Studies of DNA bending and flexibility using gel electrophoresis

Single-Molecule Methods for Investigating the Double-Stranded DNA Bendability

The various DNA-protein interactions associated with the expression of genetic information involve double-stranded DNA (dsDNA) bending. Due to the importance of the formation of the dsDNA bending structure, dsDNA bending properties have long been investigated in the biophysics field. Conventionally, DNA bendability is characterized by innate averaging data from bulk experiments. The advent of single-molecule methods, such as atomic force microscopy, optical and magnetic tweezers, tethered particle motion, and single-molecule fluorescence resonance energy transfer measurement, has provided valuable tools to investigate not only the static structures but also the dynamic properties of bent dsDNA. Here, we reviewed the single-molecule methods that have been used for investigating dsDNA bendability and new findings related to dsDNA bending. Single-molecule approaches are promising tools for revealing the unknown properties of dsDNA related to its bending, particularly in cells.

OUP accepted manuscript

DNA mechanical properties play a critical role in every aspect of DNA-dependent biological processes. Recently a high throughput assay named loop-seq has been developed to quantify the intrinsic bendability of a massive number of DNA fragments simultaneously. Using the loop-seq data, we develop a software tool, DNAcycP, based on a deep-learning approach for intrinsic DNA cyclizability prediction. We demonstrate DNAcycP predicts intrinsic DNA cyclizability with high fidelity compared to the experimental data. Using an independent dataset from in vitro selection for enrichment of loopable sequences, we further verified the predicted cyclizability score, termed C-score, can well distinguish DNA fragments with different loopability. We applied DNAcycP to multiple species and compared the C-scores with available high-resolution chemical nucleosome maps. Our analyses showed that both yeast and mouse genomes share a conserved feature of high DNA bendability spanning nucleosome dyads. Additionally, we extended our analysis to transcription factor binding sites and surprisingly found that the cyclizability is substantially elevated at CTCF binding sites in the mouse genome. We further demonstrate this distinct mechanical property is conserved across mammalian species and is inherent to CTCF binding DNA motif.

Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology

The mechanical properties of DNA have enabled it to be a structural and sensory element in many nanotechnology applications. While specific base-pairing interactions and secondary structure formation have been the most widely utilized mechanism in designing DNA nanodevices and biosensors, the intrinsic mechanical rigidity and flexibility are often overlooked. In this article, we will discuss the biochemical and biophysical origin of double-stranded DNA rigidity and how environmental and intrinsic factors such as salt, temperature, sequence, and small molecules influence it. We will then take a critical look at three areas of applications of DNA bending rigidity. First, we will discuss how DNA's bending rigidity has been utilized to create molecular springs that regulate the activities of biomolecules and cellular processes. Second, we will discuss how the nanomechanical response induced by DNA rigidity has been used to create conformational changes as sensors for molecular force, pH, metal ions, small molecules, and protein interactions. Lastly, we will discuss how DNA's rigidity enabled its application in creating DNA-based nanostructures from DNA origami to nanomachines.

Nuclear magnetic resonance analysis of protein-DNA interactions

Recent methodological and instrumental advances in solution-state nuclear magnetic resonance have opened up the way to investigating challenging problems in structural biology such as large macromolecular complexes. This review focuses on the experimental strategies currently employed to solve structures of protein-DNA complexes and to analyse their dynamics. It highlights how these approaches can help in understanding detailed molecular mechanisms of target recognition.

Determining protein-induced DNA bending in force-extension experiments: theoretical analysis

Computer simulations were used to investigate the possibility of determining protein-induced DNA bend angles by measuring the extension of a single DNA molecule. Analysis of the equilibrium sets of DNA conformations showed that shortening of DNA extension by a single protein-induced DNA bend can be as large as 35 nm. The shortening has a maximum value at the extending force of approximately 0.1 pN. At this force, the DNA extension experiences very large fluctuations that dramatically complicate the measurement. Using Brownian dynamics simulation of a DNA molecule extended by force, we were able to estimate the observation time needed to obtain the desired accuracy of the extension measurement. Also, the simulation revealed large fluctuations of the force, acting on the attached magnetic bead from the stretched DNA molecule.

Unique Physical Signature of DNA Curvature and Its Implications for Structure and Dynamics

A particularly sensitive birefringence technique is used to analyze a curved DNA fragment with 118 bp and a standard DNA with 119 bp. At salt concentrations from 0.5 to 10 mM, both fragments show the usual negative stationary birefringence and monotonic transients - differences are relatively small. At 100 mM salt the curved DNA shows a positive stationary birefringence and non-monotonic transients with processes having amplitudes of opposite sign, whereas signals of the standard DNA remain as usual. Transients induced by reversal of the field vector indicate the existence of a permanent dipole for the curved DNA. 2-MHz-ac pulses induce a negative stationary birefringence in both DNAs. These results are consistent with calculations on models for curved DNA predicting a quasi-permanent dipole and a positive dichroism/birefringence. The quasi-permanent dipole results from the loss of symmetry in the charge distribution of the curved polyelectrolyte. The appearance of the unique signature of curvature at high salt is mainly due to a strong decrease of the polarizability by about 2 orders of magnitude. The special mode of orientation resulting from the quasi-permanent dipole is expected to contribute to the gel migration anomaly. The time constants of birefringence decay for the curved fragment are shorter than those of the 119 bp fragment by a factor of approximately 1.10 at 0.6 mM salt, whereas this factor is approximately 1.20 at 100 mM Na+. If both fragments were normal DNA with 3.4 A rise per base pair, the factor would be approximately 1.02. At high salt and high electric field strengths the factor increases up to 1.37. The implications for the bending dynamics and the potential to distinguish static from dynamic persistence by field reversal experiments are discussed. The dependence of the curvature on the salt concentration indicated by the time constants is consistent with a clear decrease of the electrophoretic anomaly at decreasing salt concentration.

