An extremely stable and orthogonal DNA base pair with a simplified three-carbon backbone

Article abstract of DOI:10.1021/ja043904j

A nucleotide C₃HQ with a minimal three-carbon backbone displays unprecedented pairing strength and orthogonality in a homopair C₃HQ:C₃HQ in the presence of one equivalent of Cu²⁺. The pairing stability in DNA ev

Full text of DOI:10.1021/ja043904j

Published on Web 12/13/2004
An Extremely Stable and Orthogonal DNA Base Pair with a Simplified
Three-Carbon Backbone
Lilu Zhang and Eric Meggers*
Department of Chemistry, UniVersity of PennsylVania, 231 South 34th Street, Philadelphia, PennsylVania 19104
Received October 6, 2004; E-mail: meggers@sas.upenn.edu
DNA plays an increasingly important role in bioorganic chem-
istry, biotechnology, and material science due to its ingeniously
simple complementary base-pairing rule: A pairs with T, and G
with C. It is apparent that modifying the chemical and physical
properties of DNA without affecting the complementary base
pairing will have a tremendous impact on future applications. For
example, increasing the electrical conductivity of DNA by chemical
modification of the base pairs may allow for the self-assembly of
complex molecular-scale electrical devices.1
We started out with the goal to design functional unnatural
nucleotides that are structurally simplified and thus much easier to
access in large quantities, while retaining the desired base-pairing
properties. For example, a simple acyclic DNA-like backbone would
reduce the synthetic complexity dramatically. However, Schneider
and Benner demonstrated more than a decade ago, that even a single
flexible acyclic nucleotide in DNA already leads to a strong
destabilization of the duplex.2 We envisioned that it may still be
possible to use a simplified backbone by overcompensating the
potential loss of preorganization with interstrand base-pairing
strength. We here present a surprising outcome of this design
strategy which resulted in an exceptionally stable and orthogonal
artificial base pair having a minimal acyclic three-carbon backbone.
First, we designed a base-pairing scheme with superior stability.
Base-pairing schemes with alternate H-bonding,3 pairing through
hydrophobic packing,4 and metal coordination-driven base pairing5
Figure 1. Design rationale for a simplified completely artifical base pair
in DNA.
have been developed. We decided to create a DNA base pair with
superior stability by combining hydrophobic forces and strong metal
coordination in one base pair as shown in Figure 1. We chose
8-hydroxyquinoline as a promising candidate because it has an
extended hydrophobic aromatic surface, ideal for undergoing
hydrophobic stacking in DNA, in addition to being an exceptionally
strong bidentate ligand for a variety of transition metal ions.6
The nucleotide HQ containing a regular 2′-deoxyribose backbone
(see Figure 1) was synthesized following a lengthy standard route
(13 steps in the longest linear sequence plus one diastereomer
separation) and incorporated in the middle of a 15mer deoxyoli-
gonucleotide as shown in Figure 2. In the absence of any transition
metal ions, a 1:1 mixture of complementary 15mer oligonucleotides
containing the HQ:HQ homopair displays a melting temperature
(TM) of 36.1 °C, as determined by UV-monitored thermal dena-
Figure 2. UV-melting curves of duplex deoxyoligonucleotides with
different base pairs at position X:Y. (A) HQ:HQ (TM ) 36.1 °C without
Cu2+, TM ) 65 °C with 1 equiv of Cu2+), dA:dT (TM ) 41.3 °C), dG:dC
(TM ) 44.6 °C). (B) Melting curves of mismatches with HQ in the presence
of 1 equiv of Cu2+. HQ:T (TM < 30 °C), HQ:C (TM ) 32.5 °C), HQ:A
(TM ) 34.7 °C), HQ:G (TM ) 35.4 °C). The hyperchromicity was in all
cases 15-24%. Experiments were performed in 10 mM sodium phosphate,
pH 7.0, 50 mM NaClO4, with 2 µM of each single strand, and under argon
atmosphere to prevent photooxidation of HQ. Cu(NO3)2 was used as the
turation. For comparison, the duplexes containing a dA:dT or dG:
dC instead of HQ:HQ melt at 41.3 °C and 44.6 °C, respectively.
Mismatches between natural bases show stabilities of 31 °C (dG:
dT) or less under our experimental conditions. Thus, HQ:HQ forms
quite stable base pairing even in absence of any transition metal
ions. This effect can be attributed to the high hydrophobicity of
HQ.
Upon the addition of just one equivalent of Cu2+, the melting
point increases by 29 °C reaching a TM of 65 °C. The TM of HQ:
HQ in the presence of Cu2+ is more than 20 °C higher compared
to the natural base pairs dA:dT and dG:dC (Figure 2A). To the
source for Cu2+
.
best of our knowledge, a base pair with such strong interstrand
pairing properties is unprecedented. It can be expected that in this
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J. AM. CHEM. SOC. 2005, 127, 74-75
10.1021/ja043904j CCC: $30.25 © 2005 American Chemical Society

