Synthesis and nonenzymatic template-directed polymerization of 2′-amino-2′-deoxythreose nucleotides

Article abstract of DOI:10.1021/ja411950n

Threose nucleic acid (TNA) is a potential alternative genetic material that may have played a role in the early evolution of life. We have developed a novel synthesis of 2′-amino modified TNA nucleosides (2′-NH ₂-TNA) based on a cycloaddition reaction between a glycal and an azodicarboxylate, followed by direct nucleosidation of the cycloadduct. Using this route, we synthesized the thymine and guanine 2′-NH₂-TNA nucleosides in seven steps with 24% and 12% overall yield, respectively. We then phosphorylated the guanine nucleoside on the 3′-hydroxyl, activated the phosphate as the 2-methylimidazolide, and tested the ability of the activated nucleotide to copy C₄ RNA, DNA, and TNA templates by nonenzymatic primer extension. We measured pseudo-first-order rate constants for the first nucleotide addition step of 1.5, 0.97, and 0.57 h^-1 on RNA, DNA, and TNA templates, respectively, at pH 7.5 and 4 C with 150 mM NaCl, 100 mM N-(hydroxylethyl)imidazole catalyst, and 5 mM activated nucleotide. The activated nucleotide hydrolyzed with a rate constant of 0.39 h^-1, causing the polymerization reaction to stall before complete template copying could be achieved. These extension rates are more than 1 order of magnitude slower than those for amino-sugar ribonucleotides under the same conditions, and copying of the TNA template, which best represented a true self-copying reaction, was the slowest of all. The poor kinetics of 2′-NH ₂-TNA template copying could give insight into why TNA was ultimately not used as a genetic material by biological systems.

Full text of DOI:10.1021/ja411950n

Article
pubs.acs.org/JACS
Synthesis and Nonenzymatic Template-Directed Polymerization of
2′-Amino-2′-deoxythreose Nucleotides
J. Craig Blain,† Alonso Ricardo,† and Jack W. Szostak*
Howard Hughes Medical Institute and Department of Molecular Biology and Center for Computational and Integrative Biology,
Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
S
* Supporting Information
ABSTRACT: Threose nucleic acid (TNA) is a potential
alternative genetic material that may have played a role in the
early evolution of life. We have developed a novel synthesis of
2′-amino modified TNA nucleosides (2′-NH2-TNA) based on a
cycloaddition reaction between a glycal and an azodicarbox-
ylate, followed by direct nucleosidation of the cycloadduct.
Using this route, we synthesized the thymine and guanine 2′-
NH2-TNA nucleosides in seven steps with 24% and 12% overall
yield, respectively. We then phosphorylated the guanine
nucleoside on the 3′-hydroxyl, activated the phosphate as the 2-methylimidazolide, and tested the ability of the activated
nucleotide to copy C4 RNA, DNA, and TNA templates by nonenzymatic primer extension. We measured pseudo-first-order rate
constants for the first nucleotide addition step of 1.5, 0.97, and 0.57 h−1 on RNA, DNA, and TNA templates, respectively, at pH
7.5 and 4 °C with 150 mM NaCl, 100 mM N-(hydroxylethyl)imidazole catalyst, and 5 mM activated nucleotide. The activated
nucleotide hydrolyzed with a rate constant of 0.39 h−1, causing the polymerization reaction to stall before complete template
copying could be achieved. These extension rates are more than 1 order of magnitude slower than those for amino-sugar
ribonucleotides under the same conditions, and copying of the TNA template, which best represented a true self-copying
reaction, was the slowest of all. The poor kinetics of 2′-NH2-TNA template copying could give insight into why TNA was
ultimately not used as a genetic material by biological systems.
nucleobases on the order of minutes14 and they are compatible
INTRODUCTION
■
with fatty acid vesicles.15
The early development of life must have proceeded through
simple cells capable of Darwinian evolution to the complex life
forms that exist today. To better understand this process, efforts
(L)-α-Threose nucleic acid (TNA) (Figure 1B), based on the
four carbon sugar threose, has also generated considerable
interest since Eschenmoser and colleagues discovered that it is
able to form stable Watson−Crick duplexes with itself, DNA,
and RNA.16−18 Since TNA could have been synthesized by the
same potentially prebiotic processes that have been proposed
are underway to synthesize model protocells composed of a
self-replicating compartment and self-replicating genetic ma-
terial.1 Simple processes of growth and division have been
developed for fatty acid vesicles.2 However, despite recent
advances in autocatalytic RNA synthesis3,4 and ribozyme-
catalyzed RNA-dependent RNA polymerization,5 no self-
replicating nucleic acid system capable of open-ended evolution
has yet been developed.
As an alternative to ribozyme-mediated replication, activated
nucleotides can be used to copy sequences without enzymatic
catalysis. Building on the pioneering work of Leslie Orgel and
colleagues,6−8 we and others have been developing non-
enzymatic, template-directed primer extension using amino-
sugar nucleotides as models for genetic replication, since these
nucleotides show enhanced rates of polymerization due to the
greater nucleophilicity of the amine.9−15 In particular, we have
studied the polymerization of the acyclic 2′-amino-2′-
deoxyglycerol nucleotides,12 2′-amino-2′,3′-dideoxyribose nu-
cleotides,13,15 and 3′-amino-2′,3′-dideoxy-ribose nucleotides.14
These systems are attractive as models of genetic self-
replication, since they have the potential to copy all four
Figure 1. Chemical structures of (A) RNA (DNA), (B) threose
nucleic acid (TNA), and (C) 2′-amino-2′-deoxythreose nucleic acid
(2′-NH2-TNA).