IS911 transpososome assembly as analysed by tethered particle motion

Initiation of transposition requires formation of a synaptic complex between both transposon ends and the transposase (Tpase), the enzyme which catalyses DNA cleavage and strand transfer and which ensures transposon mobility. We have used a single-molecule approach, tethered particle motion (TPM), to observe binding of a Tpase derivative, OrfAB[149], amputated for its C-terminal catalytic domain, to DNA molecules carrying one or two IS911 ends. Binding of OrfAB[149] to a single IS911 end provoked a small shortening of the DNA. This is consistent with a DNA bend introduced by protein binding to a single end. This was confirmed using a classic gel retardation assay with circularly permuted DNA substrates. When two ends were present on the tethered DNA in their natural, inverted, configuration, Tpase not only provoked the short reduction in length but also generated species with greatly reduce effective length consistent with DNA looping between the ends. Once formed, this 'looped' species was very stable. Kinetic analysis in real-time suggested that passage from the bound unlooped to the looped state could involve another species of intermediate length in which both transposon ends are bound. DNA carrying directly repeated ends also gave rise to the looped species but the level of the intermediate species was significantly enhanced. Its accumulation could reflect a less favourable synapse formation from this configuration than for the inverted ends. This is compatible with a model in which Tpase binds separately to and bends each end (the intermediate species) and protein-protein interactions then lead to synapsis (the looped species).

Effect of organic cosolvents on the free solution mobility of curved and normal DNA molecules

The free solution mobilities of curved and normal 199-bp DNA fragments have been measured in buffer solutions containing various quantities of the organic cosolvents methanol, ethanol, 2-propanol, 2-methyl-2,4-pentanediol (MPD), ethylene glycol, and ACN, using CE. The curved fragment, taken from the VP1 gene of SV40, contains five unevenly spaced A- and T-tracts in a centrally located "curvature module"; the A- and T-tracts have been mutated to other sequences in the normal 199-bp fragment. The free solution mobility of the curved 199-bp fragment is significantly lower than that of its normal counterpart in aqueous solutions [Stellwagen, E., Lu, Y. J., Stellwagen, N. C., Nucleic Acids Res. 2005, 33, 4425-4432]. The mobilities of both the curved and normal fragments decrease with increasing cosolvent concentration, due to the effect of the cosolvent on the viscosity and dielectric constant of the solution. The mobility differences between the curved and normal 199-bp fragments and the mobility ratios decrease approximately linearly with the increasing mole fraction of cosolvent in the solution. Hence, MPD and other organic cosolvents affect DNA electrophoretic mobility by a common mechanism, most likely the preferential hydration of the DNA surface that occurs in aqueous cosolvents. The gradual loss of the anomalously slow mobility of the curved 199-bp fragment with increasing cosolvent concentration, combined with other data in the literature, suggests that preferential hydration gradually widens the narrow A-tract minor groove, releasing site-bound counterions in the minor groove and shifting the conformation toward that of normal DNA.

Topological measurement of an A-tract bend angle: effect of magnesium

Sequences of four to six adenine residues, termed A-tracts, have been shown to produce curvature in the DNA double helix. A-tracts have been used extensively as reference standards to quantify bending induced by other sequences as well as by DNA binding proteins when they bind to their sites. However, the ability of an A-tract to serve as such a standard is hampered by the wide variation of values reported for the amount of bend conferred by an A-tract. One experimental condition that differs in these studies is the presence of divalent cation. To evaluate this effect, a new application of a topological method, termed rotational variant analysis, is used here to measure for the first time the effect of the presence of magnesium ion on the bend angle conferred by an A-tract. This method, which has the unique ability to measure a bend angle in the presence or absence of magnesium ion, demonstrates that magnesium ion markedly increases the bend angle. For example, when measured in a commonly used gel electrophoretic buffer, the bend angle conferred by a tract of six adenine residues increases from about 7 degrees in the absence of magnesium ion to 19 degrees in the presence of 3.9 mM magnesium ion. This quantitative demonstration of substantial magnesium ion dependence has several important implications. First, it explains discrepancies among bend values reported in various previous studies, particularly those employing gel electrophoretic versus other solution methods. In addition, these findings necessitate substantial revisions of the conclusions in a large number of studies that have used A-tract DNA as the bend angle reference standard in comparison measurements. Finally, any such future studies employing this comparison methodology will need to use the same sequence analyzed in the original measurements as well as replicate the original measurement conditions (e.g. ionic composition and temperature).

Analysis of DNA bending by transient electric birefringence

Transient electric birefringence has been used to analyze DNA bending in six restriction fragments containing 171, 174, 207, 263, 289, and 471 bp in three different low ionic strength buffers. The target fragments contain sequences corresponding to the apparent bend centers in pUC19 and Litmus 28, previously identified by the circular permutation assay (Strutz, K.; Stellwagen, N. C. Electrophoresis 1996, 17, 989-995). The target fragments migrate anomalously slowly in polyacrylamide gels and exhibit birefringence relaxation times that are shorter than those of restriction fragments of the same size, taken from nonbent regions of the same plasmids. Apparent bend angles ranging from 30 degrees to 41 degrees were calculated for the target fragments by tau-ratio method. The bend angles of four of the target fragments were independent of temperature from 4 degrees C to 20 degrees C, but decreased when the temperature was increased to 37 degrees C. The bend angles of the other two target fragments were independent of temperature over the entire range examined, 4 degrees -37 degrees C. Hence, the thermal stability of sequence-dependent bends in random-sequence DNA is variable. The bend angles of five of the six target fragments were independent of the presence or absence of Mg2+ ions in the solution, indicating most of the target fragments were stably bent or curved, rather than anisometrically flexible. Restriction fragments containing 219 and 224 bp, with sequences somewhat offset from the sequence of the 207 bp fragment, were also studied. Comparison of the tau-ratios of these overlapping fragments allowed both the bend angle and bend position to be independently determined. These methods should be useful for analyzing sequence-dependent bending in other random-sequence DNAs.

