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Mathematical method for determining the distribution of substituted DNA zone lengths with reference to equilibrium density profiles
Author(s) -
Delcroix C.,
Cantraine F. R. L.,
Hardt N.
Publication year - 1978
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.1978.360171209
Subject(s) - generalization , density gradient , dna , chemistry , distribution (mathematics) , matrix (chemical analysis) , algorithm , biological system , mathematics , chromatography , mathematical analysis , physics , biology , biochemistry , quantum mechanics
A method of calculation to determine the profile in density‐gradient sedimentation of bromodeoxyuridine‐substituted DNA lengths prior to sonication is developed. The method may be summarized as follows: (1) A description of a formulation of random cleavage of a substituted zone i in fragments of length m ; (2) generalization and application of this formulation to all substituted zone lenghts simultaneously present in a given DNA extract, such generalization being performed by means of a matrix calculation; (3) adjustment of this formulation for the limits of the experimental method, i.e., number of gradient fractions which can be recovered, and for the evolution of the DNA fragment lengths which drop in the course of successive sonications; (4) simulation of the radioactive profiles. By this method it is possible to obtain certain indications concerning the types of initial (i.e., presonication) distributions that are compatible with observed profiles and to test the validity of assumptions relating to the initial distribution. This method has been applied in analyzing DNA synthesis in lymphocytes stimulated by Concanavalin and allowed us to determine the significance of the discontinuties appearing in the elongation with a suboptimal stimulating dose. The proposed method could also be applied to the analysis of all random populations of mixed sequences.