Received: November 22, 2013
Published: January 10, 2014
© 2014 American Chemical Society
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for RNA,19,20 it may have played a role in the early evolution of
life.21 In support of this hypothesis, TNA has been used as a
template for the nonenzymatic polymerization of activated
ribonucleotides,22 and in vitro selection techniques have been
used to isolate functional TNA sequences23,24 based on the
enzymatic copying of DNA to TNA and vice versa.25−29
Since TNA has a shortened five atom repeating backbone
unit, the interphosphate distance in a TNA−TNA duplex is
only 5.9 Å.30 As a result, it has a shallow and wide minor
groove, similar to A-form DNA and RNA,30 and binds more
tightly to RNA than DNA.31 TNA residues adopt a unique 4′-
exo sugar pucker with the 2′- and 3′-hydroxyl groups axial,
which maximizes the interphosphate distance.31,32 Since the
backbone unit has only four fully rotatable bonds, as opposed
to five in RNA, the entropic cost of trapping a single-stranded
TNA oligonucleotide into a duplex is less than with RNA or
DNA.33,34 As a result, we hypothesized that single-stranded
TNA might form a structure preorganized for favorable
nucleotide binding and primer extension. Template preorgani-
zation has previously been shown to enhance the rate of
nonenzymatic polymerization for altritol (ANA), hexitol
(HNA), and locked (LNA) nucleic acids.13,35,36
of 2-amino carbohydrates.38−40 Although this reaction had not
been used to synthesize nucleosides or four carbon sugars, the
general scheme was compatible with our needs.
We synthesized the glycal 4 from (R)-β-hydroxy-γ-butyr-
olactone (1), which can be obtained in >99% e.e. As shown in
Scheme 1, we first protected the hydroxyl group with a tert-
Scheme 1. Synthesis of the Nucleosidation Precursor by [4 +
a
2] Cycloaddition
a
Reagents and conditions: (a) TBDPSCl, imidazole, DMF, 20 °C, 23
Given the desirable properties of TNA and its potential
importance in the origin of life, we became interested in testing
the activated nucleotides of 2′-amino-2′-deoxythreose nucleic
acid (2′-NH2-TNA) (Figure 1C) in nonenzymatic primer
extension experiments. The Eschenmoser group has synthe-
sized the adenine and thymine residues of the 2′- and 3′-amino-
modified versions of TNA and shown that they have similar
base-pairing properties to regular TNA, although the 2′-amino
derivative formed significantly weaker duplexes.33,34 They have
also shown that the 2′-amino modification enhances the rate of
nonenzymatic ligation of two TNA oligonucleotides on a TNA
template.37 Similar to 2′-aminodideoxyribonucleosides,13 the
threose ring would hold the activated phosphate and
nucleophilic amine of a monomer apart from each other to
minimize cyclization, a known issue with amino-sugar
nucleotides.12,14
In the route developed by Eschenmoser et al., the thymine
2′-NH2-TNA nucleotide (8t) was synthesized from the
thymine TNA nucleoside, and the adenine 2′-NH2-TNA
nucleoside was synthesized by trans-nucleosidation of 8t.34
We first sought to develop a direct route for the synthesis of the
guanine 2′-NH2-TNA nucleoside (8g). We based our synthesis
on a [4 + 2] cycloaddition reaction between an azodicarbox-
ylate and glycal that was previously developed to synthesize
trans 2-amino, 3-hydroxyl carbohydates38−40 due to its high
efficiency and stereo- and regioselectivities. We then synthe-
sized the 3′-phosphor-2-methylimidazolide derivative (2-
MeImpntG) and tested it in nonenzymatic primer extension
experiments on C4 RNA, DNA, and TNA templates. This work
provides a novel synthetic approach to amino-sugar nucleosides
and a better understanding of the potential role threose-based
nucleic acids could play as the genetic material in a model
protocell.
h, 95%; (b) DIBAL-H, THF, −78 °C, 1 h, 95%; (c) MsCl, Et3N,
CH2Cl2, −40 °C, 1 h; (d) reflux, 10 h, 74%; (e) BTCEAD, irradiate
350 nm, cyclohexane, 20 °C, 16 h, 83%.
butyldiphenylsilyl (TBDPS) group, since it is bulky and
nonelectron withdrawing. Next, we reduced the lactone to
lactol 3 with diisobutylaluminum hydride (DIBAL-H) and
converted the 1-hydroxy group to a good leaving group by
mesylation, after which thermal elimination afforded glycal 4.
These three steps were performed at greater than 5 g scale with
a 67% overall yield. For the cycloaddition reaction, we mixed
the glycal with bis(2,2,2-trichloroethyl) azodicaroboxylate
(BTCEAD) in cyclohexane with constant 350 nm irradiation
to allow conversion of the trans azodicarboxylate to the more
reactive cis isomer.41 Previous reports have used dichloro-
methane as a cosolvent;39 however, we obtained higher yields
in neat cyclohexane.
Conveniently, the cycloaddition product 5 proved to be an
effective electrophile for one-pot nucleosidation catalyzed by
trimethylsilyl trifluoromethanesulfonate (TMSOTf)42 (Scheme
2). Both the thymine and guanine nucleobases were
glycosylated with high selectivity for the desired α anomer,
likely indicating a mechanism involving direct displacement at
C1. For guanine, we used the O6-diphenylcarbamoyl protected
nucleobase for high N9 regioselectivity.43 For the thymine
hydrazide 6t, the reported reduction conditions39 with zinc
powder in acetic acid with one equivalent of acetone were
effective in producing the protected nucleoside 7t. However,
with the guanine hydrazide 6g these conditions resulted in
product degradation and reduction of the N2-acetyl group to an
ethyl group.