Analysis of the intrinsic bend in the M13 origin of replication by atomic force microscopy

Atomic force microscopy (AFM) has been used to image a 471-bp bent DNA restriction fragment derived from the M13 origin of replication in plasmid LITMUS 28, and a 476-bp normal, unbent fragment from plasmid pUC19. The most probable angle of curvature of the 471-bp DNA fragment is 40-50 degrees, in reasonably good agreement with the bend angle determined by transient electric birefringence, 38 degrees +/- 7 degrees. The normal 476-bp DNA fragment exhibited a Gaussian distribution of bend angles centered at 0 degrees, indicating that this fragment does not contain an intrinsic bend. The persistence length, P, was estimated to be 60 +/- 8 and 62 +/- 8 nm for the 471- and 476-bp fragments, respectively, from the observed mean-square end-to-end distances in the AFM images. Since the P-values of the normal and bent fragments are close to each other, the overall flexibility of DNA fragments of this size is only marginally affected by the presence of a stable bend. The close agreement of AFM and transient electric birefringence results validates the suitability of both methods for characterizing DNA bending and flexibility.

Reflections on apparent DNA bending by charge variants of bZIP proteins

Basic-leucine zipper (bZIP) proteins have been studied intensely as transcription factors. It has been proposed that the bZIP domain might modulate transcription activation through the induction of conformational changes in the DNA binding site. We have been interested in using bZIP peptides as convenient models with which to study the role of asymmetric phosphate neutralization in DNA bending. DNA bending experiments have yielded discordant results for bZIP peptides studied by electrophoretic- vs solution-based assays. We review the history of DNA bending assays involving bZIP peptides and introduce the reader to examples of discordant results. Our recent published experiments designed to clarify this field of study will then be reviewed. The engineering of protein fusions has established that electrophoretic phasing assays are relatively insensitive to precise protein structure/conformation and instead appear to report DNA bending, as influenced by protein charge. New applications of time-resolved fluorescence resonance energy transfer (FRET) have allowed for the first time corroboration of electrophoretic phasing assays with solution-based FRET measurements. We report that two conventional DNA bending assays that rely on DNA ligation cannot be applied to analysis of the bZIP peptides we studied due to ligation inhibition.

Topological measurement of an A-tract bend angle: comparison of the bent and straightened states

It is well established that an A-tract imparts curvature to the DNA double helix. Constructs of such A-tracts have been used as bend standards in a large number of both structural and functional studies, and A-tracts can confer significant activation in transcription. An accurate value for the bend angle induced by an A-tract is centrally important to all such studies, but the estimates reported for the bend angle of an A-tract differ by greater than threefold. To address this problem, we have used the rotational variant method to measure the angle of DNA curvature conferred by a tract of six adenine bases (A6 tract). The original version of the method measured a protein-induced bend angle independent of external standards. It compared the effect of bent and straight forms of the sequence on the topology of a DNA plasmid in which the sequence is cloned as a series of tandem repeats. To adapt the approach to the measurement of an intrinsic bend, high temperature was used to generate the straightened reference state, with the required topological relaxation being performed by a hyperthermophile topoisomerase. Appropriate plasmids containing tandem repeats of A-tracts were constructed and topologically analyzed in this manner. The bend value measured at 4 degrees C was 26(+/-2), and decreased linearly to 17(+/-2) at 37 degrees C. The relationship to other estimates and the application of these values are discussed.

Atomic force microscopy reveals kinks in the p53 response element DNA

p53 is a 53 kDa nuclear phosphoprotein. Its function as a tumor suppressor critically lies in its ability to recognize its target DNA response elements as a tetramer. Here, we report the structural theme intrinsic to the response element DNA that governs this recognition phenomenon. The intrinsic flexibility or dynamic bending between two distinctly different, but naturally occurring p53 response elements has been compared by ring closure. Results show that DNA binding sites containing helically phased d(CATG.CATG) tetra-nucleotide sequences at the centers of quasi-dyad symmetry in each half-response site are more intrinsically flexible (i.e. preferentially bent under axial stress) than their d(CTTG.CTTG) counterparts. Intriguingly, p53 binding sites containing these more flexible d(CATG.CATG) sequence elements also exhibit a stronger tendency for tetrameric binding of the p53 DNA binding domain peptide. Examination of the shapes of DNA microcircles obtained by circularization of oligomers constructed from such flexible p53 target DNA sequences in tandem using MacMode atomic force microscopy directly revealed sequence-specific kinks in solution. The tetra-nucleotide sequence d(CATG.CATG) is highly conserved in most functional p53 response elements. Consequently, we propose that the sequence-specific kinks originating from d(CATG.CATG) sequences could be a common structural theme in p53 response elements and as evident from the results reported here, could be a determinant of binding site recognition by the p53 protein and the subsequent stability of the p53-DNA complex.

