Quantitative comparison of DNA looping in vitro and in vivo: chromatin increases effective DNA flexibility at short distances.
The probability that two sites on a linear DNA molecule will contact each other by looping depends on DNA flexibility. Although the flexibility of naked DNA in vitro is well characterized, looping in chromatin is poorly understood. By extending existing theory, we present a single equation that describes DNA looping over all distances. We also show that DNA looping in vitro can be measured accurately by FLP recombination between sites from 74 bp to 15 kb apart. In agreement with previous work, a persistence length of 50 nm was determined. FLP recombination of the same substrates in mammalian cells showed that chromatin increases the flexibility of DNA at short distances, giving an apparent persistence length of 27 nm.
Ringrose
L
L
Gene Expression Program, European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.
Chabanis
S
S
Angrand
P O
PO
Woodroofe
C
C
Stewart
A F
AF
D001483:Base Sequence; D002460:Cell Line; D002843:Chromatin / Q000235:genetics*; D004247:DNA / Q000737:chemistry*; D004254:DNA Nucleotidyltransferases / Q000737:chemistry; D004262:DNA Restriction Enzymes / Q000378:metabolism; D006801:Humans; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011995:Recombination, Genetic; D013997:Time Factors
D002843:Chromatin; D004247:DNA; D004254:DNA Nucleotidyltransferases; C045119:FLP recombinase; D004262:DNA Restriction Enzymes