Templated synthesis of peptide nucleic acids via sequence-selective base-filling reactions

Article abstract of DOI:10.1021/ja904712t

(Chemical Equation Presented) The templated synthesis of nucleic acids has previously been achieved through the backbone ligation of preformed nucleotide monomers or oligomers. In contrast, here we demonstrate templated nucleic acid synthesis using a base

Full text of DOI:10.1021/ja904712t

Published on Web 07/23/2009
Templated Synthesis of Peptide Nucleic Acids via Sequence-Selective
Base-Filling Reactions
Jennifer M. Heemstra and David R. Liu*
Howard Hughes Medical Institute and the Department of Chemistry and Chemical Biology, HarVard UniVersity,
12 Oxford Street, Cambridge, Massachusetts 02138
Received June 9, 2009; E-mail: drliu@fas.harvard.edu
Template-directed nucleic acid synthesis is an essential compo-
nent of living systems (and their early precursors) that allows genetic
information to be passed down to subsequent generations. The desire
to understand early nucleic acid replication systems has inspired
the search for nonenzymatic routes to templated nucleic acid
polymerization in the laboratory.1 Previous examples of templated
nucleic acid synthesis have coupled nucleotide monomers or short
nucleotide oligomers by joining backbone functional groups in
reactions including, or analogous to, phosphodiester formation
(Figure 1a). While these reactions can yield the desired products,
they often produce additional nontemplated products and can exhibit
modest sequence specificity.1b
We envisioned base filling, the addition of individual bases to
an abasic backbone (Figure 1b), as an alternative route to the
nonenzymatic templated synthesis of nucleic acids.2,3 Compared
with the backbone ligation approach, a base-filling approach offers
at least two advantages: (i) the nucleobase monomers do not contain
complementary functional groups and therefore are not self-reactive,
potentially reducing nontemplated reactions; and (ii) the reaction
site is as close as possible to the site of base pairing, potentially
Figure 2. Base-filling chemistries. (a) Base filling of DNA by N-glycosidic
bond formation. (b) Base filling of PNA by reductive amination to generate
dPNA. (c) Base filling of PNA by amine acylation to generate native PNA.
increasing sequence specificity. Here we describe the templated
synthesis of both native and modified peptide nucleic acids (PNAs)
through base filling.
The incorporation of a single dPNA monomer in the middle of a
PNA-DNA duplex has been found to dramatically lower Tm values.8
When the modification is at the end of the strand, however, there is
little effect on Tm,9 likely due to the greater structural flexibility at the
end of the duplex. In light of these observations, we designed and
synthesized PNA templates and substrates 1-15 that collectively
represent the base filling of each of the four nucleobases at a site in
the middle of a PNA duplex, as well as at a site at the end of the
duplex (Table 1). Dimethyl lysine was added at each terminus to
improve water solubility and to prevent aggregation. Template and
Figure 1. Two strategies for the templated polymerization of nucleic acids:
(a) backbone ligation and (b) base filling.
Early hypotheses on the mechanism of prebiotic nucleic acid
replication considered the addition of bases to an abasic backbone
to be unlikely given the unfavorable equilibrium of N-glycosidic
bond formation in water,4,5 although Bartel and co-workers more
recently demonstrated the ability of a ribozyme to catalyze the
addition of uracil to activated ribose pyrophosphate.6 Over the past
few decades, however, researchers have introduced several nucleic
acid analogues, including some for which prebiotic syntheses have
been proposed, that may support base filling through reactions more
favorable than N-glycosidic bond formation. One of the most well
studied of these nucleic acid variants is PNA.7 We considered PNA
to be a promising candidate for replication by base filling since
the abasic reaction site is a versatile secondary amine. Base filling
with nucleobase acetic acids by amine acylation would provide
native PNA, and base filling with nucleobase acetaldehydes by
reductive amination would generate deoxyPNA (dPNA) (Figure 2).
substrate strands were capped at their N-termini with a hexanoyl (Hex)
or acetyl (Ac) group, respectively, to make the products and templates
distinguishable by mass spectrometry.
With these PNA strands in hand, we conducted a series of Tm
experiments and observed that the dPNA monomer lowered melting
temperature significantly when present in the middle of a PNA-PNA
duplex (∆Tm ) -9.8 °C), but to a much lesser extent at the end of
the duplex (∆Tm ) -0.9 °C), consistent with the previous studies
on DNA-PNA duplexes.8,9 We found that incorporation of an
abasic site had a parallel, though more dramatic effect on Tm (∆Tm
) -15.7 °C when present in the middle of the duplex, and ∆Tm )
-3.8 °C when present at the end of the duplex) (Table 1).
Next we tested the ability of PNA bases to fill a single abasic
site in the middle of a PNA strand, where the incoming base benefits
from both Watson-Crick base pairing and base-stacking interac-
tions. PNA strands 3, 4, 5, or 6 were combined with their
9
10.1021/ja904712t CCC: $40.75  2009 American Chemical Society
J. AM. CHEM. SOC. 2009, 131, 11347–11349 11347