The use of gel and capillary electrophoresis to investigate some of the fundamental physical properties of DNA

Electrophoresis is a powerful technique which can be used not only for the size-based separation of DNA in slab gels and sieving liquid polymers, but also for the analysis of sequence-dependent variations in DNA conformation and structure. Polyacrylamide gels are useful for conformational analysis, because bent or curved DNA molecules migrate anomalously slowly in this gel medium. Bending is often (but not always) associated with runs of adenine residues (A-tracts) that occur in phase with the helix repeat. The unique structure responsible for DNA bending "melts out" at a temperature considerably below that of strand separation. The circular permutation assay is another polyacrylamide gel-based method of detecting bending. It has usually been applied to small restriction fragments, but can also be used to detect bending in plasmid-sized DNA molecules. The apparent bends in plasmid DNAs tend to be located near biologically important regions of the sequence, such as the origin of replication, the start site of transcription, and the promoters of certain genes. Finally, capillary electrophoresis in free solution (without sieving liquid polymers) can be used to determine the diffusion coefficients of small DNA molecules, detect DNA-buffer interactions, and analyze the sequence dependence of counterion binding. Counterions appear to be preferentially bound to DNA oligomers containing A-tracts, especially the A(n)T(n) sequence motif. Typical examples of these applications of gel and capillary electrophoresis to the study of DNA conformation and structure are described.

Conformation and rigidity of DNA microcircles containing waf1 response element for p53 regulatory protein

The tumor-suppressor activity of p53 is closely related to its DNA-binding properties. It binds a number of DNA response-elements and it is likely that these share a common structural feature. Here, we present a new, general method to determine the absolute twist of flexible DNA promoter sequences based on direct imaging of the topology of microcircles containing the sequences. We have used magnetically driven dynamic force microscopy ("MacMode" AFM) to observe, in solution, the conformation of 168 base-pair DNA microcircles, each containing four equally spaced copies of the waf1/cip1/p21 p53 response-element. Analysis of the images showed that the microcircles are markedly puckered with a small excess of negatively writhed molecules. The average measured values of writhe are 0.109+/-0.013 (for 60 positively writhed molecules) and -0.098+/-0.011 (for 65 negatively writhed molecules). These values lead directly to a difference in linking number for the positively and negatively writhed molecules prior to ligation, from which we derive a twist mismatch of 178 degrees (overtwist). This is 44.5 degrees for each 42-mer precursor containing a single waf1/cip1/p21 p53 response-element, in good agreement with the range of values deduced by indirect biochemical techniques. The two values of writhe may also be used to determine the ratio of the bending (B) to twisting (C) rigidity, yielding B/C=0.23. This is about one-third of the value for long, random-sequence DNA, suggesting that the waf1/cip1/p21 p53 response-element is extremely flexible, a result that is also consistent with indirect biochemical experiments. These results support the idea, proposed by us earlier, that torsional stress may play a role in the regulation of p53 binding through modulation of twist at the binding site.

Relating independent measures of DNA curvature: electrophoretic anomaly and cyclization efficiency

Electrophoretic methods are often used to measure DNA curvature and protein-induced DNA bending. Though convenient and widely-applied, quantitative analyses are generally limited to assays for which empirical calibration standards have been developed. Alternatively, solution-based cyclization of short DNA duplexes allows analysis of DNA curvature and bending from first principles, but a detailed understanding of this assay is still lacking. In this work, we demonstrate that calibration with an independent electrophoretic assay of DNA curvature permits interpretation of cyclization assay results in a quantitatively meaningful way. We systematically measure intrinsic DNA curvature in short duplexes using a well-established empirical ligation ladder assay. We then compare the results to those obtained from the analysis of the distribution of circular products obtained in simple enzymatic cyclization assays of the same duplexes when polymerized. A strong correlation between DNA curvature estimates from these two assays is obtained for DNA fragments between 150-300 bp in length. We discuss how this result might be used to improve quantitative analysis of protein-mediated bending events evaluated by cyclization methods. Our results suggest that measurements of DNA curvature obtained under similar conditions, in solution and in an acrylamide gel matrix, can be compared directly. The ability to correlate results of these simple assays may prove convenient in monitoring DNA curvature and flexibility.

Conformational isomers of curved DNA molecules can be observed by polyacrylamide gel electrophoresis

Dimers, trimers and higher multimers of two 147-base pair restriction fragments called 12 A and 12B, obtained from the MspI digest of plasmid pBR322, migrate as sharp bands in agarose and dilute polyacrylamide gels, indicating that they are homogeneous in molecular weight. However, the electrophoretic bands corresponding to multimers of the curved fragment 12A are split into sharp sub-bands in more concentrated polyacrylamide gels. The relative intensities and spacing of the sub-bands depend on the number of monomers in the multimer, the pH of the buffer, and the presence or absence of divalent cations in the solution. Since band splitting is not observed for the normal 12B multimers under any gel-running conditions, the sub-bands observed for multimers of the curved fragment 12A must be attributed to conformational isomers which are in slow exchange on the electrophoretic time scale. Band splitting is also observed for multimers of a curved DNA fragment containing the kinetoplast bending locus and for plasmid pUC19 linearized by digestion with certain restriction enzymes. Plasmid pUC19 contains two nearly equidistant regions of intrinsic curvature (Strutz, K., Stellwagen, N. C., Electrophoresis 1996, 17, 989-995). Hence, DNA molecules containing two or more regions of curvature exist as discrete subpopulations of conformational isomers which can be observed as separate bands migrating in polyacrylamide gels.