We therefore screened various alternative reduction strat-
egies and ultimately found that refluxing a mixture of indium
powder and aluminum foil in ethanol−saturated aqueous
ammonium chloride44−46 gave the highest yield of protected
nucleoside 7g. Finally, we fully deprotected the intermediates
to the free amino nucleosides 8g and 8t. Overall, the yields of
8g and 8t from lactone 1 were 12% and 24%, respectively, in
seven steps. The structure of each was solved by single-crystal
X-ray diffraction (Figure 2). The pseudorotation phase angle47
RESULTS
■
Synthesis of 2′-NH2-TNA Nucleosides. We sought to
develop an efficient synthesis that could yield multiple 2′-NH2-
TNA nucleosides from a common intermediate with high
enantiomeric purity. To this end, we decided to base our
synthesis on a [4 + 2] cycloaddition reaction between a glycal
and an azodicarboxylate, previously developed for the synthesis
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Previously, we have synthesized activated amino-sugar nucleo-
tides using phosphorus(V) oxychloride without protecting the
nucleobase.13,14 However, since the 3′-hydroxyl group of
nucleoside 8g is a secondary hydroxyl and is further sterically
hindered by its proximity to the nucleobase, this reaction was
sluggish and not selective. Since the 3′-hydroxyl of TNA
nucleosides has proven reactive toward phosphitylation
reagents,34 we accessed 2-MeImpntG through phosphityla-
tion-oxidation of the 3′-hydroxyl of protected 8g followed by
activation according to the standard procedure developed by
Orgel and colleagues.48 We measured the rate of hydrolysis of
2-MeImpntG by 31P NMR spectroscopy under the primer
extension reaction conditions and observed a pseudo-first-order
rate constant of 0.39 h−1, corresponding to a half-life of 1.8 h
(Figure 3B).
Scheme 2. Synthesis of 2′-Amino-2′-deoxythreose
a
Nucleosides from Cycloadduct 5
Primer Extension of 2-MeImpntG on RNA, DNA, and
TNA Templates. Once we had synthesized the activated 2′-
NH2-TNA nucleotide 2-MeImpntG, we tested its reactivity in
nonenzymatic template-directed primer extension experiments.
To allow for a direct comparison to previous results from other
amino-modified nucleic acid systems,13,14 we used the same
reaction conditions: 5 mM monomer, pH 7.5, 150 mM NaCl,
and 100 mM N-(hydroxyethyl)imidazole (HEI). The HEI
additive is an imidazole derivative that catalyzes both
aminonucleotide polymerization and degradation,13,14 likely
by exchanging with 2-methylimidazole to form a highly reactive
zwitterionic intermediate. We used a DNA primer with a 3′-
amino dideoxyribose terminal nucleotide and 3′-C4A2-5′ RNA,
DNA, and TNA templates (Figure 4A).
a
Reagents and conditions: (a) N2-acetyl-O6-(diphenylcarbamoyl)-
guanine, BSA, CH3CN, 80 °C, 10 min, cooled to 0 °C and added 5
and then TMSOTf, 0 °C, 15 min, 20 °C, 1.5 h, 79%; (b) indium
powder, aluminum foil, 2:1 EtOH−sat. aq. NH4Cl, reflux, 3 h, 45%;
(c) TBAF, THF, 20 °C, 3 h; (d) NH4OH, 35 °C, 22 h, 62%; (e) 5,
thymine, BSA, CH3CN, 80 °C, 10 min, cooled to 0 °C and added
TMSOTf, 0 °C, 30 min, 20 °C, 45 min, 91%; (f) zinc powder, acetic
acid, 20 °C, 1 h; (g) acetone, zinc powder, 5 h, 71%; (h) TBAF, THF,
20 °C, 3 h, 68%.
Activated nucleotide 2-MeImpntG was an effective monomer
for nonenzymatic primer extension, with only 28% of the
primer remaining after 1 h and 42% converted to full-length
product after 6 h on the RNA template (Figure 4). To compare
the reaction rates on the different templates, we first fit the
fraction of primer remaining to a first-order exponential decay
and obtained pseudo-first-order rate constants of 1.5, 0.97, and
0.57 h−1 for the RNA, DNA, and TNA templates, respectively
(Figure 4B). As expected, the RNA template, which binds more
tightly to TNA,17 was a more effective template than DNA.
However, the TNA template, which we expected to form a
preorganized single strand for favorable primer extension, was
the least effective template. The reactions reached a plateau
with 8−9% primer remaining, possibly indicating a population
of primer that was chemically modified or not properly bound
to the template. In the absence of HEI catalyst, the rate of
polymerization was 19 times slower on average, and hydrolysis
was 87 times slower (Figure S1, Supporting Information).
Figure 2. X-ray crystal structures of the 2′-amino-2′-deoxythreose
nucleosides with a (A) guanine (8g) and (B) thymine (8t) nucleobase.
Both furanose rings have a C3′-endo sugar pucker.
for nucleoside 8g and the two molecules of 8t in the crystal
asymmetric unit ranged from 0° to 23°, indicating a C3′-endo
sugar pucker characteristic of residues in A-form DNA and
RNA.
Synthesis of 2-MeImpntG. After synthesizing the nucleo-
sides, we turned our attention to the synthesis of the activated
nucleotide 2-MeImpntG (Scheme S1, Supporting Information
and Figure 3A) for use in primer extension reactions.
DISCUSSION
■
We have developed a novel synthesis of 2′-NH2-TNA
nucleosides 8g and 8t in 12% and 24% overall yield,
respectively, from lactone 1 in seven steps (Schemes 1 and
2). For comparison, Eschenmoser and colleagues synthesized
8t in nine steps from L-ascorbic acid in 10% overall yield.17,18,34
Both nucleosides crystallized with a C3′-endo sugar pucker
characteristic of residues in A-form DNA and RNA (Figure 2).
However, TNA residues prefer a C4′-exo sugar pucker in the
context of a duplex.30−32 The C3′-endo and C3′-exo sugar
puckers have also been reported in crystallized N6-benzoylade-
nine and thymine TNA nucleosides,17 respectively, suggesting
that the C4′-exo sugar pucker is preferred only in the context of
a duplex. Since both the C3′-endo and C4′-exo sugar puckers
hold the 2′- and 3′-substituents in an extended axial
Figure 3. (A) Structure of the activated 2′-NH2-TNA nucleotide 2-
MeImpntG. (B) Plot of the hydrolysis of 2-MeImpntG measured by
31P NMR with 100 mM HEPES pH 7.5, 150 mM NaCl, 100 mM HEI,
5 mM potassium phosphate reference, and 10% D2O at 4 °C. The
natural logarithm of the fraction of activated nucleotide remaining was
fit to a line; the slope yielded a pseudo-first-order rate constant of 0.39
h−1.