C O M M U N I C A T I O N S
Table 1. Effect of PNA Modifications on Melting Temperaturea
the impurities in the adenine addition can be attributed to formation
of a T:G wobble pair.
For middle-of-strand base filling by amine acylation (Table 2,
entries a-d), we observed a much broader range of results than
for reductive amination depending on the identity of the substrate
base and the acylation reagents used. Using EDC and sNHS, we
observed good selectivity for all four reactions but good yield
(66-78%) only when adding guanine or cytosine. Adenine addition
proceeds with a significantly lower yield (38%), and the yield for
thymine addition is poor (8%). Switching the acylation reagent to
DMT-MM increases the yield for purine addition but lowers the
yields and the sequence specificity for pyrimidine additions.
These variations in acylation efficiency and selectivity likely arise
from the different steric and π-stacking characteristics of the
activated ester intermediates. Our results also suggest that, for
middle-of-strand base filling, G:C base pairing supports more
efficient product formation than A:T base pairing. Further, despite
producing canonical PNA, acylation is generally less efficient and
selective than reductive amination. A similar trend has been
observed for other DNA-templated reaction substrates1f and is likely
a consequence of the reversible formation of an iminium intermedi-
ate during reductive amination.1d
We next investigated base filling of a single abasic site at the
end of the PNA strand (Table 2, entries e-h). These reactions are
more challenging, since the base-stacking interaction between the
incoming base and the template should be significantly weaker than
the case in the middle of a strand. Under reductive amination
conditions, we observed moderate yields for the additions of guanine
and adenine (47-58%) and low yields for the additions of cytosine
and thymine (2-7%). Under acylation conditions, we observed no
significant addition of any of the four bases using EDC/sNHS, but
DMT-MM provided moderate yields (39-42%) for the additions
of guanine and adenine and poor yields (4-28%) for the additions
of cytosine and thymine. The selectivities of all of the reactions
were significantly lower than those observed for the middle-of-
strand additions. The universally lower yields for the end-of-strand
reactions in Table 2 implicate base-stacking interactions and the
a Conditions: 3 mM each PNA, 10 mM potassium phosphate buffer,
pH 6.2. b The Lys(Me2) and capping groups are omitted for clarity.
complementary template (1 or 2) and either an equimolar mixture
of all four aldehyde monomers 16a-d10 under reductive amination
conditions, or an equimolar mixture of all four carboxylic acid
monomers 17a-d under amide bond-forming conditions (Figure
3), and the reactions were monitored by MALDI mass spectrometry.
Representative MALDI spectra for the selective addition of guanine
to 3 by either reductive amination or acylation are shown in Figure
4. All reactions were performed in duplicate, and five MALDI
spectra obtained from each for a total of 10 measurements per
reaction. Product yields were calculated from the average ratio of
observed product and template ion counts using a standard curve
generated from independently quantitated and synthesized authentic
product (see Supporting Information).11
Addition of a single base to an abasic site at the middle of the
PNA strand using reductive amination proceeds with good to
excellent yield (78-98%) and good selectivity (g7:1 ratio of the
matched product to each possible mismatch product) for each of
the four bases (Table 2, entries a-d). Small amounts of mismatched
products are observed in the additions of adenine and thymine, but
Figure 4. MALDI spectra of sequence-specific base filling of a guanine
nucleobase (16a or 17a) at the abasic site in 3 via (a) reductive amination
and (b) amine acylation. See Table 2 for reaction conditions.
Figure 3. Nucleobase substrates for base-filling reactions.
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C O M M U N I C A T I O N S
