Modified curved DNA that could allow local DNA underwinding at the nucleosomal pseudodyad fails to position a nucleosome in vivo.
In competitive in vitro reconstitution experiments synthetic DNA composed of tandem repeats of the repetitive sequence (A/T)3NN(G/C)3NN, specifically the 20 bp 'TG sequence' (5'-TCGGTGTTAGAGCCTGTAAC-3'), was reported to associate with the histone octamer with an affinity higher than that of nucleosomally derived DNA. However, at least two groups have independently shown that tandem repeats of the TG sequence do not accommodate a stably positioned nucleosome in vivo. It was suggested that the anisotropic flexibility of the TG sequence, governed by a 10 bp sequence periodicity, is incompatible with the required underwinding of the DNA helix at the nucleosome pseudodyad while maintaining a bending preference that can be accommodated in the remainder of the nucleosome. Here we test this hypothesis directly by studying the in vivo nucleosomal structure of modified TG sequences designed to accommodate underwinding at the pseudodyad. We show that these modifications are not sufficient to allow stable incorporation of the TG sequence repeat into a nucleosome in vivo, but do note invasion from one end of the TG heptamer of a translationally random but rotationally constrained nucleosome. We discuss possible reasons for the absence of nucleosomes from the TG sequence in vivo.
D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D003850:Deoxyribonuclease I; D006657:Histones / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000378:metabolism*; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis / Q000737:chemistry / Q000378:metabolism; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics
D006657:Histones; D009707:Nucleosomes; D009838:Oligodeoxyribonucleotides; D004247:DNA; D003850:Deoxyribonuclease I