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Figure 4. Nonenzymatic primer extension of 2-MeImpntG on C4 RNA, DNA, and TNA templates. (A) Schematic diagram of the primer extension
reaction. A 5′-TAMRA-labeled DNA primer with a 3′-amino terminus was hybridized to each template and incubated with 5 mM 2-MeImpntG
monomer at pH 7.5 and 4 °C with 150 mM NaCl and 100 mM HEI as catalyst. (B) Plot of the amount of primer remaining as a fraction of the total
lane integration against time. The plot was fit to a single exponential decay to measure pseudo-first-order rate constants of 1.5, 0.97, and 0.57 h−1 and
■
▲
plateau values of 8%, 9%, and 9% for the RNA (•), DNA ( ), and TNA ( ) templates, respectively. (C) PAGE analysis of the products of the
primer extension reactions.
conformation required for the duplex, the C4′-exo sugar pucker
is likely required for the optimal orientation of the nucleobase
and phosphodiester backbone. The 2′-amino group may also
affect the preferred conformation.
present at intermediate time points (Figure 4C). A similar
trend was observed for the 3′-amino-2′,3′-dideoxyribose
system14 and may be due to a change in helical geometry as
the amino nucleotides extend from the DNA primer.
Alternatively, the monomers could form short oligomers that
subsequently add to the primer. The monomer hydrolyzed
surprisingly quickly with a half-life of 1.8 h (Figure 3B), making
it only slightly more stable than its 3′-amino-2′,3′-dideoxyr-
ibose analogue, which cyclizes with a half-life of 1.2 h.14
Interestingly, the ranking of the polymerization rates on the
different templates was RNA > DNA > TNA. We expected
polymerization to be faster on the A-form RNA template than
the B-form DNA template, since TNA prefers an A-form
geometry due to its shortened backbone.31 However, we
similarly expected polymerization to be fastest on the TNA
template. TNA is also a worse template than RNA for the
polymerization of activated ribonucleotides.22 The restrained
geometry of TNA either makes it less able to bind tightly to
nucleotides or for them to adopt the geometry necessary for
phosphoryl transfer once bound. These alternate hypotheses
could be tested by measuring the rate of polymerization at a
range of monomer concentrations on the different templates,
combined with direct physical measurements of monomer
binding to templates.
The cycloaddition−nucleosidation−reduction scheme we
have developed could potentially be applied to other 2′-
amino nucleosides. Stereoselectivity of the cycloaddition
reaction has been maintained with 3-deoxy glycals by using
more distal bulky protecting groups.40 Therefore, it could
potentially be used to access the 2′-amino-2′,3′-dideoxyribose
nucleoside series, which performs well in nonenzymatic
polymerization experiments but is currently difficult to
synthesize.13 The more common 2′-hydroxyl nucleosides
could potentially be accessed by using phenanthrenequinone
instead of azodicarboxylates. It has previously been shown that
phenanthrenequinone can undergo similar stereoselective [4 +
2] cycloaddition chemistry with glycals to form new C1−O and
C2−O bonds,49 although it is not known if the cycloadduct
formed is a good substrate for nucleosidation.
The monomer 2-MeImpntG was able to extend a primer on
C4 RNA, DNA, and TNA templates (Figure 4). This finding
demonstrates the first nonenzymatic polymerization of a
threose-based nucleotide, a reaction that is critical for its
potential use as a self-replicating genetic material. The pseudo-
first-order rate constants for the first addition to the primer
ranged from 0.57 to 1.5 h−1 (Figure 4B). For comparison, in
the 2′-amino and 3′-amino-2′,3′-dideoxyribose systems, the
activated guanine nucleotides completely copy a C4 RNA
template in under 5 min with the same conditions, indicating a
rate constant of at least 42 h−1. It is possible that the
constrained sugar of 2-MeImpntG limits its ability to adopt the
geometry necessary for the phosphoryl transfer when bound to
the template. We also found that the addition steps did not
progress evenly, with less +2 product than +1, +3, and +4
Taken together, our results show that 2′-NH2-TNA could
potentially be used as a self-replicating genetic material, but its
slow rate of polymerization compared to monomer hydrolysis,
especially on the TNA template, makes other systems more
attractive. Furthermore, the limited reactivity of the 3′-hydroxyl
group could make the prebiotic phosphorylation of TNA
nucleosides difficult. If these results hold for TNA monomers,
TNA would be inferior to RNA as a genetic polymer in the
origin of life, which may be why it was ultimately not used
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dry ice bath. A 1 M solution of DIBAL-H in toluene (38 mL, 38
mmol) was added dropwise over 1 h. The reaction was quenched with
methanol (3 mL) and then warmed to room temperature. Saturated
sodium potassium tartrate (150 mL) was added, and the mixture was
poured into 400 mL of EtOAc and stirred for 2 h. The organic layer
was washed with water (150 mL), washed with brine (150 mL), dried
over MgSO4, and filtered, and the crude was purified by flash
chromatography (5−20% EtOAc in hexanes) to afford protected lactol
3 (9.58 g, 95%) as a clear oil: Rf = 0.28, 1:4 EtOAc−hexanes; 1H NMR
(400 MHz, DMSO-d6) anomer 1: δ 7.63−7.54 (m, 4H, H-Ph), 7.48−
7.37 (m, 6H, H-Ph), 6.06 (d, J = 5.1 Hz, 1H, H−O−C1), 5.44 (m, 1H,
H−C1), 4.49 (m, 1H, H−C3), 3.76 (dd, J = 9.1, 4.9 Hz, 1H, H−C4),
3.55 (dd, J = 9.2, 2.4 Hz, 1H, H−C4), 1.94 (m, 1H, H−C2), 1.77
(ddd, J = 13.3, 6.3, 3.0 Hz, 1H, H−C2), 0.97 (s, 9H, H-t-Bu); anomer
2: δ 7.63−7.54 (m, 4H, H-Ph), 7.48−7.37 (m, 6H, H-Ph), 6.11 (d, J =
5.0, 1H, H−O−C1), 5.20 (m, 1H, H−C1), 4.28 (m, 1H, H−C3),
3.68−3.60 (m, 2H, H−C4), 2.10 (m, 1H, H−C2), 1.67 (m, 1H, H−
C2), 0.98 (s, 9H, H-t-Bu); 13C NMR (100 MHz, DMSO-d6) δ 135.2,
135.1, 133.3, 133.2, 129.9, 127.9, 97.6, 97.3, 72.9, 72.6, 72.1, 71.5, 43.3,
42.4, 26.7, 18.7, 18.6; HRMS (m/z): [M + Na+]+ calcd. for
C20H26O3Si, 365.1543, obsd. 365.1544.
