Glycerol nucleoside triphosphates: Synthesis and polymerase substrate activities

Article abstract of DOI:10.1021/ol062232u

The synthesis of (S)-glycerol nucleoside triphosphates (gNTPs) and the analysis of their substrate activities for enzymatic polymerization is described. NTPs with simplified carbohydrate backbones such as the tNTPs (α-L-threose-NTPs) are polymerase substr

Full text of DOI:10.1021/ol062232u

ORGANIC
LETTERS
2006
Vol. 8, No. 23
5345-5347
Glycerol Nucleoside Triphosphates:
Synthesis and Polymerase Substrate
Activities
Allen T. Horhota,† Jack W. Szostak,‡ and Larry W. McLaughlin*,†
Department of Chemistry, Merkert Chemistry Center, Boston College,
Chestnut Hill, Massachusetts 02467, and Howard Hughes Medical Institute and
Department of Molecular Biology, Massachusetts General Hospital,
Boston, Massachusetts 02114
mclaughl@bc.edu
Received September 8, 2006
ABSTRACT
The synthesis of (S)-glycerol nucleoside triphosphates (gNTPs) and the analysis of their substrate activities for enzymatic polymerization is
described. NTPs with simplified carbohydrate backbones such as the tNTPs ( -threose-NTPs) are polymerase substrates and offer the
potential to create non-natural aptamer sequences with simplified backbones through enzymatic means. The acyclic (S)-GNA was modeled
after the shortened -threofuranosyl backbone. Here we describe the synthesis of (S)-glycerol NTPs and initial enzymatic testing of this
r-L
r
further simplified nucleic acid backbone.
Glycerol nucleic acid (GNA), which has a simple acyclic
nucleic acid backbone, is of current interest1 as a potential
evolutionary progenitor of RNA. Simplified nucleic acid
backbones have been the focus of recent study. Since RNA
systems are structurally more complex, there are questions
regarding the ability of RNA polymers to have evolved
directly from a prebiotic enviroment.2,3 Eschenmoser et al.
have synthesized and screened a number of nucleic acid
systems based on alternative carbohydrate backbones and
examined their ability to self-pair and to pair with RNA/
DNA.4 The shortened and simplified R-L-threofuranosyl
backbone (TNA) possesses the ability to form both types of
duplexes.5,6 Threose nucleoside triphosphates (tNTPs) were
also shown to be remarkably efficient substrates for template-
directed enzymatic polymerization by Therminator DNA
polymerase; the investigation of TNA aptamers is now
feasible.7,8
Since TNA forms duplexes with RNA and DNA, the six-
bond backbone repeat that is characteristic of RNA and DNA
is not a critical requirement for progenitor nucleic acid
systems. Polymers based on simpler backbones may also
(4) Eschenmoser, A. Science 1999, 284, 2118.
(5) Scho¨ning, K.-U.; Scholz, P.; Wu, X.; Guntha, S.; Delgado, G.;
Krishnamurthy, R.; Eschenmoser, A. HelV. Chim. Acta 2002, 85, 4111.
(6) Scho¨ning, K.-U.; Scholz, P.; Guntha, S.; Wu, X.; Krishnamurthy,
R.; Eschenmoser, A. Science 2000, 290, 1347.
(7) Horhota, A.; Zou, K.; Ichada, J. K.; McLaughlin, L. W.; Szostak, J.
W.; Chaput, J. C. J. Am. Chem. Soc. 2005, 127, 7427.
† Boston College.
‡ Massachusetts General Hospital.
(1) (a) Zhang, L.; Peritz, A; Meggers, E. J. Am. Chem. Soc. 2005, 127,
4174. (b) Zhang, L.; Pertiz, A. E.; Carroll, P. J.; Meggers, E. Synthesis
2006, 645.
(2) Joyce, G. F. Nature 2002, 418, 214.
(3) Orgel, L. Crit. ReV. Biochem. Mol. Biol. 2004, 39, 99.
(8) Ichada, J. K.; Zou, K.; Horhota, A.; Yu, B.; McLaughlin, L. W.;
Szostak, J. W. J. Am. Chem. Soc. 2005, 127, 2802.
10.1021/ol062232u CCC: $33.50
© 2006 American Chemical Society
Published on Web 10/17/2006