Dynamic bending rigidity of a 200-bp DNA in 4 mM ionic strength: a transient polarization grating study

DNA may exhibit three different kinds of bends: 1) permanent bends; 2) slowly relaxing bends due to fluctuations in a prevailing equilibrium between differently curved secondary conformations; and 3) rapidly relaxing dynamic bends within a single potential-of-mean-force basin. The dynamic bending rigidity (kappa(d)), or equivalently the dynamic persistence length, P(d) = kappa(d)/k(B)T, governs the rapidly relaxing bends, which are responsible for the flexural dynamics of DNA on a short time scale, t < or = 10(-5) s. However, all three kinds of bends contribute to the total equilibrium persistence length, P(tot), according to 1/P(tot) congruent with 1/P(pb) + 1/P(sr) + 1/P(d), where P(pb) is the contribution of the permanent bends and P(sr) is the contribution of the slowly relaxing bends. Both P(d) and P(tot) are determined for the same 200-bp DNA in 4 mM ionic strength by measuring its optical anisotropy, r(t), from 0 to 10 micros. Time-resolved fluorescence polarization anisotropy (FPA) measurements yield r(t) for DNA/ethidium complexes (1 dye/200 bp) from 0 to 120 ns. A new transient polarization grating (TPG) experiment provides r(t) for DNA/methylene blue complexes (1 dye/100 bp) over a much longer time span, from 20 ns to 10 micros. Accurate data in the very tail of the decay enable a model-independent determination of the relaxation time (tau(R)) of the end-over-end tumbling motion, from which P(tot) = 500 A is estimated. The FPA data are used to obtain the best-fit pairs of P(d) and torsion elastic constant (alpha) values that fit those data equally well, and which are used to eliminate alpha as an independent variable. When the relevant theory is fitted to the entire TPG signal (S(t)), the end-over-end rotational diffusion coefficient is fixed at its measured value and alpha is eliminated in favor of P(d). Neither a true minimum in chi-squared nor a satisfactory fit could be obtained for P(d) anywhere in the range 500-5000 A, unless an adjustable amplitude of azimuthal wobble of the methylene blue was admitted. In that case, a well-defined global minimum and a reasonably good fit emerged at P(d) = 2000 A and <deltazeta(2)>(1/2) = 25 degrees. The discrimination against P(d) values <1600 A is very great. By combining the values, P(tot) = 500 A and P(d) = 2000 A with a literature estimate, P(pb) = 1370 A, a value P(sr) = 1300 A is estimated for the contribution of slowly relaxing bends. This value is analyzed in terms of a simple model in which the DNA is divided up into domains containing m bp, each of which experiences an all-or-none equilibrium between a straight and a uniformly curved conformation. With an appropriate estimate of the average bend angle per basepair of the curved conformation, a lower bound estimate, m = 55 bp, is obtained for the domain size of the coherently bent state. Previous measurements suggest that this coherent bend is not directional, or phase-locked, to the azimuthal orientation of the filament.

TATA box DNA deformation with and without the TATA box-binding protein

DNA ring closure methods have been applied to TATA box DNA and its complex with the TATA box-binding protein (TBP). The J factors for cyclization (effective concentrations of one DNA end about the other) have been measured using cyclization kinetics, with and without bound TBP, for 18 DNA constructs containing the adenovirus major late promoter TATA box (TATAAAAG) separated by a variable helical phasing adapter from sequence-induced A-tract DNA bends. Six phasing lengths were used at three overall DNA lengths each. Cyclization kinetics were also measured in the absence of protein for the same set of molecules bearing a mutant TATA box (TACAAAAG). The results suggest that the TATA box DNA itself is strongly bent and anisotropically flexible, in a direction opposite to the bend induced by TBP, and that the mutant TACA box is much less bent/flexible. The bending and flexibility of the free DNA may govern the energetics of recognition of different DNA sequences by TBP, and the intrinsic bend may act to repress transcription complex assembly in the absence of TBP. The cyclization kinetics of TBP-DNA complexes in solution predict a geometry generally consistent with crystal structures, which show dramatic bending and unwinding. The novel observation of TBP-induced topoisomers suggests that this minicircle approach is able to distinguish TBP-induced unwinding from writhe (these cancel out in larger DNA), and this in turn suggests that changes in supercoiling in small topological domains can control TBP binding.

Damage increases the flexibility of duplex DNA

It is proposed that much of the recognition of specific types of damaged DNAs is based on accessible structural features, while much of the recognition of damaged DNAs, as a class, is based on flexibility. The more flexible a DNA the faster its diffusion rate. The diffusion rates of each member of a series of damaged duplex DNAs has been found to be significantly faster than that of the corresponding undamaged duplex DNA. The damaged sites studied include apurinic and apyrimidinic a basic sites, thymine glycol and urea. The presence of mismatched sites also increases the diffusion. Thus, damaged DNAs appear to have sufficient flexibility for recognition and the flexibility may allow damaged sites to act as a universal joint or hinge that allows distant sites on the DNA to come together.