(R)-tert-Butyl((2,3-dihydrofuran-3-yl)oxy)diphenylsilane (4).
Protected lactol 3 (8.94 g, 27.6 mmol) and Et3N (14.6 mL, 104.7
mmol) were dissolved in anhydrous CH2Cl2 (200 mL) under argon
and then cooled to −40 °C with an acetonitrile−dry ice bath. MsCl
(2.7 mL, 34.9 mmol) was added slowly, and the reaction was stirred at
−40 °C for 1 h, warmed to room temperature, and refluxed for 10 h.
The reaction mixture was concentrated to 100 mL and then purified
by flash chromatography (1:1 CH2Cl2−hexanes) to afford protected
glycal 4 (6.59 g, 74%) as a clear oil: Rf = 0.57, 1:1 CH2Cl2−hexanes;
1H NMR (400 MHz, CDCl3) δ 7.68−7.64 (m, 4H, H-Ph), 7.45−7.41
(m, 2H, H-Ph), 7.40−7.36 (m, 4H, H-Ph), 6.49 (apt. d, J = 2.6 Hz,
1H, H−C1), 5.01 (dddd, J = 7.2, 2.6, 2.6, 0.9 Hz, 1H, H−C3), 4.96
(dd, J = 2.6, 2.6 Hz, 1H, H−C2), 4.23 (dd, J = 10.5, 2.6 Hz, 1H, H−
C4), 4.04 (dd, J = 10.5, 7.20 Hz, 1H, H−C4), 1.04 (s, 9H, H-t-Bu);
13C NMR (100 MHz, DMSO-d6) δ 150.5, 135.5, 135.4, 133.8, 133.6,
despite the likely coproduction of threose- and ribose-based
nucleosides through prebiotic chemistry.19,20
MATERIALS AND METHODS
■
General. All reagents and solvents were purchased from Sigma−
Aldrich, Alfa Aesar, or Toronto Research Chemicals, except for
deuterated solvents, which were purchased from Cambridge Isotope
Laboratories. Flash chromatography was performed on a Biotage SP1
instrument with HP-Sil columns. NMR spectroscopy was performed
on a 400 MHz Varian spectrometer (Oxford AS-400) operating at 25
°C, unless otherwise specified. Spectra were referenced to the solvent
peak according to published values,50 except for 31P spectra, which
were referenced to orthophosphate or phosphoric acid (0 ppm). High-
resolution mass spectrometry was carried out on a Waters Q-TOF
micro LC-MS or an Agilent 6520 QTOF LC-MS. Low resolution
electrospray ionization mass spectrometry (ESI-MS) was performed
on a Bruker Esquire 6000 with direct injection. Preparative high-
performance liquid chromatography (HPLC) purification was
performed on a Varian ProStar instrument with a Dynamax Microsorb
C18 column (250 mm × 21.4 mm). Data analysis was performed using
Prism software (GraphPad).
Primer Extension Reaction. The conditions for the primer
extension reaction were as follows: 200 mM HEPES pH 7.5, 150 mM
NaCl, 100 mM HEI pH 7.5, 5 mM 2-MeImpntG, 0.3 μM primer, 1.5
μM template, 4 °C. The primer sequence was 5′-TAMRA-GCG TAG
ACT GAC TGG-3′-NH2. The sequence of the RNA, DNA, and TNA
templates was 5′-AAC CCC CCA G(U/T)C AG(U/T) C(U/T)A
CGC-3′, with the C4 template region in bold. The TNA template was
composed of DNA, except for the underlined region. The primer was
provided by Dr. Sergei Gryaznov (Geron Corp.), the TNA template
was provided by Dr. John Chaput (Arizona State University), and the
RNA and DNA templates were purchased from IDT DNA.
The total reaction volume was 30 μL. At each time point, a 5 μL
aliquot was taken, mixed with 10 μL of kill buffer (100 mM EDTA, 4.8
M urea, 1X TBE), and precipitated by ethanol. Time points were taken
at 1, 2, 3, 4.5, 6, and 24 h. Samples were analyzed by 20% urea−TBE
denaturing polyacrylamide gel electrophoresis (PAGE) and imaged on
a Typhoon Scanner 9400 (GE Healthcare) and integrated using
ImageQuant TL software (GE Healthcare).
Kinetics of 2-MeImpntG Hydrolysis. The kinetics of 2-
MeImpntG hydrolysis were measured under the same conditions as
the primer extension reaction, except with 3 mM 2-MeImpntG, 100
mM HEPES pH 7.5, 5 mM potassium phosphate reference, and 10%
D2O. Time points were taken over the course of 6 h. At each time
point, a 31P NMR spectrum was measured, the phosphate signal was
set to a chemical shift of 0 ppm and an integration of 1, and the
integrations of the activated (−12.02 ppm) and hydrolyzed (1.15
ppm) nucleotide were then measured and normalized to the initial
integration.
