The organization and repair of DNA in the mammalian chromosome. I. Calibration procedures and errors in the determination of the molecular weight of a native DNA

Abstract

SynopsisThe semiautomated sucrose gradient system of Lange and Liberman (1974) (Anal. Biochem. 59,129-145) has been used to determine an accurate value of the exponent K of the Burgi and Hershey equation (1963) (Biophys. J. 3,309-321) under conditions of 1M salt. A complete analysis of the variance of k was done for data from both systems. The results lead to the conclusion that the value k = 0.401 (f0.012 for reproducibility; f0.019 for total error) obtained here is considerably more accurate than that of Burgi and Hershey (even when corrected for DNA concentration effects and the improved size estimates of T4 DNA size). The use of the Burgi and Hershey relationship and a T4 DNA metric to determine molecular weights of mammalian DNA requires the utmost precision in the exponent if useful estimates are to be obtained. This also has implications for double-strand breakage and repair estimates.

Cell-cell interactions in spheroids maintained in suspension

“…The standard error is the standard deviation divided by the square root of the number of observations, and is properly used when comparing mean values with each other rather than data points with the mean (for which the standard deviation should be used). The standard errors of ratios (as in plating efficiencies and surviving fractions) are determined using the chain rule for equipartition of variance, which takes into account the proper weight of the uncertainty contributions of both the numerator and the denominator [23,24].…”

The organization and repair of DNA in the mammalian chromosome. III. Determination of the molecular weight of a mammalian native DNA

“…(9) and (10) from part I (Ref. 9) to deduce that M , = 4.9 X lo9 (To simplify notation, the subscript "r" has been deleted from M, wherever other identifying subscripts have been necessary, but is still to be understood, i.e., M, is really M,,, the number average molecular weight ratio, etc.). However, this conclusion would be valid only if our sedimentation distance (86.9% of the total gradient length) were for DNA at zero concentration, and it was not; the concentration was about 1.10 pg/ml.…”

“…Therefore, instead, we made use of the relationship (2) where c is the DNA concentration (in g/dl), [q] is the intrinsic viscosity of the DNA being measured (in dl/g), and K = 0.723 f 0.121 as determined in part I (Ref. 9). Again, as in part I,9 replacing S by D (sedimentation distance, as per cent of total gradient length) we could rewrite eqs.…”