DNA bending induced by the archaebacterial histone-like protein MC1

The conformational changes induced by the binding of the histone-like protein MC1 to DNA duplexes have been analyzed by dark-field electron microscopy and polyacrylamide gel electrophoresis. Visualisation of the DNA molecules by electron microscopy reveals that the binding of MC1 induces sharp kinks. Linear DNA duplexes (176 bp) which contained a preferential site located at the center were used for quantitative analysis. Measurements of the angle at the center of all duplexes, at a fixed DNA concentration, as a function of the MC1 concentration, were very well fitted by a simple model of an isotropic flexible junction and an equilibrium between the two conformations of DNA with bound or unbound MC1. This model amounts to double-folded Gaussian distributions and yields an equilibrium deflection angle of theta0=116 degrees for the DNA with bound MC1. It allowed measurements of the fraction of DNA with bound MC1 to be taken as a function of MC1 concentrations and yields an equilibrium dissociation constant of Kd=100 nM. It shows that the flexibility of DNA is reduced by the binding of MC1 and the formation of a kink. The equilibrium dissociation constant value was corroborated by gel electrophoresis. Control of the model by the computation of the reduced chi2 shows that the measurements are consistent and that electron microscopy can be used to quantify precisely the DNA deformations induced by the binding of a protein to a preferential site.

DNA bending and the curious case of Fos/Jun

DNA bending has been implicated as an important regulatory mechanism in several processes involving protein-DNA interactions. Various methods for examining intrinsic and protein-induced DNA bending may lead to different conclusions. For the Fos and Jun transcription factors, this has resulted in controversy over whether these factors significantly bend DNA at all.

Evidence for intrinsic DNA bends within the human cdc2 promoter

Cyclin-dependent protein kinases (Cdks) are key regulatory proteins of the eukaryotic cell cycle. The product of the cdc2 gene, p34cdc2 (cdk1), is the catalytic subunit of a serine/ threonine protein kinase that is expressed in S phase and functions in the G2 to M phase transition. Previous studies indicate that the human cdc2 gene expression is dependent on cell growth, and is transcriptionally regulated in a complex manner involving multiple transcription factors binding to specific sites in the promoter. One possible mechanism by which these transcription factors regulate transcription is that by binding to their cognate sites they induce bends in the DNA helix, thereby allowing their interaction with the basal transcription machinery through protein-protein contacts. Such protein-induced DNA bending is also influenced by intrinsic bends in the regulatory region. Using both theoretical and experimental approaches, the study reports that the human cdc2 promoter has an intrinsic DNA bend with a broad locus of curvature.

Strained DNA is kinked by low concentrations of Zn2+

A novel atomic force microscope with a magnetically oscillated tip has provided unprecedented resolution of small DNA fragments spontaneously adsorbed to mica and imaged in situ in the presence of divalent ions. Kinks (localized bends of average angle 78 degrees) were observed in axially strained minicircles consisting of tandemly repeated d(A)5 and d(GGGCC[C]) sequences. The frequency of kinks in identical minicircles increased 4-fold in the presence of 1 mM Zn2+ compared with 1 mM Mg2+. Kinking persisted in mixed Mg2+/Zn2+ electrolytes until the Zn2+ concentration dropped below 100 microM, indicating that this type of kinking may occur under physiological conditions. Kinking appears to replace intrinsic bending, and statistical analysis shows that kinks are not localized within any single sequence element. A surprisingly small free energy is associated with kink formation.

Identification and characterization of genomic nucleosome-positioning sequences

Positioned nucleosomes are believed to play important roles in transcriptional regulation and for the organization of chromatin in cell nuclei. Here, we have isolated the DNA segments in the mouse genome that form the most stable nucleosomes yet characterized. In separate molecules we find phased runs of three to four adenine nucleotides, extensive CA repeats, and in a few cases phased TATA tetranucleotides. The latter forms the most stable nucleosome yet characterized. One sequence with CAG repeats was also found. By fluorescence in situ hydridization the selected sequences are shown to be localized at the centromeric regions of mouse metaphase chromosomes.

Polymorphic curvature of satellite DNA in three subspecies of the beetle Pimelia sparsa

The curvature of the monomeric repeats of satellite DNAs from three subspecies of the beetle Pimelia sparsa (Coleoptera, Tenebrionidae) has been analysed. Evidence of curvature was inferred from their retarded migration in native polyacrylamide gels, which was confirmed by direct electron microscopy visualisation. Sequence-comparison analysis, which included sequence alignments and modelling studies, was used to reveal the patterns of local bending and curvature. The effects of the minor-groove-binding drugs distamycin and berenil on the curvature were assayed, and analysed with respect to their (A+T)-rich sequence preferences. Since our study deals with satellite DNAs from closely related organisms (three subspecies), we correlated the differences in sequence, and also the high similarity conserved in the (A+T)-rich regions, with the changes in the patterns of curvature.

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.

The organic crystallizing agent 2-methyl-2,4-pentanediol reduces DNA curvature by means of structural changes in A-tracts

Contemporary predictive models for sequence-dependent DNA structure provide a good estimation of overall DNA curvature in most cases. However, the two current models differ fundamentally in their view of the origin of DNA curvature. An earlier model that associates DNA bending primarily, although not exclusively, with stretches of adenines (A-tracts) is based on results of comparative gel retardation, cyclization kinetics, hydroxyl radical cutting, and other solution measurements. It represents an intersection of wedge and junction models. More recently, a non-A-tract bending model has been proposed, built on structural results from x-ray crystallography and molecular modeling. In this view, A-tracts are proposed to be straight and rigid, whereas mixed sequence DNA is bent. Because a key premise of the non-A-tract bending model is the crystallographic observation that A-tracts are straight, we have examined the effect in solution of 2-methyl-2,4-pentanediol (MPD), an organic solvent used in crystal preparation for crystallographic DNA structure determinations. Using cyclization analysis, DNase I cutting, chemical probing, and electron microscopy on DNA oligomers with and without A-tracts, we show that the presence of MPD in solution dramatically affects A-tracts and that the effect is specific to these sequence elements. Combined with the previous observation that MPD affects gel mobility of curved sequences with A-tracts, our findings support the bent A-tract model and call for caution in the interpretation of crystallographic results on DNA structure as these are presently obtained.