130.2, 130.1, 128.3, 128.2, 103.7, 77.1, 74.8, 27.0, 19.0; ESI-MS (m/z):
[M + Na+]+ calcd. for C20H24O2Si, 347.1, obsd. 347.1.
(4aR,7R,7aR)-2,2,2-Trichloroethyl-7-((tert-butyl-
diphenylsilyl)oxy)-3-(2,2,2-trichloroethoxy)-4a,6,7,7a-tetrahy-
dro-1H-furo[3,2-e][1,3,4]oxadiazine-1-carboxylate (5). Pro-
tected glycal 4 (1.00 g, 9.25 mmol) and bis(2,2,2-trichloroethyl)-
azodicarboxylate (1.65 g, 13.0 mmol) were dissolved in 18 mL of
anhydrous cyclohexane under argon in a sealed 40 mL glass vial. The
solution was irradiated at 350 nm while stirred at room temperature
(rt) for 16 h. Volatiles were removed in vacuo, and the crude residue
was purified by flash chromatography (0−10% EtOAc in hexanes) to
afford cycloadduct 5 (1.83 g, 83%) as a colorless foam: Rf = 0.52, 3:7
1
ether−hexanes; H NMR (400 MHz, CDCl3) δ 7.6−7.3 (m, 10H, H-
Ph), 5.69 (d, J = 4.6 Hz, 1H, H−C1), 5.20 (dd, J = 4.6, 6.6 Hz, 1H,
H−C2), 4.70 (br. s, 4H, H2C), 4.43 (apt. q, J = 6.4 Hz, 1H, H−C3),
3.90 (dd, J = 9.3, 7.0 Hz, 1H, H−C4), 3.80 (dd, J = 9.4, 5.9 Hz, 1H,
H−C4), 1.07 (s, 9H, H3C); 13C NMR (100 MHz, CDCl3) δ 135.8,
135.8, 135.3, 134.9, 132.2, 130.4, 130.3, 129.8, 128.1, 128.1, 127.9,
99.3, 95.2, 94.2, 74.2, 26.9, 26.7, 19.2; HRMS (m/z): [M + H+]+ calcd.
for C26H28Cl6N2O6Si, 702.9921, obsd. 702.9895.
(R)-4-((tert-Butyldiphenylsilyl)oxy)dihydrofuran-2(3H)-one
(2). A mixture of lactone 1 (10 g, 94.0 mmol) and imidazole (16.7 g,
245 mmol) in DMF (36 mL) under argon was cooled on ice, and then,
TBDPSCl (32 mL, 119 mmol) was added slowly. The mixture was
warmed to 20 °C, stirred for 23 h, and then, poured into ddH2O (400
mL). The product was extracted with CH2Cl2 (3 × 250 mL), and the
combined organic fractions were washed with brine (200 mL), dried
over MgSO4, filtered, and concentrated to 100 mL. The concentrate
was filtered through a bed of silica with CH2Cl2 and then triturated
with hexanes to afford protected lactone 2 (28.3 g, 95%) as a white
Bis(2,2,2-trichloroethyl) 1-((3R,4R)-2-(2-Acetamido-6-((di-
phenylcarbamoyl)-oxy)-9H-purin-9-yl)-4-((tert-butyl-
diphenylsilyl)oxy)tetrahydrofuran-3-yl)hydrazi-ne-1,2-dicar-
boxylate (6g). N2-Acetyl-O6-(diphenylcarbamoyl)-guanine (2.15 g,
5.54 mmol) was suspend in anhydrous acetonitrile (40 mL) under
argon. Bis(trimethylsilyl)acetamide (2.8 mL, 11.5 mmol) was added,
and the suspension was stirred at 80 °C for 10 min to dissolve the
silylated guanine. The solution was cooled to 0 °C, and then,
cycloadduct 5 (3.26 g, 4.62 mmol) was added in acetonitrile (30 mL)
followed by the dropwise addition of TMSOTf (1.08 mL, 5.98 mmol).
The reaction was stirred at 0 °C for 15 min and then at rt for 1.5 h.
Volatiles were removed in vacuo, and the residue was dissolved in
EtOAc (100 mL), washed with 5% NaHCO3 (2 × 100 mL), washed
with brine (100 mL), dried over MgSO4, filtered, and concentrated in
1
solid: Rf = 0.69, CH2Cl2; H NMR (400 MHz, CDCl3) δ 7.62 (d, J =
6.9 Hz, 4H, H-Ph), 7.46 (dd, J = 7.2 Hz, 2H, H-Ph), 7.40 (dd, J = 7.1
Hz, H-Ph), 4.56 (m, 1H, H−C3), 4.21 (dd, 1H, J = 9.8, 2.5 Hz, H−
C4), 4.16 (dd, 1H, J = 9.8, 4.6 Hz, H−C4), 2.50 (d, 2H, J = 3.9 Hz,
H−C2), 1.06 (s, 9H, H-t-Bu); 13C NMR (100 MHz, CDCl3) δ 175.9,
135.8, 133.0, 130.4, 128.2, 75.9, 69.2, 38.1, 26.9, 19.2; HRMS (m/z):
[M + H+]+ calcd. for C20H24O3Si, 341.1568, obsd. 341.1563.
(4R)-4-((tert-Butyldiphenylsilyl)oxy)tetrahydrofuran-2-ol (3).
