The helical periodicity of DNA on the nucleosome

Organization of internucleosomal DNA in rat liver chromatin.

“…A value close to 10.0 bp/turn has since been supported by a mapping of DNase I cutting sites in three dimensions (Klug and Lutter, 1981) and by a measurement of the periodicity with which exo III digests nucleosomal DNA (Prunell, in preparation). This value of the pitch, taken together with the five nucleotide shift of inter-versus intranucleosomal fragments, leads to a model opposite to that of Lohr and Van Holde (1979), in which nucleosomes share the same orientation on the DNA.…”

“…As observed by Prunell et al (1979), a value of 10.0 bp/turn for the pitch of nucleosomal DNA will result in the observed cleavage periodicity of -10.5 nucleotides if directions of cutting are no longer perpendicular to the axis of the DNA superhelix but oriented as shown in Figure 6c. More specifically, average directions of cutting will vary regularly from the perpendicular at the mid position to the maximum angle off the perpendicular at the edges of the particle as drawn in Figure 6d (Klug and Lutter, 1981). An estimate for the maximal change in the cleavage direction angle can be simply obtained from the length difference between 14 turns of a DNA double helix with 10.0 bp/turn (140 bp) and the actual DNA content of a core particle (-145 bp; Lutter, 1979), which gives a figure of -5 bp or 180°(see Klug and Lutter, 1981, for detailed discussion).…”

“…More specifically, average directions of cutting will vary regularly from the perpendicular at the mid position to the maximum angle off the perpendicular at the edges of the particle as drawn in Figure 6d (Klug and Lutter, 1981). An estimate for the maximal change in the cleavage direction angle can be simply obtained from the length difference between 14 turns of a DNA double helix with 10.0 bp/turn (140 bp) and the actual DNA content of a core particle (-145 bp; Lutter, 1979), which gives a figure of -5 bp or 180°(see Klug and Lutter, 1981, for detailed discussion). With parallel nucleosomes, internucleosomal fragments corresponding to a full repeat length (1 -6, 2-7, etc., in Figure 6d) contain an integral number of turns of the double helix, in contrast to the largest intranucleosomal fragments (1-5, 6-10 in Figure 6d) which, as mentioned above, correspond to an integral number of turns plus approximately half a turn.…”

DNase II digestion of the nucleosome core: precise locations and relative exposures of sites

“…However, one must be cautious in identifying these exact periodicities directly with the structural periodicity of the DNA double helix, as has been done, for example, in reference 18. We have pointod out previously (10) as well as in the accompanying paper (20) that, due to the possibility that a nuclease may exhibit different angles of attack at different sites, a distance of e.g. 10.7 bases between two given sites does not necessarily mean the screw of the DNA is 10.7 base-pairs per turn between those two sites.…”

Telomeric DNA-protein interactions of Oxytricha macronuclear DNA.

“…2B, lane 1). The 10.4-bp periodicity of the nucleosomal digestion pattern (Noll 1974;Prunell et al 1979) arises from the passage of the nucleosomal DNA around the outside of the histone octamer (Klug and Lutter 1981). To ascertain whether the telomeric DNA might be involved in similar DNA-protein interactions, the periodicity of the DNase I digestion pattern from the telomeric complex was determined accurately.…”