C O M M U N I C A T I O N S
Figure 3. Synthesis of the C3-nucleotide 4 for the automated nucleic acid
synthesis. (a) First, addition of sec-BuLi (THF, -78 °C) to 2, followed by
MgBr2 (in situ prepared from BrCH2CH2Br and Mg), and cat. CuI, followed
by the addition of epoxide 1 (69%). (b) TBSCl, DMAP, imidazole. (c) Cs2-
CO3. (d) tBuCOCl, DMAP. (e) TBAF (f) (iPr2N)(OCH2CH2CN)PCl,
(iPr)2EtN (49% over steps b-f).
Figure 4. (A) UV-melting curves of the shown duplex above (2 µM each
strand) containing the acyclic nucleobase pair C3HQ:C3HQ without and
with one equivalent of Cu2+ (TM ) 70.5 °C). The hyperchromicity is 16%
and 18%, respectively. (B) CD-spectra of the same duplex (10 µM each
strand) in the presence of 1 equiv of Cu2+ at 80, 70, 60, 50, 40, and 25 °C.
Experiments were performed in 10 mM sodium phosphate, pH 7.0, 50 mM
NaClO4, and under argon atmosphere. Cu(NO3)2 was used as the source
base pair the two 8-hydroxyquinoline ligands coordinate a central
Cu2+ ion in an approximately square planar fashion as indicated in
Figure 1.5b
To test the pairing specificity of the Cu2+-dependent HQ:HQ
base pair, we measured the TM’s of all mismatches with the natural
strands. The melting curves are shown in Figure 2B. Compared to
HQ:HQ(+Cu2+) the mispairs with natural bases lead to a strong
decrease in melting temperatures of more than 30 °C. Thus, the
base pair HQ:HQ(+Cu2+) shows exceptionally strong base-pairing
strength and orthogonality and is therefore a promising candidate
to reduce the complexity of the backbone in the next step.
We chose the three-carbon derivative C3HQ as shown in Figures
1 and 3. This backbone is derived from Eschenmoser’s L-R-
threofuranosyl nucleoside7 by eliminating a CH2O unit from the
tetrahydrofuran ring, and we envisioned that this scaffold is
economically accessible by ring opening of “spring-loaded” ep-
oxides.8
for Cu2+
.
equivalent of Cu2+. It is quite a surprise that the pairing stability
and selectivity even exceeds those of the related base pair HQ:
HQ, having the regular deoxyribose backbone. This discovery of
a synergy between an artificial backbone and base-pairing scheme
opens new avenues for the economical design of modified oligo-
nucleotides with tailored properties.
Acknowledgment. We thank the University of Pennsylvania,
LRSM-MRSEC, and the ACS Petroleum Research Fund (Type G
Grant) for supporting this research. We are also grateful for support
from the laboratories of Dr. Ivan J. Dmochowski (UV-melting) and
Dr. Feng Gai (CD-measurements). We thank Dr. Adam Peritz for
support with oligonucleotide synthesis.
Accordingly, inexpensive commercially available S-(-)-glycidol
was tritylated to 1 and the epoxide regioselectively ring-opened
with metalated 2 to yield 3 in 69% yield (Figure 3). Exchange of
the protection group at the 8-hydroxyquinoline followed by
introduction of a phosphoramidite yielded the building block 4 for
the automated oligonucleotide synthesis. This procedure is short
and simple and does not require any separation of isomers.
We next investigated the stability of this new homopair C3HQ:
