Synthesis and Characterization of Stacked and Quenched Uridine Nucleotide Fluorophores
IR@IICB: CSIR-Indian Institute of Chemical Biology, Kolkata
View Archive Info| Field | Value | |
| Title |
Synthesis and Characterization of Stacked and Quenched Uridine
Nucleotide Fluorophores
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| Creator |
Dhar, Goutam
Bhaduri, Amar Nath |
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| Subject |
Infectious Diseases and Immunology
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| Description |
Intramolecular aromatic interactions in aqueous solution
often lead to stacked conformation for model organic
molecules. This designing principle was used to
develop stacked and folded uridine nucleotide analogs
that showed highly quenched fluoroscence in aqueous
solution by attaching the fluorophore 1-aminonaphthalene-
5-sulfonate (AmNS) to the terminal phosphate via a
phosphoramidate bond. Severalfold enhancement of
fluorescence could be observed by destacking the molecules
in organic solvents, such as isopropanol and dimethylsulfoxide
or by enzymatic cleavage of the pyrophosphate
bond. Stacking and destacking were
confirmed by 1-H NMR spectroscopy. The extent of
quenching of the uridine derivatives correlated very
well with the extent of stacking. Taking 5-H as the monitor,
temperature-variable NMR studies demonstrated
the presence of a rapid interconversionary equilibrium
between the stacked and open forms for uridine-5*-
diphosphoro-b-1-(5-sulfonic acid) naphthylamidate
(UDPAmNS) in aqueous solution. DH was calculated
to be 22.3 Kcal/mol, with 43–50% of the population
in stacked conformation. Fluorescence lifetime for
UDPAmNS in water was determined to be 2.5 ns as
against 11 ns in dimethyl sulfoxide or 15 ns for the pyrophosphate
adduct of AmNS in water. Such a greatly
reduced lifetime for UDPAmNS in water suggests collisional
interaction between the pyrimidine and thefluorophore
moieties to be responsible for quenching. The
potential usefulness of such stacked and quenched nucleotide
fluorophores as probes for protein-ligand interaction
studies has been briefly discussed.
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| Publisher |
American Society for Biochemistry and Molecular Biology
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| Date |
1999
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| Type |
Article
PeerReviewed |
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| Format |
application/pdf
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| Identifier |
http://www.eprints.iicb.res.in/681/1/JOURNAL_OF_BIOLOGICAL_CHEMISTRY_274(_21)_14568%2D14572;1999[50].pdf
Dhar, Goutam and Bhaduri, Amar Nath (1999) Synthesis and Characterization of Stacked and Quenched Uridine Nucleotide Fluorophores. The Journal of Biological Chemistry, 274 (21). pp. 14568-14572. |
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| Relation |
http://dx.doi.org/10.1074/jbc.274.21.14568
http://www.eprints.iicb.res.in/681/ |
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