Stable minihairpin structures forming at minisatellite DNA isolated from yellow fin sea bream Acanthopagrus latus.
The lengths of simple repeat sequences are generally unstable or polymorphic (highly variable with respect to the numbers of tandem repeats). Previously we have isolated a family of minisatellite DNA (GenBank accession AF422186) that appears specifically and abundantly in the genome of yellow fin sea bream Acanthopagrus latus but not in closely-related red sea bream Pagrus major, and found that the numbers of tandem arrays in the homologous loci are polymorphic. This means that the minisatellite sequence has appeared and propagated in A. latus genome after speciation. In order to understand what makes the minisatellite widespread within the A. latus genome and what causes the polymorphic nature of the number of tandem repeats, the structural features of single-stranded polynucleotides were analyzed by electrophoresis, chemical modification, circular dichroism (CD), differential scanning calorimetry (DSC) and electron microscopy. The results suggest that a portion of the repeat unit forms a stable minihairpin structure, and it can cause polymerase pausing within the minisatellite DNA.
Kato
Mikio
M
Department of Biological Science, Osaka Prefecture University Graduate School of Science, 1-1 Gakuencho, Naka-ku, Sakai 599-8531, Japan. mkato@b.s.osakafu-u.ac.jp
Haku
Takeshi
T
Hibino
Takeshi
T
Fukada
Harumi
H
Mishima
Yumiko
Y
Yamashita
Ichiro
I
Minoshima
Shinsei
S
Nagayama
Kuniaki
K
Shimizu
Nobuyoshi
N
D000818:Animals; D001483:Base Sequence; D002942:Circular Dichroism; D004247:DNA / Q000378:metabolism; D004261:DNA Replication; D004276:DNA, Satellite / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000235:genetics; D053842:Microsatellite Instability; D018598:Minisatellite Repeats; D008969:Molecular Sequence Data; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D016133:Polymerase Chain Reaction; D021541:Sea Bream / Q000235:genetics*; D019914:Taq Polymerase; D013696:Temperature
D004276:DNA, Satellite; D004277:DNA, Single-Stranded; D009838:Oligodeoxyribonucleotides; D004247:DNA; D019914:Taq Polymerase