Large-scale oscillation of structure-related DNA sequence features in human chromosome 21.
Human chromosome 21 is the only chromosome in the human genome that exhibits oscillation of the (G+C) content of a cycle length of hundreds kilobases (kb) ( 500 kb near the right telomere). We aim at establishing the existence of a similar periodicity in structure-related sequence features in order to relate this (G+C)% oscillation to other biological phenomena. The following quantities are shown to oscillate with the same 500 kb periodicity in human chromosome 21: binding energy calculated by two sets of dinucleotide-based thermodynamic parameters, AA/TT and AAA/TTT bi- and tri-nucleotide density, 5'-TA-3' dinucleotide density, and signal for 10- or 11-base periodicity of AA/TT or AAA/TTT. These intrinsic quantities are related to structural features of the double helix of DNA molecules, such as base-pair binding, untwisting or unwinding, stiffness, and a putative tendency for nucleosome formation.
Li
Wentian
W
The Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore LIJ Health System, 350 Community Drive, Manhasset, New York 11030, USA. wli@nslij-genetics.org
Miramontes
Pedro
P
D001482:Base Composition / Q000235:genetics*; D001483:Base Sequence; D001683:Biological Clocks / Q000235:genetics*; D002891:Chromosomes, Human, Pair 21 / Q000737:chemistry* / Q000235:genetics*; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA; D013329:Structure-Activity Relationship
D004247:DNA