Start Date
16-3-2018 1:15 PM
End Date
16-3-2018 2:30 PM
Abstract Text
Molecular beacons are important bioanalytical probes which are most often
constructed from a single-stranded oligonucleotide which has been labeled at
opposite termini with a fluorophore and a quencher. When the fluorophore and
quencher are in close proximity, no fluorescence is observed due to FRET
(Fluorescence Resonance Energy Transfer). DABCYL (4-dimethylaminoazobenzene-
4'-carboxylic acid) has been used as a quencher in the molecular beacon to absorbs
excitation energy from a fluorophore and to dissipate the energy as heat. However,
DABCYL is unable to form a base-pair and is conventionally placed as an overhanging
residue. This produces a derivative wherein the chromophore has substantial mobility
and limits the types of other conjugates that can be prepared. In order to overcome
these limitations, we have embarked on the synthesis of deoxyribonucleoside and
peptide nucleic acid (PNA) analogue possessing DMPAU (5-[(4-dimethylaminophenyl)
diazenyl]uracil) as the nucleobase. DMPAU has DABCYL-like properties due to the
installation of an azo moiety at the 5-position of the uracil base. This base is designed
to have the ability to form a complementary base pair with adenosine by canonical
hydrogen bonding and also to quench the fluorescence emission in a molecular
beacon construct. Both DMPAUridine and DMPAU PNA analogue are determined to
have same UV-Vis absorbance ranges as DABCYL and reasonable quenching effect
to the fluorophore.
Supervisor Consent
yes
Included in
Biochemistry Commons, Nucleic Acids, Nucleotides, and Nucleosides Commons, Organic Chemistry Commons
A Chimeric Nucleobase - Phenylazo Derivative as an Intrinsic Nucleobase Quencher
Molecular beacons are important bioanalytical probes which are most often
constructed from a single-stranded oligonucleotide which has been labeled at
opposite termini with a fluorophore and a quencher. When the fluorophore and
quencher are in close proximity, no fluorescence is observed due to FRET
(Fluorescence Resonance Energy Transfer). DABCYL (4-dimethylaminoazobenzene-
4'-carboxylic acid) has been used as a quencher in the molecular beacon to absorbs
excitation energy from a fluorophore and to dissipate the energy as heat. However,
DABCYL is unable to form a base-pair and is conventionally placed as an overhanging
residue. This produces a derivative wherein the chromophore has substantial mobility
and limits the types of other conjugates that can be prepared. In order to overcome
these limitations, we have embarked on the synthesis of deoxyribonucleoside and
peptide nucleic acid (PNA) analogue possessing DMPAU (5-[(4-dimethylaminophenyl)
diazenyl]uracil) as the nucleobase. DMPAU has DABCYL-like properties due to the
installation of an azo moiety at the 5-position of the uracil base. This base is designed
to have the ability to form a complementary base pair with adenosine by canonical
hydrogen bonding and also to quench the fluorescence emission in a molecular
beacon construct. Both DMPAUridine and DMPAU PNA analogue are determined to
have same UV-Vis absorbance ranges as DABCYL and reasonable quenching effect
to the fluorophore.