Intrinsic curvature of plasmid DNAs analyzed by polyacrylamide gel electrophoresis

The electrophoretic mobility of two small DNA plasmids, pUC19 and Litmus 28, linerarized by digestion with a variety of single-cut restriction enzymes, has been studied. The permuted sequence isomers migrate with identical mobilities in agarose gels, as expected, but exhibit different mobilities in large-pore polyacrylamide gels, suggesting that the parent plasmids contain sequence-specific sites of curvature and/or anisotropic flexibility. Both plasmids contain apparent bend centers near their origin(s) of replication; pUC19 also has a major apparent bend center near the promoter of the ampicillin resistance gene. These apparent bend centers are observed under a variety of experimental conditions, suggesting that they correspond to sites of stable curvature in the parent plasmids. Both plasmids also contain minor bend centers that are observed under a sub-set of electrophoretic conditions and disappear when divalent cations are added to the solution, suggesting that these apparent bend centers may correspond to localized regions of variable flexibility.

The effects of sequence context on DNA curvature

Recent experiments have exposed significant discrepancies between experimental data and predictive models for DNA structure. These results strongly suggest that DNA structural parameters incorporated in the models are not always sufficient to account for the influence of sequence context and of specific ion effects. In an attempt to evaluate these two effects, we have investigated repetitive DNA sequences with the sequence motif GAGAG.CTCTC located in different helical phasing arrangements with respect to poly(A) tracts and GGGCCC.GGGCCC sequence motifs. Methods used are ligase-mediated cyclization and gel mobility experiments along with DNase I cutting and chemical probe studies. The results provide new evidence for curvature in poly(A) tracts. They also show that the sequence context in which bending and flexible sequence elements are found is an important aspect of sequence-dependent DNA conformation. Although dinucleotide models generally have good predictive power, this work demonstrates that in some instances sequence elements larger than the dinucleotide must be taken into account, and hence it provides a starting point for the appropriate modification and refinement of existing structural models for DNA.

Influence of optical probing with YOYO on the electrophoretic behavior of the DNA molecule

The influence of the fluorescent dye YOYO (1,1'-(4,4,8,8,-tetramethyl- 4,8-diazaundecamethylene)bis[4-[[3-methyl-benzo-1,3-oxazol-2 -yl] methylidene]-1,4-dihydroquinolinium] tetraiodide) on the electrophoretic behavior of the DNA molecule was investigated. This is important when using YOYO as a probe in capillary electrophoresis or in fluorescence microscopy studies of DNA with the purpose of studying the migration mechanism of DNA on the molecular level. We have measured the mobility and orientation dynamics (using the linear dichroism technique) for both pure DNA and the YOYO-DNA complex in agarose gel in order to compare their electrophoretic properties. Mobility decreases, the degree of orientation becomes lower, and the orientational dynamics slower, when YOYO binds to DNA. However, the dependence on field strength of the mobility, orientation and orientational dynamics, are similar for DNA and YOYO-DNA, indicating that the mode of migration does not change significantly upon binding YOYO to DNA. Furthermore, since our results show that the effect of YOYO on both the degree of orientation and orientational dynamics of the DNA can be measured and therefore be compensated for, it can be concluded that YOYO is an excellent optical probe for the study of the migrational behavior of DNA.

Theoretical permutation gel electrophoretic analysis of a curved DNA fragment located in circular permutation

Using the theoretical model for DNA curvature, we analyzed a set of fragments with a curved insert located in circular permutation. The theoretical permutation analysis of each of the cyclically located fragments reveals the presence of a shifting molecular bend locus. The delineation of the molecular bend locus associated with the fragments obtained by a second permutation helps in providing an explanation for the differential mobility behavior of the fragments.

Electric birefringence of kilobase-sized DNA molecules

Transient electric birefringence has been used to characterize the rotational diffusion of linear, circularly permuted pBR322 and SV40 DNA molecules. The birefringence relaxation times vary with the site of linearization, suggesting that the circularly permuted DNAs have different conformations in solution. The longest relaxation times are observed for DNA sequence isomers linearized at the major bend centers identified by gel electrophoresis. SV40 sequence isomers linearized at other locations have faster, but approximately equal, terminal relaxation times, suggesting that their free solution conformations are relatively independent of the location of the bend center within the sequence. By contrast, the terminal relaxation times of the various pBR322 sequence isomers vary approximately in accord with their electrophoretic mobilities in large-pore polyacrylamide gels, suggesting that the different mobilities may reflect real conformational differences between the sequence isomers.

Bending and torsional flexibility of G/C-rich sequences as determined by cyclization assays

The structural polymorphism of DNA is a vital aspect of its biological function. However, it has become increasingly apparent in recent years that DNA polymorphism is a complicated, multidimensional phenomenon that includes not only static sequence-directed structures but dynamic effects as well, including influences of counterions and sequence context. In order to address some of these additional factors that govern DNA conformation, we have used T4 ligase-mediated cyclization to investigate bending in a series of DNA sequences containing the GGGCCC.GGGCCC motif in different sequence contexts including various helical phasings with (A)5-tracts. We present evidence for curvature in GGGCCC.GGGCCC and (A)5-tract motifs in the presence of physiological levels of Mg2+ and show that these motifs curve through similar but oppositely directed bending angles under these ionic strength conditions. Although these two sequence motifs appear to bend similarly, our results suggest significant differences in stiffness and stability of curvature between them. We also show that under the same experimental conditions, the CTAG-CTAG sequence element possesses unusual torsional flexibility and that this appears to be associated with the central TA.TA dinucleotide. The results underscore the need to include sequence context and specific ion effects as well as a dynamic basis in more complete predictive models for functionally related DNA polymorphism.

