of the gel electrophoretic manifestations of sequence-dependent DNA superstructures is illustrated. The model is based on the calculation of the curvature dispersion as evaluated by integrating the orientational parameters of the base pairs along the chain. Such a quantity is proportional to the straightening activation energy of the curved DNA in the direction of the average orientation of the helical axis and was found to be proportional to the logarithm of the gel electrophoretic retardation. The model is capable of consistently explaining the different electrophoretic manifestations of DNA superstructures, such as the retardation of a large ensemble of multimeric oligonucleotides with different sequences, periodicities, and lengths, and the permutation gel assays as well as the mobility changes consequent to extensive point mutations in a DNA tract.

A structural analysis of the bent kinetoplast DNA from Crithidia fasciculata by high resolution chemical probing

The chemical probes potassium permanganate (KMnO4) and diethylpyrocarbonate (DEPC) have been used to study the conformation of bent kinetoplast DNA from Crithidia fasciculata at different temperatures. Chemical reactivity data shows that the numerous short A-tracts of this bent DNA adopt a similar structure at 43 degrees C. This conformation appears to be very similar to the conformation of A-tracts in DNA exhibiting normal gel mobility. The A-tract structure detected by chemical probing is characterized by a high degree of base stacking on the thymine strand, and by an abrupt conformational change at the 3' end of the adenine strand. In general, no major alteration of this A-tract specific structure was detected between 4-53 degrees C. However, probing with KMnO4 revealed two unusual features of the C. fasciculata sequence that may contribute to the highly aberrant gel mobility of this DNA: 1) the B DNA/A-tract junction 5' dC/A3-6 3'. 5' dT3-6/G 3' is disproportionately represented and is conformationally distinct from other 5' end junctions, and 2) low temperature favors a novel strand-specific conformational distortion over a 20 base pair region of the bent kinetoplast DNA. Presence of the minor groove binding drug distamycin had little detectable effect on the A-tract conformation. However, distamycin did inhibit formation of the novel KMnO4 sensitive low temperature structure and partially eliminated the anomalous gel mobility of the kinetoplast DNA. Finally, we describe a simple and reproducible procedure for the production of an adenine-specific chemical DNA sequence ladder.

In vitro evolution of intrinsically bent DNA

DNA fragments which are intrinsically bent or curved migrate anomalously during electrophoresis through polyacrylamide gels. Starting with an initial population of approximately 10(12) unique DNA sequences, DNA which exhibited the kind of anomalous mobility associated with DNA bending was selected and enriched using a variation of the SELEX procedure. After seven rounds of selection and amplification, the vast majority of the remaining population of DNA fragments migrated as bent DNA. Cloning and sequencing of 30 individual sequences from this population has yielded information regarding the relationship between DNA sequence and bending. Some of the previous conclusions on DNA bending have been confirmed while others have been modified, by the results presented here. In addition, the dinucleotide base step CA/TG, which had not been thought to be a major factor in DNA bending, appears to be important.

Theoretical prediction of the gel electrophoretic retardation changes due to point mutations in a tract of SV40 DNA

The changes of gel electrophoretic retardation due to single base substitutions in a 173 bp fragment of Sv40 DNA were predicted by using a theoretical model based on conformational energy calculations. As described in previous papers, this model allows successful prediction of the gel electrophoretic retardation of synthetic as well as natural DNAs reported in literature. The experimental retardations related to 195 point-mutated DNAs were reproduced with a standard deviation of 0.05 comparable with the experimental one of 0.04. This result, which represents a very critical test for the proposed model, indicates that DNA superstructures can be satisfactorily predicted on the simple physical basis of the integration of the nearest-neighbour perturbations in the dinucleotide steps. Thus, cooperative effects appear, in the majority of cases investigated, to play a second order role.

Curved DNA without AA/TT dinucleotide step

The evidence is accumulating that dinucleotide steps other than AA/TT affect DNA flexure of AnTm (m + n greater than = 4) containing fragments. However, it is not clear whether macroscopic DNA flexure without AA/TT steps might occur. In this paper we demonstrate the anomaly in electrophoretic mobility of non AA/TT repetitive DNA sequences which is a function of sequence phasing. Therefore, our results show that PyPu (TA) and AG/CT steps, angulary separated by close to 180 degrees from Pu/Py (GC) and GG/CC steps, bend DNA, even in the absence of AnTm tracts.

The curvature vector in nucleosomal DNAs and theoretical prediction of nucleosome positioning

Using our model for predicting DNA superstructures from the sequence, the average distribution of the phases of curvature along the sequences of the set of the 177 nucleosomal DNAs investigated by Satchwell et al. (J. Mol. Biol. 191 (1986) 659) was calculated. The diagram obtained shows very significant features which allow the visualization of the intrinsic nucleosomal superstructure characterized by two quasi-parallel tracts of a flat left-handed superhelical turn connected by a left-handed inflection in a perpendicular direction; such a superstructure appears to be closely related to the nucleosome model of Travers and Klug (Phil. Trans. R. Soc. Lond. 317 (1987) 537). The nucleosomal curvature phase diagram was then adopted as a sensitive determinant for the nucleosome virtual positioning in DNAs via correlation function, obtaining a good agreement with the experimental mapping of SV40 regulatory region as recently investigated by Ambrose et al. (J. Mol. Biol. 209 (1989) 255). This analysis shows also the presence of a constant phase relation between the virtual nucleosome positions which suggests its possible implication in the nucleosome condensation in chromatin.