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.

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Mar 16th, 1:15 PM Mar 16th, 2:30 PM

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.