Nucleic Acids in Chemistry and Biology

164 Chapter 4

N

O

R5'O Base

ONRP 2

OR3'

Morpholino phosphorodiamidate nucleoside

Figure 4.26 Structure of a morpholino phosphorodiamidate nucleotide residue

benzhydryloxycarbonyl (Bhoc) group that is cleaved with aqueous trifluoracetic acid (Figure 4.25).^41 In both
these systems, the coupling reactions are similar to those used in solid phase peptide synthesis to form an
amide bond. Sinceunmodified PNA is rather insoluble in water, it is usual to incorporate a few cationic
amino acids (especially lysines) to aid solubility. One advantage of PNA is that amino acids or peptides
can be synthesised as direct conjugates with the DNA analogue. Such PNA–peptide conjugates are being
explored in antisense applications for direct delivery of PNA into cells.
PNA forms particularly strong hybrids with DNA and RNA oligonucleotides and the inter-base distance
in PNA when bound to such oligonucleotides is approximately the same as in the natural nucleotide
strand. When bound to RNA, RNase H is not induced and therefore PNA is only used in steric block anti-
sense approaches (see Section 5.7.1) or in microarray diagnostic applications (see Section 5.5.4). In add-
ition, when targeted at DNA duplexes, PNA is able to displace one strand of the duplex to form a
PNA:DNA:PNA triplex (see Section 2.3.6).

4.4.3.9 Phosphorodiamidate Morpholino Modifications. One final modification that has been

used is the double replacement of the pentose by a morpholino-group and the phosphate non-bridging oxygen

N

NH

O

O

N

OO

ONHFmoc

N

NH

O

O

N

O

O

ONH

O

N NHFmoc

O

NO

NHBhoc

N

OO

ONH 2

N

NH

O

O N

N

O

O

N

O

ONHFmoc

NHBhoc

C 6 F 5

PNA

1. deblock,
   20% piperidine


2. Activate and couple
   Diisopropylethylamine/lutidine
   PyAOP, DMF


3. Cap, acetic anhydride/lutidine


4. Cyclentimes


5. Deprotect
   trifluoroacetic acid

Figure 4.25 Synthesis of PNA by the Fmoc method. Bhoc: benzhydryloxycarbonyl, PyBOP: 7-azabenzotriazol-1-
yloxytris (pyrrolidino)phosphonium hexafluorophosphate

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