2 research outputs found
Structural and Dynamical Impact of a Universal Fluorescent Nucleoside Analogue Inserted Into a DNA Duplex
Recently,
a 3-hydroxychromone based nucleoside 3HCnt has been developed
as a highly environment-sensitive nucleoside surrogate to investigate
proteinâDNA interactions. When it is incorporated in DNA, the
probe is up to 50-fold brighter than 2-aminopurine, the reference
fluorescent nucleoside. Although the insertion of 3HCnt in DNA was
previously shown to not alter the overall DNA structure, the possibility
of the probe inducing local effects cannot be ruled out. Hence, a
systematic structural and dynamic study is required to unveil the
3HCntâs limitations and to properly interpret the data obtained
with this universal probe. Here, we investigated by NMR a 12-mer duplex,
in which a central adenine was replaced by 3HCnt. The chemical shifts
variations and nOe contacts revealed that the 3HCnt is well inserted
in the DNA double helix with extensive stacking interactions with
the neighbor base pairs. These observations are in excellent agreement
with the steady-state and time-resolved fluorescence properties indicating
that the 3HCnt fluorophore is protected from the solvent and does
not exhibit rotational motion. The 3HCnt insertion in DNA is accompanied
by the extrusion of the opposite nucleobase from the double helix.
Molecular dynamics simulations using NMR-restraints demonstrated that
3HCnt fluorophore exhibits only translational dynamics. Taken together,
our data showed an excellent intercalation of 3HCnt in the DNA double
helix, which is accompanied by localized perturbations. This confirms
3HCnt as a highly promising tool for nucleic acid labeling and sensing
Structural and Dynamical Impact of a Universal Fluorescent Nucleoside Analogue Inserted Into a DNA Duplex
Recently,
a 3-hydroxychromone based nucleoside 3HCnt has been developed
as a highly environment-sensitive nucleoside surrogate to investigate
proteinâDNA interactions. When it is incorporated in DNA, the
probe is up to 50-fold brighter than 2-aminopurine, the reference
fluorescent nucleoside. Although the insertion of 3HCnt in DNA was
previously shown to not alter the overall DNA structure, the possibility
of the probe inducing local effects cannot be ruled out. Hence, a
systematic structural and dynamic study is required to unveil the
3HCntâs limitations and to properly interpret the data obtained
with this universal probe. Here, we investigated by NMR a 12-mer duplex,
in which a central adenine was replaced by 3HCnt. The chemical shifts
variations and nOe contacts revealed that the 3HCnt is well inserted
in the DNA double helix with extensive stacking interactions with
the neighbor base pairs. These observations are in excellent agreement
with the steady-state and time-resolved fluorescence properties indicating
that the 3HCnt fluorophore is protected from the solvent and does
not exhibit rotational motion. The 3HCnt insertion in DNA is accompanied
by the extrusion of the opposite nucleobase from the double helix.
Molecular dynamics simulations using NMR-restraints demonstrated that
3HCnt fluorophore exhibits only translational dynamics. Taken together,
our data showed an excellent intercalation of 3HCnt in the DNA double
helix, which is accompanied by localized perturbations. This confirms
3HCnt as a highly promising tool for nucleic acid labeling and sensing