Complex of osmium tetroxide with 1,10-phenanthroline binds covalently to double-stranded DNA

Complex of osmium tetroxide with 1,10-phenanthroline (Os,phen) reacts with double-stranded B-DNA in contrast to osmium tetroxide, pyridine and other osmium structural probes which show a strong preference for single-stranded DNA (ssDNA) (Palecek, E. in Abelson, J.N., and Simon, M.I. (eds), Lilley, D.M.J., and Dahlberg, J.E., (volume eds.), Methods in Enzymology, Vol. 212, DNA Structures, part B., Academic Press, 139-155 (1992)). Modification of negatively supercoiled DNA (scDNA) with Os,phen changes the DNA electrophoretic mobility inducing the DNA relaxation at lower degrees of modification followed by formation of positive supercoils at higher modification extents. Electrophoretic mobility of the Os,phen-modified DNA fragments in agarose gel is almost unchanged while a strong retardation of the same fragments is observed in polyacrylamide gels. Os,phen-modified DNA is hypersensitive to nuclease S1. Cleavage of this DNA by restriction enzymes is selectively inhibited showing a preference of Os,phen for TA and AT dinucleotide steps. DNA modification by Os,phen is inhibited by low and moderate concentrations of MgCl2. The covalent binding of Os,phen to double-stranded DNA (dsDNA) is preceded by noncovalent interactions (probably intercalation) inducing DNA structural changes; the shape of the Os,phen-modified DNA molecule appears to be severely deformed.

Four p53 DNA-binding domain peptides bind natural p53-response elements and bend the DNA

Recent structural studies of the minimal core DNA-binding domain of p53 (p53DBD) complexed to a single consensus pentamer sequence and of the isolated p53 tetramerization domain have provided valuable insights into their functions, but many questions about their interacting roles and synergism remain unanswered. To better understand these relationships, we have examined the binding of the p53DBD to two biologically important full-response elements (the WAF1 and ribosomal gene cluster sites) by using DNA circularization and analytical ultracentrifugation. We show that the p53DBD binds DNA strongly and cooperatively with p53DBD to DNA binding stoichiometries of 4:1. For the WAF1 element, the mean apparent Kd is (8.3 +/- 1.4) x 10(-8) M, and no intermediate species of lower stoichiometries can be detected. We show further that complex formation induces an axial bend of at least 60 degrees in both response elements. These results, taken collectively, demonstrate that p53DBD possesses the ability to direct the formation of a tight nucleoprotein complex having the same 4:1 DNA-binding stoichiometry as wild-type p53 which is accompanied by a substantial conformational change in the response-element DNA. This suggests that the p53DBD may play a role in the tetramerization function of p53. A possible role in this regard is proposed.

High-affinity binding sites for histone H1 in plasmid DNA

The interaction of histone H1 isolated from chicken erythrocytes with restriction fragments from plasmids pBR322 and pUC19 was studied by gel electrophoresis. Certain restriction fragments exhibited unusually high affinity for the histone, forming high molecular mass complexes at protein to DNA ratios at which the other fragments did not show evidence for binding. The highly preferred fragments are intrinsically curved, as judged by their electrophoretic mobility in polyacrylamide gels, by computer modeling, and by imaging with scanning force microscopy. However, control experiments with either curved portions of the same fragments or highly curved kinetoplast DNA fragments showed that the presence of curvature alone was not sufficient for preferential binding. By using various restriction fragments centered around the highly preferred sequence, it was found that the high-affinity binding required in addition the presence of specific sequences on both sides of the region of curvature. Thus, both curvature and the presence of specific sites seem to be required to generate high affinity.

Use of polyacrylamide gel electrophoresis to detect structural variations in kilobase-sized DNAs

The electrophoresis of linear, kilobase-sized DNA molecules with permuted sequences has been studied in polyacrylamide and agarose gels. Plasmid pBR322, bacteriophage phi X174, and the SV40 minichromosome were each digested with a series of single-cut restriction enzymes. The linearized, permuted isomers of all three DNAs exhibit different mobilities in large-pore polyacrylamide gels, suggesting that all three DNAs contain sites of anisotropic, sequence-dependent curvature. Various experimental parameters such as acrylamide concentration, crosslinker ratio and buffer composition affect the magnitude of the observed differential mobilities. Band sharpness appears to be optimal in polyacrylamide gels containing 6.9-8.1%T and 0.5-1%C. Only small mobility differences are observed for the linearized, permuted sequence isomers in agarose gels.

Sequence dependent migration behavior of double-stranded DNA in capillary electrophoresis

Capillary electrophoresis (CE) with a replaceable linear polyacrylamide (LPA) sieving matrix was used to examine sequence-dependent migration of double-stranded DNA fragments. It has been found that DNA conformational effects were significant under high electric field separations, especially using high resolution matrices. Compared to linear DNA-ladder standards, both anomalously slow and rapid DNA fragments were observed, with the degree of anomalous migration depending on the electric field strength, polymer concentration, column temperature, and background electrolyte (denaturants, sodium and magnesium ions, DNA-intercalating dyes). By selecting a combination of electrophoretic conditions (e.g. 3% T LPA, elevated capillary temperature, lower electric field strength and addition of DNA intercalating dyes), molecular weight dependent separations were closely restored.