Protected lactone 2 (10.02 g, 29.4 mmol) was dissolved in anhydrous
THF (100 mL) under argon and cooled to −78 °C with an acetone−
2037
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Journal of the American Chemical Society
Article
vacuo to a crude. The crude was purified by flash chromatography
(20−60% EtOAc in hexanes) to afford protected hydrazide 6g as a
white foam (4.01 g, 79%). Rf = 0.72, 6% MeOH in CH2Cl2; 1H NMR
(400 MHz, DMSO-d6, 40 °C) Note: broad multiplets were observed
due to stable rotamers δ 8.47 (br d, 1H, H−C8), 7.77−7.32 (m, 20H,
H-Ph), 6.20 (s, 1H, H−C1′), 5.65 (br s, 1H, H−C3′), 5.00−4.30 (br
m, 6H, H−C4′ and H-Troc), 3.87 (br m, 1H, H−C2′), 2.29 (br s, 3H,
H−Ac), 1.04 (br s, 9H, H-tBu); 13C NMR (100 MHz, DMSO-d6, 60
°C) δ 169.9, 155.2, 153.8, 152.1, 149.7, 143.9, 143.5, 141.4, 135.5,
135.3, 135.0, 132.4, 132.1, 130.0, 129.9, 129.6, 129.5, 129.3, 128.8,
127.7, 127.3, 126.8, 126.4, 120.3, 95.1, 94.5, 74.9, 59.4, 54.5, 26.5, 26.3,
18.4; HRMS (m/z): [M + H+]+ calcd. for C46H44Cl6N8O9Si,
1091.1204, obsd. 1091.1254.
2-Acetamido-9-((3R,4R)-3-amino-4-((tert-butyl-
diphenylsilyl)oxy)tetrahydro-furan-2-yl)-9H-purin-6-yl diphe-
nylcarbamate (7g). Protected hydrazide 6g (4.54 g, 4.15 mmol),
indium powder (1.90 g, 16.6 mmol), and aluminum foil (1.29 g, 47.9
mmol) were suspended in EtOH (67 mL) and sat. aq. NH4Cl (33 mL)
and refluxed under argon with vigorous stirring for 3 h. The hot
reaction mixture was then filtered through a short bed of Celite,
diluted with water (200 mL), adjusted to pH 11 with 1 M NaOH, and
then, extracted with CH2Cl2 (3 × 100 mL). The combined organic
phase was dried over MgSO4, filtered, and concentrated in vacuo to a
crude. The crude was purified by flash chromatography (0−4% MeOH
in CH2Cl2) to afford protected aminonucleoside 7g as a white foam
(1.35 g, 45%). Rf = 0.29, 6% MeOH in CH2Cl2; 1H NMR (400 MHz,
DMSO-d6) δ 8.56 (s, 1H, H−C8), 7.57−7.27 (m, 20H, H-Ph), 5.80
(d, J = 2.7 Hz, 1H, H−C1′), 4.17 (dd, J = 7.4, 3.3 Hz, 1H, H−C3′),
4.11 (dd, J = 9.1, 3.1 Hz, 1H, H−C4′), 4.04 (dd, J = 9.4, 5.1 Hz, 1H,
H−C4′), 4.01 (m, 1H, H−C2′), 2.22 (s, 3H, H−Ac), 0.88 (s, 9H, H-
tBu); 13C NMR (100 MHz, DMSO-d6) δ 169.1, 155.1, 154.2, 152.1,
150.1, 143.5, 141.7, 135.3, 135.2, 132.6, 132.6, 130.1, 130.0, 128.0,
127.9, 120.4, 91.3, 78.4, 74.7, 63.6, 26.6, 24.8, 18.5; HRMS (m/z): [M
+ H+]+ calcd. for C40H41N7O5Si, 728.3011, obsd. 728.2943.
9-(2′-Amino-2′-deoxy-α-L-threofuranosyl)guanine (8g). Pro-
tected aminonucleoside 7g (234 mg, 321 mmol) was dissolved in THF
(15 mL) under argon. A 1 M solution of TBAF in THF (0.48 mL, 480
mmol) was added, and the reaction was stirred at rt for 3 h. Volatiles
were removed in vacuo, and the residue was transferred to a pressure
vessel in MeOH (5 mL), 28% NH4OH (15 mL) was added, and the
sealed flask was heated at 35 °C for 22 h. Volatiles were removed in
vacuo, and the residue was purified by flash chromatography (2−20%
MeOH in CH2Cl2) to afford aminonucleoside 8g (50 mg, 62%) as a
white solid. Rf = 0.04, 3:7 methanol−dichloromethane; 1H NMR (400
MHz, DMSO-d6) δ 7.88 (s, 1H, H−C8), 5.54 (d, J = 3.4 Hz, 1H, H−
C1′), 4.06 (dd, J = 8.8, 4.8 Hz, 1H, H−C4′), 4.00 (m, 1H, H−C3′),
3.89 (dd, J = 8.8, 3.2 Hz, 1H, H−C4′), 3.55 (apt. t, J = 3.1 Hz, 1H, H−
C2′); 13C NMR (100 MHz, DMSO-d6) δ 157.7, 154.5, 152.0, 137.0,
117.4, 90.5, 77.4, 75.0, 65.0; HRMS (m/z): [M + H+]+ calcd. for
C9H12N6O3, 253.1044, obsd. 253.1045. Cambridge Crystallographic
Data Centre deposition number 967793.
9.3 Hz, H−C3′), 3.76 (br s, 1H, H−C2′), 1.73 (s, 3H, H2−CC5), 1.04
(s, 9H, H-tBu); 13C NMR (100 MHz, DMSO-d6) δ 163.8, 155.0,
153.0, 150.2, 135.2, 132.4, 130.2, 128.0, 95.4, 95.0, 83.4, 75.2, 73.9,
70.8, 26.6, 18.6, 12.2; HRMS (m/z): [M + H+]+ calcd. for
C31H34Cl6N4O8Si, 829.0350, obsd. 829.0341.
