title: New energy transfer dyes for DNA sequencing.
abstract: We have synthesized a set of four energy transfer dyes and demonstrated their use in automated DNA sequencing. The donor dyes are the 5- or 6-carboxy isomers of 4'-aminomethylfluorescein and the acceptor dyes are a novel set of four 4,7-dichloro-substituted rhodamine dyes which have narrower emission spectra than the standard, unsubstituted rhodamines. A rigid amino acid linker, 4-aminomethylbenzoic acid, was used to separate the dyes. The brightness of each dye in an automated sequencing instrument equipped with a dual line argon ion laser (488 and 514 nm excitation) was 2-2.5 times greater than the standard dye-primers with a 2 times reduction in multicomponent noise. The overall improvement in signal-to-noise was 4- to 5-fold. The utility of the new dye set was demonstrated by sequencing of a BAC DNA with an 80 kb insert. Measurement of the extinction coefficients and the relative quantum yields of the dichlororhodamine components of the energy transfer dyes showed their values were reduced by 20-25% compared with the dichlororhodamine dyes alone.
authors.affiliation: PE Applied Biosystems, 850 Lincoln Centre Drive, Foster City, CA 94404, USA. leelg@perkin-elmer.com
authors.forename: L G
authors.initials: LG
authors.lastname: Lee
authors.forename: S L
authors.initials: SL
authors.lastname: Spurgeon
authors.forename: C R
authors.initials: CR
authors.lastname: Heiner
authors.forename: S C
authors.initials: SC
authors.lastname: Benson
authors.forename: B B
authors.initials: BB
authors.lastname: Rosenblum
authors.forename: S M
authors.initials: SM
authors.lastname: Menchen
authors.forename: R J
authors.initials: RJ
authors.lastname: Graham
authors.forename: A
authors.initials: A
authors.lastname: Constantinescu
authors.forename: K G
authors.initials: KG
authors.lastname: Upadhya
authors.forename: J M
authors.initials: JM
authors.lastname: Cassel
mesh_terms: D001483:Base Sequence; D004247:DNA; D017931:DNA Primers; D004735:Energy Transfer; D005452:Fluoresceins / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry*; D008969:Molecular Sequence Data; D015394:Molecular Structure; D012235:Rhodamines / Q000737:chemistry*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D017931:DNA Primers; D005452:Fluoresceins; D005456:Fluorescent Dyes; D012235:Rhodamines; C024098:6-carboxyfluorescein; D004247:DNA