exhibit useful enzymatic activity. A further simplification
of the TNA backbone involves opening the cyclic sugar to
yield an acyclic or glycerol (GNA) backbone that conserves
the five-bond backbone repeat of TNA (Figure 1). Oligomers
triphosphates from these dihydroxy monomers with POCl3
as the phosphorylating agent met with limited success.11,12
After POCl3 phosphorylation, rapid intramolecular cycliza-
tion by the secondary hydroxyl, prior to pyrophosphate
addition, generated the cyclic phosphodiester, likely as the
result of both proximity effects and backbone flexibility
(Scheme 1). To block this reaction pathway, the nucleobases
Scheme 1. Syntheses of gNTPs
Figure 1. RNA, TNA, and (S)-GNA polymers. (S)-Glycerol nucleic
acids are simplified nucleic acids containing the same 5-bond
repeating, but acyclic, backbone as TNA.
and secondary hydroxyls of the GNA monomers were
protected. Treatment of the monomers with DMT-Cl fol-
lowed by acetic anhydride placed the trityl group on the
primary hydroxyl and acetylated the secondary hydroxyl and,
when present, the nucleobase amino groups. Removal of the
trityl groups was accomplished by using 3% dichloroacetic
in dry dichloromethane and the products were purified by
flash chromatography with use of dry dichloromethane for
three column volumes before eluting with a methanol:di-
chloromethane mixture. With a protected secondary hydroxyl
(and nucleobase), we could phosphorylate using Eckstein’s13
phosphite method and these procedures resulted in excellent
overall yields of the desired gNTPs (Scheme 1).
Single and multiple nucleotide incorporation assays were
conducted to test substrate activities for gNTP monomers
with various polymerases. Primer extensions were carried
out by using radio-labeled primer annealed to appropriate
templates and incubated with a polymerase and one or more
gNTPs. The reactions were quenched by using stop buffer
and analyzed by 20% denaturing PAGE (Figure 3).
Polymerases and reverse transcriptases from differing
families (Therminator, Vent, Deep Vent, AMV-RT, M-
MuLV, HIV-RT, KF, KFexo-, Bst, and Taq) were tested for
polymerization activity on DNA primers and templates.
These enzymes exhibited the ability to readily incorporate
one gNTP, with Therminator DNA polymerase accomplish-
ing the N + 1 extension in the shortest time, but we have
not observed further extension of GNA attached to the DNA
or RNA primers.
based upon the GNA monomers have been prepared, and of
the two possible enantiomers, (S)-GNA forms the more stable
heteroduplexes with RNA.1
The synthesis of three-carbon nucleic acid backbones was
initially described by Holy9 and phosphoramidites were later
described by Andrews.10 R-(+)-Glycidol was used to define
the stereochemisty of the final product, obtained by ring
opening of the chiral epoxide. The propane-2,3-diol phos-
phoramidite monomers were compatible with standard solid-
phase coupling chemistries used to create GNA oligomers.
Meggers employed these strategies to construct poly-A and
poly-T GNA oligomers for their base-pairing studies.1 Here
we describe the syntheses of the acyclic glycerol-based gNTP
monomers (Figure 2), which we have used for enzymatic
incorporation into a primer/template complex.
Figure 2. (S)-Glycerol nucleoside triphosphates (gNTPs) of the
four common nucleobases.
The difficulty in forming longer strands may be due to a
number of factors: (i) loss of contacts between the primer/
template and polymerase as the growing strand incorporates
After ring opening of the R-(+)-glycidol with the four
common nucleobases, initial attempts to synthesize the
(10) Acevedo, O. L.; Andrews, R. S. Tetrahedron Lett. 1996, 37, 3931.
(11) Vaish, N. K.; Fraley, A. W.; Szostak, J. W.; McLaughlin, L.W.
Nucleic Acids Res. 2000, 28, 3316.
(9) (a) Holy, A.; Ivanova, G. S. Nucleic Acids Res. 1974, 1, 19. (b) Holy,
A. Collect. Czech. Chem. Commun. 1975, 40, 187.
(12) Burgerss, K.; Cook, D. Chem. ReV. 2000, 100, 2047.
(13) Ludwig, J.; Eckstein, F. J. Org. Chem. 1989, 54, 631.
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Org. Lett., Vol. 8, No. 23, 2006