1-((3R,4R)-3-Amino-4-((tert-butyldiphenylsilyl)oxy)-tetrahy-
drofuran-2-yl)-5-methylpyrimidine-2,4(1H,3H)-dione (7t). Pro-
tected hydrazide 6t (250 mg, 301 μmol) was dissolved in glacial acetic
acid (10 mL) under argon. Zinc powder (950 mg) was added, and the
suspension was stirred vigorously for 1 h at rt. Acetone (0.04 mL, 544
μmol) was added, and the reaction was stirred for another 1 h. Finally,
more zinc powder (750 mg) was added, and the reaction was stirred
for another 4 h. The suspension was filtered, washed with MeOH,
concentrated in vacuo, and coevaporated with toluene to obtain a
crude foam. The crude was purified by flash chromatography (0 to 2%
MeOH in CH2Cl2 with 0.1% Et3N to afford protected nucleoside 7t as
1
a white foam (99 mg, 71%). Rf = 0.35, 6% MeOH in CH2Cl2; H
NMR (400 MHz, DMSO-d6, 40 °C) δ 7.62−7.42 (m, 11H, H-Ph and
H−C6), 5.50 (d, J = 2.1 Hz, H−C1′), 4.10−4.00 (m, 3H, H−C4′ and
H−C3′), 3.43 (m, 1H, H−C2′), 1.73 (d, J = 1.2, H3C−C5), 0.98 (s,
9H, H-tBu); 13C NMR (100 MHz, DMSO-d6) δ 163.9, 150.5, 136.4,
135.2, 132.6, 130.0, 128.0, 108.3, 92.6, 78.5, 75.4, 64.4, 26.5, 18.6, 12.3;
ESI-MS (m/z): [M + H+]+ calcd. for C25H31N3O4Si, 466.2, obsd.
466.1.
1-(2′-Amino-2′-deoxy-α-L-threofuranosyl)thymine (8t). Pro-
tected nucleoside 7t (203 mg, 450 μmol) was dissolved in anhydrous
THF (15 mL) under argon. A 1 M solution of tetrabutylammonium
fluoride in THF (0.67 mL, 670 μmol) was added, and the solution was
stirred at rt for 3 h. The solution was concentrated in vacuo, and the
crude was purified by flash chromatography (2−8% MeOH in
CH2Cl2) and then precipitated from ether and trituration with CH2Cl2
to remove excess tetrabutylammonium to afford nucleoside 8t as a
1
white powder (70 mg, 68%). Rf = 0.08, 8% MeOH in CH2Cl2; H
NMR (400 MHz, DMSO-d6) δ 7.61 (d, J = 1.2 Hz, 1H, H−C6), 5.55
(d, J = 3.1 Hz, 1H, H−C1′), 4.04 (dd, J = 5.0, 9.7 Hz, 1H, H−C4′),
3.93 (m, J = 2.5 Hz, 1-H, H−C4′), 3.92 (m, 1H, H−C3′), 3.23 (dd, J =
2.7 Hz, 1H, H−C2′), 1.76 (d, J = 1.2 Hz, 3H, H3C−C5); 13C NMR
(100 MHz, DMSO-d6) δ 163.9, 150.7, 137.1, 108.3, 91.8, 75.9, 74.5,
64.0, 12.3; HRMS (m/z): [M + H+]+ calcd. for C9H13N3O4, 228.0979,
obsd. 228.0990. Cambridge Crystallographic Data Centre deposition
number 967794.
ASSOCIATED CONTENT
* Supporting Information
■
S
Scheme of the synthesis of the activated 2′-NH2-TNA
nucleotide 2-MeImpntG, figure of the nonenzymatic primer
extension and hydrolysis of 2-MeImpntG in the absence of HEI
with associated procedures, thermal ellipsis representations of
X-ray crystal structures, experimental procedures and character-
ization data for the synthesis of 2-MeImpG, experimental
procedures for X-ray crystallography, and X-ray crystallography
data in cif file format. This material is available free of charge via
the Internet at http://pubs.acs.org.
Bis(2,2,2-trichloroethyl)-1-((3R,4R)-4-((tert-butyl-
diphenylsilyl)oxy)-2-(5-methyl-2,4-dioxo-3,4-dihydro-pyrimi-
din-1(2H)-yl)tetrahydrofuran-3-yl)hydrazine-1,2-dicarboxylate
(6t). Thymine (1.25 g, 9.91 mmol) and cycloadduct 5 were suspended
in anhydrous acetonitrile (76 mL) under argon. Bis(trimethylsilyl)-
acetamide (7.25 mL, 29.7 mmol) was added, and the suspension was
stirred at 80 °C for 10 min to dissolve the silylated thymine. The
solution was cooled to 0 °C, and then, TMSOTf (1.24 mL, 6.86
mmol) was added dropwise. The reaction was stirred at 0 °C for 30
min and then at rt for 45 min. Volatiles were removed in vacuo, and
the residue was dissolved in CH2Cl2 (400 mL) and washed with 5%
NaHCO3 (300 mL). The aqueous phase was extracted further with
CH2Cl2 (2 × 100 mL), dried over MgSO4, filtered, and concentrated
in vacuo to a crude. The crude was purified by flash chromatography
(0−2% MeOH in CH2Cl2) to afford protected hydrazide 6t as a white
AUTHOR INFORMATION
Corresponding Author
szostak@molbio.mgh.harvard.edu
■
Present Address
†Ra Pharmaceuticals, One Kendall Square, Suite B14301,
Cambridge, Massachusetts 02139, United States.
Notes
The authors declare no competing financial interest.
1
foam (3.71 g, 91%). Rf = 0.40, 5% MeOH in CH2Cl2; H NMR (400
ACKNOWLEDGMENTS
We thank Dr. John Chaput for the TNA template, Dr. Sergei
Gryaznov for the primer oligonucleotide, and members of our
■
MHz, DMSO-d6, 50 °C) δ 11.30 (s, 1H, H−N3), 10.41 (br s, 1H, H−
N-Troc), 7.63−7.35 (m, 11H, H-Ph and H−C6), 6.07 (br s, 1H, H−
C1′), 5.00−4.65 (m, 6H, H2−CCCl3 and H2−C4′), 4.07 (app d, J =
2038
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Journal of the American Chemical Society
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979.
laboratory for helpful discussions and comments on the
manuscript. We also thank Dr. Shao-Liang Zheng for his help
with X-ray data collection and structure determination. This
research was funded in part by grant CHE-0809413 from the
National Sciences Foundation. J.W.S. is an Investigator of the
Howard Hughes Medical Institute.
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