title: Capillary electrophoresis and fluorescence studies on molecular beacon-based variable length oligonucleotide target discrimination.
abstract: Molecular beacons (MBs) are oligonucleotide probes having a compact hairpin structure, with a fluorophore attached to one end and a quencher molecule attached to the other end. In its native state, the fluorophore is quenched by virtue of its proximity to the quencher molecule. Upon hybridization with its complementary oligonucleotide target, fluorescence is elicited due to a conformational change that results in separation of the fluorophore and quencher molecule. The present study describes the hybridization interaction of an MB to various complementary target sequences. The effects of temperature and length of complementary target sequences on hybridization were investigated using capillary electrophoresis and solution-based fluorescence techniques. Hybridization efficiency was dependent on the ability of the target sequences to destabilize the stem region by binding directly to the stem region. Optimal hybridization occurred between 40 and 50 degrees C for all targets tested, with the true target forming a more stable hybrid complex.
authors.affiliation: Department of Physiological Sciences, Veterinary Medicine, Oklahoma State University, Stillwater, OK 74078, USA.
authors.forename: Akhilesh
authors.initials: A
authors.lastname: Ramachandran
authors.forename: Minquan
authors.initials: M
authors.lastname: Zhang
authors.forename: David
authors.initials: D
authors.lastname: Goad
authors.forename: Glenn
authors.initials: G
authors.lastname: Olah
authors.forename: Jerry R
authors.initials: JR
authors.lastname: Malayer
authors.forename: Ziad
authors.initials: Z
authors.lastname: El-Rassi
mesh_terms: D001483:Base Sequence; D019075:Electrophoresis, Capillary / Q000379:methods*; D005456:Fluorescent Dyes; D005603:Francisella / Q000235:genetics; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization / Q000379:methods; D015345:Oligonucleotide Probes / Q000737:chemistry* / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013050:Spectrometry, Fluorescence / Q000379:methods; D013696:Temperature
chemical_list: D005456:Fluorescent Dyes; D015345:Oligonucleotide Probes; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S