Movement of fluorescence pattern after photobleaching: an accelerated procedure for DNA electrophoretic mobility analysis

A new approach which is compatible with many of the existing procedures for the analysis of DNA species in gel electrophoresis is being demonstrated. It takes advantage of fluorescence photobleaching in order to create a sharp boundary between the stained and the (partially) photobleached DNA. By arbitrarily creating a stained DNA band of narrower width, the sensitivity to detect (averaged) DNA band movements has been increased. This feature permits measurements of time-dependent electrophoretic mobility over very short time periods. The approach can be used to shorten the running time of gel electrophoresis experiment and to increase the resolution because of the sharper boundary and narrower band width. With faster running time, diffusion of both DNA and dye in the gel also becomes less serious. Movement of fluorescence pattern after photobleaching also permits measurements of localized motions when the gel pores are small in comparison with DNA sizes. Experiments demonstrating some aspects of the proposed technique, as well as the anticipated limitations, are presented and discussed.

Suppression of crossbridge motions of isolated thick myofilaments in ATP-free medium by thiourea

Thiourea is known to suppress the contractile response of Mytilus anterior byssus retractor muscle and toad sartorious muscle following electrical or chemical stimulation without abolishing of the electrical responses. In addition, it blocks the shortening of glycerinated sartorious muscle induced by Ca2+. With dynamic laser light scattering method we found that thiourea suppresses the increase of the average linewidth of the photoelectron count autocorrelation function, gamma, of isolated thick filaments of Limulus striated muscle induced by depletion of ATP. The results obtained suggest that thiourea prevents the crossbridges from moving away from the thick myofilament backbones which will, in turn, prohibit the crossbridges from interacting with the thin myofilaments.

Neurotoxicity induced by the D-1 agonist SKF 38393 following microinjection into rat brain

Microinjection of the D-1 agonist R-SKF 38393 into rat striatum resulted in extensive neurotoxic damage as revealed by the presence of large lesions upon histological analysis. These lesions were observed following a single injection of the drug into the ventrolateral striatum (30 micrograms/0.5 microliters) or nucleus accumbens (3.0 or 30 micrograms/0.5 microliters). This neurotoxic damage was also observed following microinjection of the inactive isomer S-SKF 38393. The mechanisms underlying these effects are presently unknown. The use of this compound for intracerebral microinjection studies should be re-evaluated. In view of the usefulness of central microinjections in studying the role of D-1 and D-2 receptors in behavior, it is suggested that alternative D-1 agonists, or ways of minimizing the toxicity of SKF 38393, should be considered.

Study of large DNA fragments in agarose gels by transient electric birefringence

The pulsed-field gel electrophoresis (PFG) is a newly developing technique used in the fractionation of large DNA fragments. Advances in PFG demand a better understanding in the corresponding mechanisms of DNA dynamics in the gel network. Detailed experiments are needed to verify and to extend existing theoretical predictions as well as to find optimum conditions for efficient separation of large DNA fragments. In the present study, deformation of large DNA fragments (40-70 kilobase pairs) imbedded in agarose gels were investigated by using the transient electric birefringence (TEB) technique under both singular polarity and bipolarity electric pulses at low applied electric field strengths (E less than or equal to 5 V/cm). The steady-state optical retardation (delta s) of DNA molecules is linearly proportional to E2. At a given E, the amplitude of optical retardation [delta(t)] increases monotonically with the pulse width (PW) and then reaches a plateau value [delta(t = 0) = delta s] where t = 0 denotes the time when the applied field is turned off or reversed. The field-free decay time (tau-a few minutes) is several orders of magnitudes slower than that from previous TEB observations using high electric field strengths (E-kV/cm) and short pulse widths (PW-ms). The degree of deformation (stretching and orientation) and the time of restoration to the equilibrium conformation of overall DNA chains have been related to delta and tau. In field inversion measurements, exponentially rising and linearly falling of birefringence signals in the presence of forward/inverse applied fields were observed. The rising and falling of birefringence signals were reproducible under a sequence of alternating pulses. Comparison of our results with literature findings and discussions with theories are presented.

Electrophoresis and movements of fluorescence pattern after photobleaching of large DNA fragments in agarose gels

By combining electrophoresis with movements of fluorescence pattern after photobleaching (MOFPAP), which is abbreviated as EMOFPAP, we are able to measure electrophoretic mobilities of large DNA fragments in an agarose gel within a fairly short time scale (about 10 min or even down to 1 min). The new method represents a significant improvement in experiment time when compared with the time (typically on the order of hours) required to determine the average electrophoretic mobility of large DNA fragments in agarose gels by means of either conventional gel electrophoresis or pulsed-field gel electrophoresis. In this article, we present the EMOFPAP experimental setup and consider optical conditions, including beam profile geometry and fluorescence pattern formation. A realistic formula that can explain the parameters governing the EMOFPAP method using our present optical setup has been derived. A comparison of results between experimental and computer simulation data is made, and an optimization of the EMOFPAP method is proposed.

Fiber optic detector probes for laser light scattering

An experimental investigation of the role of fiber optic detector probes in laser light scattering is presented. A quantitative comparison between different detector configurations is accomplished by measuring the time taken for one million photocounts to be accumulated in the extrapolated zeroth delay channel of the net unnormalized intensity time correlation function. A considerable reduction in the accumulation time is achieved by relaxing a rather stringent requirement for the spatial coherence of the optical field.

