M. Giacca et al., MAPPING REPLICATION ORIGINS BY QUANTIFYING RELATIVE ABUNDANCE OF NASCENT DNA STRANDS USING COMPETITIVE POLYMERASE CHAIN-REACTION, Methods, 13(3), 1997, pp. 301-312
A procedure was developed for mapping origins of DNA replication in ma
mmalian cell chromosomes based on determining the relative abundance o
f nascent DNA strands throughout a specific genomic region. The method
entails purification of short strands of nascent DNA derived from rec
ently activated origins and the quantification, within this sample, of
the relative abundances dances of different adjacent DNA segments by
a competitive polymerase chain reaction technique. It is expected that
the abundance of defined markers within the origin region is greatest
at the site where DNA replication begins. This origin map ping proced
ure (i) allows analysis of single-copy genomic regions, (ii) can be pe
rformed on cultured and primary cells in the absence of any chemical t
reatment, (iii) does not require cell synchronization, and (iv) allows
mapping origins to within a few hundred base pairs. This high degree
of resolution permits a study of the cis- and trans-acting elements re
quired for origin function. Application of this method to single-copy
sequences in mammalian cells has identified replication origins within
an similar to 500-bp segment in the human lamin B2 gene domain and wi
thin an similar to 8OO-bp segment in the hamster dihydrofotate reducta
se gene locus. (C) 1997 Academic Press.