Internal dynamics of linear and superhelical DNA as studied by photon correlation spectroscopy

The Statistical Segment Length of DNA: Opportunities for Biomechanical Modeling in Polymer Physics and Next-Generation Genomics

The development of bright bisintercalating dyes for deoxyribonucleic acid (DNA) in the 1990s, most notably YOYO-1, revolutionized the field of polymer physics in the ensuing years. These dyes, in conjunction with modern molecular biology techniques, permit the facile observation of polymer dynamics via fluorescence microscopy and thus direct tests of different theories of polymer dynamics. At the same time, they have played a key role in advancing an emerging next-generation method known as genome mapping in nanochannels. The effect of intercalation on the bending energy of DNA as embodied by a change in its statistical segment length (or, alternatively, its persistence length) has been the subject of significant controversy. The precise value of the statistical segment length is critical for the proper interpretation of polymer physics experiments and controls the phenomena underlying the aforementioned genomics technology. In this perspective, we briefly review the model of DNA as a wormlike chain and a trio of methods (light scattering, optical or magnetic tweezers, and atomic force microscopy (AFM)) that have been used to determine the statistical segment length of DNA. We then outline the disagreement in the literature over the role of bisintercalation on the bending energy of DNA, and how a multiscale biomechanical approach could provide an important model for this scientifically and technologically relevant problem.

Persistent draining crossover in DNA and other semi-flexible polymers: Evidence from hydrodynamic models and extensive measurements on DNA solutions

Although the scaling theory of polymer solutions has had many successes, this type of argument is deficient when applied to hydrodynamic solution properties. Since the foundation of polymer science, it has been appreciated that measurements of polymer size from diffusivity, sedimentation, and solution viscosity reflect a convolution of effects relating to polymer geometry and the strength of the hydrodynamic interactions within the polymer coil, i.e., "draining." Specifically, when polymers are expanded either by self-excluded volume interactions or inherent chain stiffness, the hydrodynamic interactions within the coil become weaker. This means there is no general relationship between static and hydrodynamic size measurements, e.g., the radius of gyration and the hydrodynamic radius. We study this problem by examining the hydrodynamic properties of duplex DNA in solution over a wide range of molecular masses both by hydrodynamic modeling using a numerical path-integration method and by comparing with extensive experimental observations. We also considered how excluded volume interactions influence the solution properties of DNA and confirm that excluded volume interactions are rather weak in duplex DNA in solution so that the simple worm-like chain model without excluded volume gives a good leading-order description of DNA for molar masses up to 10(7) or 10(8) g/mol or contour lengths between 5 μm and 50 μm. Since draining must also depend on the detailed chain monomer structure, future work aiming to characterize polymers in solution through hydrodynamic measurements will have to more carefully consider the relation between chain molecular structure and hydrodynamic solution properties. In particular, scaling theory is inadequate for quantitative polymer characterization.

Is DNA a Good Model Polymer?

The details surrounding the cross-over from wormlike-specific to universal polymeric behavior has been the subject of debate and confusion even for the simple case of a dilute, unconfined wormlike chain. We have directly computed the polymer size, form factor, free energy and Kirkwood diffusivity for unconfined wormlike chains as a function of molecular weight, focusing on persistence lengths and effective widths that represent single-stranded and double-stranded DNA in a high ionic strength buffer. To do so, we use a chain-growth Monte Carlo algorithm, the Pruned-Enriched Rosenbluth Method (PERM), which allows us to estimate equilibrium and near-equilibrium dynamic properties of wormlike chains over an extremely large range of contour lengths. From our calculations, we find that very large DNA chains (≈ 1,000,000 base pairs depending on the choice of size metric) are required to reach flexible, swollen non-draining coils. Furthermore, our results indicate that the commonly used model polymer λ-DNA (48,500 base pairs) does not exhibit "ideal" scaling, but exists in the middle of the transition to long-chain behavior. We subsequently conclude that typical DNA used in experiments are too short to serve as an accurate model of long-chain, universal polymer behavior.

Characterization of polybutadiene-poly(ethyleneoxide) aggregates in aqueous solution: a light-scattering and small-angle neutron-scattering study

For diblockcopolymers of polybutadiene-poly(ethyleneoxide) (PB-PEO) type, water is a selective solvent. In dependence of the length of both blocks and the block length ratio, these polymers form a multitude of self-assembled structures in solution. In the present work scattering methods are used to investigate the water-soluble polymer PB125-PEO155 . It is found to form long rodlike micelles, which are characterized with respect to the aggregate length L , the cross sectional radius RCS , the radial scattering length density profile sigma r, and the radial aggregation number Nrad. Model-independent as well as model-based approaches are used for the scattering data analysis. From dynamic light scattering (DLS) and static light scattering (SLS) experiments the weight averaged length Lw of these stiff elongated aggregates is determined to Lw=350 nm . Small angle neutron scattering (SANS) reveals a cross sectional radius of RCS=17 nm and in combination with results from the SLS the radial aggregation number is found to be Nrad=70 .

Genetically engineered polymers: status and prospects for controlled release

Genetic engineering methodology has enabled the synthesis of protein-based polymers with precisely controlled structures. Protein-based polymers have well-defined molecular weights, monomer compositions, sequences and stereochemistries. The incorporation of tailor-made motifs at specified locations by recombinant techniques allows the formation of hydrogels, sensitivity to environmental stimuli, complexation with drugs and nucleic acids, biorecognition and biodegradation. Accordingly, a special interest has emerged for the use of protein-based polymers for controlled drug and gene delivery, tissue engineering and other biomedical applications. This article is a review of genetically engineered polymers, their physicochemical characteristics, synthetic strategies used to produce them and their biomedical applications with emphasis on controlled release.

