Electro-optic scattering studies on deoxyribonucleic acid

Laser induced birefringence in liquids and solutions

An apparatus is described with which the electric vector of a suitably defined laser beam has been used to induce optical birefringence in various liquid media. Blue light from a low powered argon laser monitored the birefringence in the sample cell while the infrared (1.06 μm wavelength) radiation of a neodymium doped YAG laser interacted with the sample molecules to give rise to the birefringence effects. The principal object of the study was to manifest effects in dilute solutions of macromolecules. Initial attempts involved mechanically chopping the YAG beam whose power was some 20 W continuous output. Only thermal effects were observed. These experiments are outlined as they give effects which might easily be mistaken for particle orientation effects. By ‘ Q ’ switching the laser, the increased power in the beam was sufficient to induce birefringence in pure liquids and liquid crystals. Finally, when operated in a ‘fixed Q ’ mode, the intermediate power but increased pulse duration (100 μs) enabled the optical Kerr effect to be realized in macromolecular solutions. Typical results are given for suspensions of bentonite clay and potassium hyaluronate in water.

Interactions of nucleic acid double helices induced by electric field pulses

Electric field pulses induce a substantial increase of the light scattering intensity of double-helical DNA. The relative change of light scattering and also the reciprocal relaxation time constants under electric field pulses increase with increasing nucleotide concentration. These observations, together with a large difference between dichroism orientation time constants and light scattering time constants under electric field pulses, demonstrate that the main part of the light scattering effect is due not to field-induced orientation but to interactions between DNA helices. From the concentration dependence of the light scattering time constants we obtain, according to an isodesmic reaction model, association rate constants in the range 3 X 10(10) M-1 helices s-1 for DNA with approx. 300 base-pairs. These values are at the limit of a diffusion-controlled DNA association and do not show any dependence upon the field strength. The dissociation rate constants kd decrease strongly with increasing field strength E and thus demonstrate that the interactions between the helices are induced by the electric field. This conclusion is consistent with independent measurements which do not reveal any DNA association at zero field strength. The observed linear relation between log(kd) and E2 suggests a field-induced reaction driven by dipole changes. According to this interpretation the change of dipole moment should be in the range of approx. 1400 debye. The dissociation rates for DNA helices with approx. 300 to approx. 800 base-pairs strongly increase with increasing salt concentration (measured in the range 1-5 mM ionic strength), whereas the association rate constants remain virtually unchanged. Measurements of the linear dichroism in the same range of DNA chain length demonstrate that for long field pulses of e.g., 40 microseconds, the amplitude approaches a maximum value and then decreases. The dichroism relaxation curves observed after long field pulses exhibit a component with a positive dichroism and an increased decay time. These observations suggest the formation of a DNA aggregate with an unusual arrangement of the bases.

The flexibility of low molecular weight double-stranded DNA as a function of length. I. Isolation andphysical characterization of seven fractions

Sonicated calf thymus DNA was fractionated by rate zonal centrifugation into seven fractions with weight average molecular weights ranging from 0.28 to 1.3 X 10(6) daltons, as determined by sedimentation equilibrium and light scattering measurements (the latter are described in the accompanying paper). Electron microscopy and sedimentation equilibrium analysis revealed these fractions to be narrowly disperse with Mw/Mn ratios averaging about 1.06. Intrinsic viscosities and sedimentation rates were measured and found to vary linearly with molecular weight in double-logarithmic plots in fair agreement with previously published functions relating these parameters for low molecular weight DNA. Thso agreeing with reported estimates of this parameter for short DNA. These data will be used in the second paper of this series to calculate the persistence length of the DNA fragments in each of the seven fractions by light scattering and hydrodynamic theories for the Kratky-Porod worm-like coil.

Light-scattering studies on deoxyribonucleic acid flexibility. The solution properties of a small circular deoxyribonucleic acid molecule

Previous investigations on the persistence length of DNA in solution have revealed large discrepancies between hydrodynamic results and those from light-scattering techniques which have potentially a greater resolving power. The information obtained from experiments on a small circular DNA molecule has resolved these discrepancies. The non-superhelical circular double-stranded DNA molecule from bacteriophage [unk]X174-infected cells is small enough to permit accurate light-scattering extrapolations, and its solutions have negligible anisotropy. The persistence length obtained from experimental investigations on this molecule is comparable with that obtained by hydrodynamic techniques, even with variation of the excluded-volume factor.