polymerase binding and function. Incorporation of the initial
gNTP indicated that the monomers are sufficiently accom-
modated within the active site for successful incorporation
within a broad range of polymerases so substrate recognition
by the active site does not appear to play a limiting role.
Residues associated with duplex binding may be interesting
candidates for mutation for directed evolution of polymerases
capable of more efficient synthesis of long GNA oligo-
mers.14,15
Glycerol nucleic acids are promising molecules for
investigation of potential RNA progenitors. GNA’s simplicity
offers potential as an intermediate catalytic and/or informa-
tion storage polymer between the “Prebiotic” and “RNA”
worlds. However, a plausible prebiotic synthesis of GNA
has yet to be demonstrated. This structural simplicity also
offers ease of synthesis and functionalization which may lend
GNA to more diverse biochemical applications. Enzymatic
systems able to transcribe into or replicate long sequences
of GNA are necessary to fully investigate GNA sequence
space and their oligomer properties. To date, we have not
identified an enzyme system that possesses the ideal char-
acteristics, but we identified several polymerases that are
candidates for further evolution. The availablity of synthetic
GNA oligomers and now all four gNTPS provides the tools
needed to evolve the enzymatic machinery.
Figure 3. Single nucleotide incorporations of 2′-deoxy- (d) and
(S)-gNTPs (g) by Therminator DNA polymerase. Lane 1: 20 uL
of 250 nM radiolabeled 23-mer primer. Lanes 2-9: 20 uL of 250
nM primer annealed to an appropriate template, 74 µM Therminator
DNA polymerase, 10 mM KCl, 10 mM (NH4)2SO4, 20 mM Tris-
HCl, 2 mM MgSO4, 0.1% Triton X-100, 0.1 mg/mL BSA, 2.5 mM
DTT, at pH 8.8 and incubated at 55 °C. Lanes 2, 4, 6, and 8
contained 0.5 µM dNTP and were stopped after 1 min. Lanes 3, 5,
7, and 9 contained 500 µM gNTP and were incubated for 30 min.
Reactions were quenched with 8 M urea and 100 mM EDTA and
analyzed by 20% denaturing PAGE.
a greater number of GNA monomers; (ii) alignment of the
primer 2′-hydroxyl for attack at the R phosphate of the gNTP
after a GNA monomer has been added could be unfavorable
due to the smaller size, greater flexibility, or increased
rotational freedom along the glycerol backbone; and (iii) loss
of duplex stability with increased GNA content may result
in uncontrolled denaturation. On the other hand, no signifi-
cant differences in the elongations were observed for DNA
vs RNA templates. GNA has been reported to form a more
stable duplex with RNA than with DNA, but this did not
improve the extent of primer extension. Temperatures at or
below the reported Tm for the heteroduplexes also did not
result in improvement, though reduced enzyme efficiency
at lower temperatures may be a contributing factor.
Acknowledgment. This work was supported by awards
from the NSF to L.W.M. (MCB 0451488) and to J.W.S.
(CHE 0434507).
Supporting Information Available: Experimental pro-
cedures and characterization of all compounds along with
NMR spectra. This material is available free of charge via
the Internet at http://pubs.acs.org.
OL062232U
The structure of a GNA/RNA(DNA) duplex has yet to be
determined, so the conformation of a GNA-containing duplex
may be significantly different from that of “normal”, A- or
B-like structures, further reducing contacts availible for
(14) Henry, A. A.; Romesberg, F. E. Curr. Opin. Biotechnol. 2005, 16,
370.
(15) Holmberg, R. C.; Henry, A. A.; Romesberg, F. E. Biomed. Eng.
2005, 22, 39.
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