Table 2. Yields of base-filling reactionsa
reductive amination
yield
(%, mismatched)
acylation
matched
base
yield
(%, matched)
yield
(%, matched)
yield
(%, mismatched)
entry
PNA duplexb
a
1N′TAC TGC TAG ACGC′
3C′ATG AC_ ATC TGCN′
G
91c
78c
81c
98c
58c
47c
2c
<2c
78d
87e
<2d
2(A)e
b
c
d
e
f
1N′TAC TGC TAG ACGC′
4C′ATG ACG _TC TGCN′
A
6(G)c
38d
73e
5(G)d
7(G)e
2N′CGT CTA GCA GTAC′
5C′GCA GA_ CGT CATN′
T
11(G), 4(C)c
<2c
8d
<2d
<2e
19(A), 13(G), 5(C)e
2N′CGT CTA GCA GTAC′
6C′GCA GAT _GT CATN′
C
66d
16e
<2d
26(G), 17(A)e
2N′CGT CTA GCA GTAC′
7C′_CA GAT CGT CATN′
G
13(A), 9(C)c
29(G), 11(T), 8(C)c
4(C), 3(G), 2(A)c
4(G), 4(A), 3(T)c
39e
42e
4e
16(A), 5(C)e
1N′TAC TGC TAG ACGC′
8C′_TG ACG ATC TGCN′
A
26(G), 7(C)e
g
h
i
2N′CGT CTA GCA GTAC′
9C′GCA GAT CGT CA_N′
T
15(C), 7(G), 6(A)e
10(A), 9(G), 9(T)e
1N′TAC TGC TAG ACGC′
10C′ATG ACG ATC TG_N′
C
7c
28e
56e
9e
1N′TAC TGC TAG ACGC′
13C′ATG AC_ _TC TGCN′
G-A
C-G
38c
21c
7(G-G), 3(G-C),
3(C-A)c
23(G-G), 5 (G-C),
4(C-A), 3(A-A)e
j
14N′TGT ACG CGA TCAC′
15C′ACA TG_ _CT AGTN′
6(G-G), 4(A-G)c
16(G-G), 12(A-G),
3(T-G)e
a Yields shown each represent the mean of 10 measurements from two independent reactions and are accurate to (10%. b Lys(Me2) and capping
groups are omitted for clarity. c 3 µM template, 2.5 µM reactant strand, 150 µM each 16a-d, 15 mM NaBH3CN, 10 mM phosphate buffer, pH 6.2, 5
°C, 24 h. d 3 µM template, 2.5 µM reactant strand, 830 µM each 17a-d, 9 mM sNHS, 13 mM EDC, 100 mM MOPS buffer, pH 7.5, 5 °C, 24 h. e 3
µM template, 2.5 µM reactant strand, 830 µM each 17a-d, 13 mM DMT-MM, 100 mM MOPS buffer, pH 7.5, 2 °C, 24 h.
lower disorder of double helices away from strand termini as key
determinants of base-filling reaction efficiency.
Acknowledgment. This work was supported by the Howard
Hughes Medical Institute and the NIH/NIGMS (R01GM065865).
To explore the ability of base filling to support the transfer of multiple
consecutive bases, we attempted the addition of two neighboring bases to
the middle of the PNA strand (Table 2, entries i-j). We used PNA
template 1 to test the tandem addition of guanine and adenine and
introduced a new template (14) to test the tandem addition of cytosine
and guanine. We observed significant yields of doubly base-filled product
for both reductive amination (up to 38%) and amine acylation (up to 56%),
although yields were lower than the analogous single-base addition
reactions. Consistent with our observations above, purines added more
efficiently than pyrimidines (comparing the addition of adenine+guanine
with that of cytosine+guanine), and the reductive amination reactions
proceeded with higher selectivities than the acylation reactions.
In conclusion, we have achieved sequence-selective templated
nucleic acid synthesis through base filling. Using either reductive
amination or acylation reactions, a single base can be sequence-
specifically added to an abasic site on a PNA strand in the presence
of all four nucleobase monomers in the reaction mixture. We
observe that middle-of-strand addition is more efficient than end-
of-strand addition and that purines add more efficiently than
pyrimidines, highlighting the role of base-stacking interactions in
promoting base-filling reactions. Base-pairing interactions may also
play a significant role, as in general guanine adds more efficiently
than adenine and cytosine adds more efficiently than thymine.
Additionally, we observe that reductive amination generally provides
higher yields and selectivities than the amine acylation chemistries
tested, likely resulting from the reversible formation of a stable iminium
intermediate in the former reaction. These findings lay an experimental
foundation for the development of more complex information transfer
systems, including the possibility of exponential replication of nucleic
acids through base-filling reactions.
Supporting Information Available: Experimental procedures and
compound characterization data. This material is available free of charge
via the Internet at http://pubs.acs.org.
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