In vitro and in vivo evaluation of recombinant silk-elastinlike hydrogels for cancer gene therapy

The objectives of this study were to evaluate: (i). the influences of hydrogel geometry, DNA molecular weight, and DNA conformation on DNA release from a silk-elastinlike protein polymer (SELP) hydrogel, (ii). the bioactivity and transfection efficiency of encapsulated DNA over time in vitro, (iii). the delivery and transfection of a reporter gene in a murine model of human breast cancer in vivo, and (iv). the in vitro release and bioactivity of adenovirus containing the green fluorescent protein (gfp) gene as a marker of gene transfer. Plasmid DNA was released from SELP hydrogels in a size-dependent manner, with the average effective diffusivity ranging from 1.70+/-0.52 x 10(-12) cm(2)/s for a larger plasmid (11 kbp) to 2.55+/-0.51 x 10(-10) cm(2)/s for a smaller plasmid (2.6 kbp). Plasmid conformation also influenced the rate of release, with the rank order linear>supercoiled>open-circular. DNA retained bioactivity in vitro, after encapsulation in a SELP hydrogel for up to 28 days. Delivery of pRL-CMV from a SELP hydrogel resulted in increased transfection in a murine model of human breast cancer by 1-3 orders of magnitude, as compared to naked DNA. The release of a bioactive adenoviral vector was related to the concentration of the polymer in the hydrogel. These studies indicate that genetically engineered SELP hydrogels have potential as matrices for controlled nonviral and viral gene delivery.

Study of DNA internal dynamics by quasi-elastic light scattering

We have studied the large-scale internal fluctuations in DNA coils by using quasi-elastic light-scattering spectroscopy. We have measured the angular dependence of the first cumulant of the scattered-light autocorrelation function. Within the q (3) domain of this dependence, we observed the transition from the asymptotic behavior predicted for good solvents to the asymptotic behavior predicted for ? conditions. This allowed us to determine the screening length of volume interactions in DNA chains. Analysis of the autocorrelation functions by a regularization procedure allowed us to reconstruct the mode composition of the scattered light and to determine the relaxation time of the fluctuations in the coil size.

Light scattering studies of supercoiled and nicked DNA

Static and dynamic light scattering measurements were made of solutions of pGem1a plasmids (3730 base pairs) in the relaxed circular (nicked) and supercoiled forms. The static structure factor and the spectrum of decay modes in the autocorrelation function were examined in order to determine the salient differences between the behaviors of nicked DNA and supercoiled DNA. The concentrations studied are within the dilute regime, which is to say that the structure and dynamics of an isolated DNA molecule were probed. Static light scattering measurements yielded estimates for the molecular weight M, second virial coefficient A2, and radius of gyration RG. For the nicked DNA, M = (2.8 +/- 0.4) x 10(6) g/mol, A2 = (0.9 +/- 0.2) x 10(-3) mol cm3/g2, and RG = 90 +/- 3 nm were obtained. For the supercoiled DNA, M = (2.5 +/- 0.4) x 10(6) g/mol, A2 = (1.2 +/- 0.2) x 10(-3) mol cm3/g2, and RG = 82 +/- 2.5 nm were obtained. The static structure factors for the nicked and supercoiled DNA were found to superpose when they were scaled by the radius of gyration. The intrinsic stiffness of DNA was evident in the static light scattering data. Homodyne intensity autocorrelation functions were collected for both DNAs at several angles, or scattering vectors. At the smallest scattering vectors the probe size was comparable to the longest intramolecular distance, while at the largest scattering vectors the probe size was smaller than the persistence length of the DNA. Values of the self-diffusion coefficients D were obtained from the low-angle data. For the DNA, D = (2.9 +/- 0.3) x 10(-8) cm2/s, and for the supercoiled DNA, D = (4.11 +/- 0.21) x 10(-8) cm2/s. The contribution to the correlation function from the internal dynamics of the DNA was seen to result in a strictly bimodal decay function. The rates of the faster mode gamma int, reached plateau values at low angles. For the nicked DNA, gamma int = 2500 +/- 500 s-1, and for the supercoiled DNA, gamma int = 5000 +/- 500 s-1. These rates correspond to the slowest internal relaxation modes of the DNAs. The dependence of the relaxation rates on scattering vector was monitored with the aid of cumulants analysis and compared with theoretical predictions for the semiflexible ring molecule. The internal mode rates and the dependence of the cumulants moments reflected the difference between the nicked DNA and the supercoiled DNA dynamical behavior. The supercoiled DNA behavior seen here indicates that conformational dynamics might play a larger role in DNA behavior than is suggested by the notion of a branched interwound structure.

Structural changes in 16S RNA from Escherichia coli upon unfolding by urea

The urea-induced unfolding of 16S RNA at low ionic strength has been studied by dynamic light scattering, uv spectroscopy, and some hydrodynamic methods. Three components could be resolved in the photon correlation spectra of scattered light, using the inverse Laplace transform SIPP program [G.R. Danovich and I.N. Serdyuk (1983) in Photon Correlation Techniques in Fluid Mechanics, vol. B38, E.O. Schulz-Dubois, Ed., Springer, Berlin/Heidelberg, New York, p. 315]. One component is assigned to the center-of-mass translation of the RNA, another one to a combination of translational and internal motion, and the last to diffusion of urea clusters. The hydrodynamic dimensions of RNA increase strongly upon transition from 4 to 6 M urea. We conclude that up to 2 M urea, 16S RNA is highly elongated, and coiled above 4 M urea, with a great increase of the hydrodynamic dimensions of RNA being observed upon transition from 4 to 6 M urea. A scheme for RNA unfolding is proposed.