Chemistry Reference
In-Depth Information
PNA
DNA duplexes. The synthesis of PNA
monomers is relatively simple [21]. PNA monomers containing the A, G, C, and T bases
are commercially available from several suppliers. Numerous PNA monomers with differ-
ent pseudo-peptide backbone or with alternative nucleobases have been prepared [22]. For
example, alanyl PNA is a peptide-based nucleic acid structure with an alanyl-derived
backbone having the nucleobases attached to the b-carbon [23]. PNA oligomers are pre-
pared simply by modified solid phase synthesis using either a Boc or a Fmoc protection
strategy [24]. The attachment of amino acids or carboxylic acid derivatives of ligands or
metal complexes to the amino end of the PNA oligomers is straightforward. Positively
charged amino acids such as lysine and arginine, and hydrophilic groups such as poly-
ethylene glycol (PEG) have been introduced into PNA oligomers to improve their solubil-
ity, enabling the preparation of millimolar solutions of PNA [24]. Cysteine has also been
introduced in PNA to form self-assembled monolayers (SAMs) on gold surfaces [25].
In contrast to the chiral sugar-phosphate backbone of DNA, the amino-ethylglycine
backbone of PNA does not contain stereocenters. A preferred helical handedness can be
induced in the PNA
PNA duplexes than on PNA
DNA or DNA
PNA duplexes by the attachment of a D -or L -amino acid at the car-
boxy or C-terminus of one or both strands of a duplex [26]. X-ray crystallography showed
that the PNAPNA duplexes, which adopt a distinct “p-form” helix in both crystals and
solution, exist in crystals as a 1:1 mixture of right- and left-handed duplexes even if they
contain a L -lysine, which indicates that the chiral induction effect exerted by the lysine is
comparable in strength to the crystal packing forces [27]. A preferred handedness can also
be induced in PNA duplexes by a stereogenic center at the a-org-position of the PNA
backbone [22o,28]. The incorporation of an ( S )-Me stereogenic center at the g-backbone
position induces the formation of a right-handed structure in duplexes as well as in ss
PNA [22o,29].
Several metal complexes have been attached to PNA because they can be used as IR
[e.g., (benzene)chromiumtricarbonyl] or electrochemistry probes {e.g., ferrocene, cobal-
tocene, or [Ru(bipy) 3 ] }, or to quantify the cellular uptake of PNA. These complexes
have been linked to PNA by using metal complex-containing PNA monomers or alkyne-
containing PNA monomers to which the metal complex could be linked by click chemis-
try (Figure 10.5) [30]. Studies of the thermal stability of a DNA
PNA duplex have shown
that the duplex was destabilized by the ferrocene “clicked” at the middle of the PNA
strand of the duplex.
Oxy-LNA is an RNA analogue developed in 1998 [32], in which the ribose group of the
sugar phosphate backbone contains a methylene bridge between the 2 0 -oxygen atom of
the ribose and the 4 0 -carbon atom [33]. Unlocked nucleic acid (UNA) lacks the C2 0 -C3 0
bond normally found in ribonucleosides (Figure 10.4). Several C-glycoside analogues of
LNA have been prepared including an amino-LNA that has a 2 0 -NH group instead of the
2 0 -oxygen (Figure 10.4). This chemical modification preorganizes the LNA monomer into
a locked C3 0 -endo conformation similar to that observed in A-type DNA, and reduces the
entropic penalty for the formation of duplexes containing LNA. Consequently, LNA
LNA
and hetero LNA
DNA and LNA
RNA duplexes are more stable than DNA
DNA or
DNA
RNA ones. The NMR structures of partially- or completely-modified LNA
DNA
and LNA
RNA hybrids showed that the LNA nucleotides induce a preference for an A-
type, right-handed duplex structure because they adopt a C3 0 -endo conformation and
because they steer the sugar conformations of neighboring nucleotides into similar
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