Beilstein J. Org. Chem.2018,14, 253–281, doi:10.3762/bjoc.14.17
bases). In this section, only those that have been used in combination with PNA will be discussed. More general reviews of fluorescentbaseanalogues in the DNA/RNA context can be found elsewhere [177][178].
Fluorescent nucleobases capable of hydrogen bonding ("base discriminating fluorophores")
The
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Graphical Abstract
Figure 1:
The design of classical DNA molecular beacons.
Beilstein J. Org. Chem.2018,14, 114–129, doi:10.3762/bjoc.14.7
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Keywords: B-to-Z-DNA transition; fluorescentbaseanalogues; FRET; netropsin; nucleic acid structure and dynamics; quadracyclic adenines; tricyclic cytosines; Z-DNA; Review
Introduction
The importance of nucleic acid structure and dynamics in the understanding of vital processes in living organisms has
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In this review we will focus on the FRET between fluorescentbaseanalogues, i.e., base–base FRET, the theory behind it, the increased accuracy in orientation factor κ2 as an effect of their position inside the base-stack, other advantages and disadvantages compared to FRET in nucleic acids using
. Unfortunately, the variety of functional groups requires different protection group strategies and, moreover, changes the reactivity of the nucleobase. Since the discovery of the gold standard of fluorescentbaseanalogues, 2-AP, a multitude of adenine FBAs has emerged [22]. Notable recent examples of adenine
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Graphical Abstract
Figure 1:
a) Angles and unit vectors used to define the relative orientations of the donor and acceptor trans...