Effect of ATP depletion on the isolated thick filament of limulus striated muscle

With the dynamic light scattering method, we have shown that calcium ions increase the high-frequency internal motions of isolated thick filaments of Limulus striated muscle in the presence of ATP (Kubota, K., B. Chu, Shih-fang Fan, M.M. Dewey, P. Brink, and D. Colflesh. J. Mol. Biol. 1983. 166:329 and Fan, S.-f., M.M. Dewey, D. Colflesh, B. Gaylinn, R. Greguski, and B. Chu. Biophys. J. 1985. 47:809). If ATP is removed from the suspending medium, an increase of high-frequency internal motions also has been observed with characteristics different from those of filaments suspended in a medium containing ATP and calcium ions. These internal motions appear whether calcium ions are present or not and are suppressed by trifluoperazine (TFP). The motions differ from the calcium ion-induced motions in that (a) an energy supply is not required; (b) they are insensitive to heat treatment (42 degrees C, 10 min) and (c) they are also insensitive to phenylmethylsulfonyl fluoride which blocks the motions in the presence of ATP and calcium ions (Fan, Shih-fang, M.M. Dewey, D. Colflesh, B. Gaylinn, R. Greguski, and B. Chu. 1985. Biochim. Biophys. Acta. 827:101). Electron micrographs of negatively stained thick filaments in an ATP-free medium show that the majority of crossbridges extend out from the backbone of the filament and optical diffraction patterns from these filaments lack layer lines arising from the crossbridges. The flexibility of the thick filaments suspended in ATP-free media increases.

The active cross-bridge motions of isolated thick filaments from myosin-regulated muscles detected by quasi-elastic light scattering

Intensity fluctuation spectroscopy has been used successfully as a probe that can detect an increase in high-frequency internal motions of isolated thick filaments of Limulus muscle upon the addition of calcium ions. We have attributed such motions to cross-bridge motion instead of to an increase in the flexibility of the filament backbone. Here we show that after cleavage of the S-1 and then the S-2 moieties with papain, cross-linking the myosin heads to the filament backbone, or heat denaturation (42 degrees C, 10 min), the increase in the high frequency internal motions in the thick filaments no longer occurs. Congo Red, which has been shown to induce shortening of isolated myofibrils, also increases the high-frequency motions of the isolated filaments. Furthermore, the increase is suppressed by treating the filaments with a myosin ATPase inhibitor such as vanadate ions (10 mM) or by replacing ATP with either an equimolar CrADP or the nonhydrolyzable ATP analogue beta, gamma-imido-adenine-5'-triphosphate (AMP-PNP). Calcium ions have a similar effect on isolated thick filaments from scallop muscle, where the myosin is known to be regulatory. Calcium ions have no such effect on thick filaments isolated from frog muscle, which is believed not to be regulated by calcium binding to myosin. These results confirm our earlier supposition that the additional high frequency internal motions of the thick filaments isolated from striated muscle of Limulus are related to the energy dependent, active cross-bridge motions.

Short-term fluctuations and long-term trends in anchorage-independent multiplication among cryopreserved subpopulations of a spontaneously transformed Balb/3T3 clone

A spontaneously transformed clone of Balb/3T3 cells which produced primitive pleomorphic sarcomas in nude mice was maintained in serial passage without cryopreservation. It was also cryopreserved at an early passage and thawed out at four successive intervals. The capacity of these 5 subpopulations to form colonies while suspended in agar (CFEag) was assayed repeatedly over a period of almost 3 years. The initial CFEag and the subsequent pattern of change were unique for each of the subpopulations. When later passages of the nonfrozen subpopulation were cryopreserved and then thawed, there was only a slight change in CFEag and colony size in agar. There were differences in multiplication rates of 3 of the subpopulations on plastic surfaces in the same rank order as their CFEag, but the differences were smaller. Short-term fluctuations in CFEag, however, were not paralleled by changes in multiplication rate on plastic. The nonfrozen subpopulation assumed the appearance of nontransformed fibroblasts when crowded for several days on plastic, and these "normalized" cells had a greatly reduced CFEag when assayed in agar. Neither the change in appearance nor the decrease in CFEag with prolonged incubation of crowded cells occurred with one of the cryopreserved subpopulations which had the same CFEag and growth rate on plastic as the nonfrozen subpopulation under optimal conditions. The evidence favors an epigenetic rather than a genetic origin of the variations in appearance and behavior of the subpopulations.

Suppression of active cross-bridge motions of isolated thick myofilaments in suspension by phenylmethylsulfonyl fluoride

Studies of photoelectron count autocorrelation function of light scattered from suspensions of thick filaments of Limulus telson muscle and scallop striated adductor muscle reveal that Ca2+ can activate cross-bridge motions of these isolated filaments. By treating suspensions of activated filaments with phenylmethylsulfonyl fluoride (PMSF), we can suppress active cross-bridge motions but not affect the Ca2+-dependent ATPase activity.

Dynamic laser light scattering of papain-treated thick filaments from limulus striated muscle in suspension

Using quasielastic light scattering we have previously shown an increase in high frequency internal motion of isolated thick filament upon activation. This we have attributed to cross-bridge motion. Here we show that after cleavage of the S1 moiety of myosin from isolated filaments with papain, calcium ions no longer activate the isolated filaments to produce high-frequency motions.

Quasi-elastic light scattering of suspensions of Limulus thick myofilaments in relaxed (long) activated and rerelaxed (short) states

Photoelectron count autocorrelation function of light scattered by Limulus thick myofilament suspensions was measured as a function of scattering angle in the relaxed, activated and rerelaxed states. By using the cumulants method of data analysis, the average linewidth over large ranges of KL (up to 120), has been calculated with K and L being, respectively, the magnitude of the momentum transfer vector and the length of the myofilament. We have observed a dramatic increase in the average linewidth denoting the presence of additional high frequency components for the myofilament suspension on the activated state. By confirming our results on the size of the myofilaments from electron micrographs, we are able to attribute the high frequency (kHz) components to the "correlated" cross-bridge motions, representing, to our knowledge, the first direct experimental evidence of such movements in isolated thick myofilament suspensions.