C3HQ in duplex DNA. Without Cu2+, no stable duplex formation
is observed (Figure 4A). However, upon the addition of just one
equivalent of Cu2+, C3HQ:C3HQ gives cooperative UV-melting
with a TM of 70.5 °C. The UV-melting experiments are in agreement
with CD measurements, which demonstrate a temperature-depend-
ent melting of a B-form duplex (Figure 4B). It is very surprising
Supporting Information Available: Experimental procedures for
the synthesis of HQ, C3HQ and their incorporation into DNA. This
material is available free of charge via the Internet at http://pubs.acs.org.
References
(1) See, for example: Okamoto, A.; Tanaka, K.; Saito, I. J. Am. Chem. Soc.
2003, 125, 5066-5071.
(2) Schneider, K. C.; Benner, S. A. J. Am. Chem. Soc. 1990, 112, 453-455.
(3) Base pairs in DNA with altered H-bonding: Benner, S. A. Acc. Chem.
Res. 2004, 37, 784-797.
(4) Hydrophobic base pairs in DNA: (a) Kool, E. T.; Morales, J. C.; Guckian,
K. M. Angew. Chem., Int. Ed. 2000, 39, 990-1009. (b) Henry, A. A.;
Romesberg, F. E. Curr. Opin. Chem. Biol. 2003, 7, 727-733.
(5) Metallo-base pairing in DNA: (a) Meggers, E.; Holland, P. L.; Tolman,
W. B.; Romesberg, F. E.; Schultz, P. G. J. Am. Chem. Soc. 2000, 122,
10714-10715. (b) Atwell, S.; Meggers, E.; Spraggon, G.; Schultz, P. G.
J. Am. Chem. Soc. 2001, 123, 12364-12367. (c) Weizman, H.; Tor, Y.
J. Am. Chem. Soc. 2001, 123, 3375-3376. (d) Tanaka, K.; Yamada, Y.;
Shionoya, M. J. Am. Chem. Soc. 2002, 124, 8802-8803. (e) Tanaka, K.;
Tengeiji, A.; Kato, T.; Toyama, N.; Shiro, M.; Shionoya, M. J. Am. Chem.
Soc. 2002, 124, 12494-12498. (f) Zimmermann, N.; Meggers, E.; Schultz,
P. G.; J. Am. Chem. Soc. 2002, 124, 13684-13685. (g) Zimmermann,
N.; Meggers, E.; Schultz, P. G. Bioorg. Chem. 2004, 32, 13-25.
(6) Critically Selected Stability Constants of Metal Complexes Database,
NIST, 2001. For example, the dissociation constant of a 1:1 complex with
Cu2+ is around 1 × 10-12 M.
that the stability of the simplified base pair C3HQ:C3HQ(+Cu2+
)
surpasses that of HQ:HQ(+Cu2+) (∆TM ) + 5.5 °C). This is even
more remarkable since the C3-backbone is strongly destabilizing
for the natural A:T base pair (TM < 30 °C). We hypothesize that
the expanded C1′-C1′ distance in the 8-hydroxyquinoline base pair
can be accommodated with less strain in the slimmer acyclic
backbone. It is also noteworthy that no stable base pairing is
observed between C3HQ and the natural deoxynucleotides (TM’s
< 25 °C, 1 equiv of Cu2+).
(7) Scho¨ning, K.-U.; Scholz, P.; Guntha, S.; Wu, X.; Krishnamurthy, R.;
Eschenmoser, A. Science 2000, 290, 1347-1351.
(8) Epoxides are one of the priviledged functional group for “click chemis-
try”: Kolb, H. C.; Finn, M. G.; Sharpless, K. B. Angew. Chem., Int. Ed.
2001, 40, 2004-2021.
In summary, we have introduced a strategy for the design of a
simplified artificial base pair. The nucleotide C3HQ with a minimal
three-carbon backbone displays unprecedented pairing strength and
orthogonality in a homopair C3HQ:C3HQ in the presence of one
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