Replication initiation point mapping

Susan A. Gerbi, Anja K Bielinsky

Research output: Contribution to journalArticlepeer-review

80 Scopus citations


Replication in eukaryotes is bidirectional and semi-discontinuous. This asymmetry provides the basis for mapping the origin of bidirectional replication (OBR), which is the transition point from discontinuous to continuous synthesis. The regions of each DNA strand complementary to the leading strand or lagging strand can be measured by the methods of imbalanced DNA synthesis or Okazaki fragment distribution, respectively. The resolution of both of these hybridization-based procedures is a few hundred base pairs. Nucleotide resolution was previously achieved for viral origins by mapping the initiation sites of Okazaki fragments on sequencing gels. To overcome the background caused by nicked DNA, all DNA ends were phosphorylated, RNA primers were removed from the Okazaki fragments by NaOH hydrolysis, and the hydroxyl ends thus created were phosphorylated with 32 P. Unfortunately, this method was not sensitive enough to map eukaryotic cellular origins. A new method, replication initiation point (RIP) mapping, that is 1000-fold more sensitive and has been applied to yeast ARS1 where the OBR is mapped to an 18-bp region from within element B1 toward B2 is described here. RIP mapping utilizes Vent (exo-) polymerase to extend from a labeled primer to the DNA/RNA junctions of nascent strand template in an asynchronous population of replicating molecules. The DNA is digested with λ-exonuclease prior to primer extension to remove nicked contaminating DNA.

Original languageEnglish (US)
Pages (from-to)271-280
Number of pages10
JournalMethods: A Companion to Methods in Enzymology
Issue number3
StatePublished - Nov 1997
Externally publishedYes

Fingerprint Dive into the research topics of 'Replication initiation point mapping'. Together they form a unique fingerprint.

Cite this