Nylon/DNA: Single-stranded DNA with a covalently stitched nylon lining

Article abstract of DOI:10.1021/ja035186r

The synthesis of DNA/nylon ladder oligomers is described. Three stages of the development are addressed: the synthesis of 2′-β-substituted phosphoramidites, the deprotection/purification protocols of ODNs modified with both amino and carboxyl groups, and

Full text of DOI:10.1021/ja035186r

Published on Web 08/05/2003
Nylon/DNA: Single-Stranded DNA with a Covalently Stitched Nylon Lining
Lei Zhu, Philip S. Lukeman, James W. Canary,* and Nadrian C. Seeman*
Department of Chemistry, New York UniVersity, New York, New York 10003
Received March 16, 2003; E-mail: james.canary@nyu.edu; ned.seeman@nyu.edu
During the past half-century the known functions of nucleic acids
have expanded from genetic information carriers and messengers
to include catalysis and regulation of a number of cellular
processes.1 In addition, many nucleic acid-based structures have
been developed with medicinal applications, catalytic properties,
and prebiotic chemistry implications.1 Notable examples are anti-
sense agents2, e.g., peptide nucleic acid (PNA),3 deoxynucleic
guanidine (DNG),4 and locked DNA (LNA).5 DNAzymes have been
developed with functionalized nucleotidyl groups to enhance
catalytic abilities.6 TNA, (3′,2′)-R-L-threose nucleic acid, has been
suggested as an evolutionary progenitor of RNA or DNA or both.7
We wish to develop new nucleic acid-based materials to expand
the applications and scope of DNA nanotechnology.8 A number of
topological targets, objects, devices, and two-dimensional (2D)
Figure 1. Schematic illustration of a ladder oligomer synthesis. R1:
-DMTr; R2: -P(NiPr2)(OCH2CH2CN); green and blue dots are carboxyl
arrays have been prepared from conventional DNA molecules with
defined sequences and unusual structural motifs.9 Analogous DNA/
organic polymer conjugates of these structures offer practical
interest. For example, DNA 2D arrays10 may serve as platforms,
to assemble molecular electronic devices with nanometer precision,
or as templates to synthesize non-DNA polymeric 2D networks
that would enjoy the stability and other favorable properties of
organic materials. Single-stranded DNA has been used to direct
polymerization of DNA oligos with unnatural linkages.11,19 Our goal
would be to harness the full power of DNA nanotechnology, which
depends on both secondary and tertiary DNA structural motifs, to
assemble organic materials with unique structures. Our approach
also entails regiospecific chemistry between non-DNA entities.
Here, we report the first nucleic acid-based structure in which a
DNA backbone has been covalently linked to an organic polymer,
nylon. The synthesis was accomplished in three stages: preparation
of 2′-â-substituted phosphoramidites, synthesis of oligonucleotides
(ODNs) with appended amine and carboxylate groups, and coupling
of the pendent groups to form oligopeptide strands covalently linked
at each base pair to give a nylon/DNA ladder polymer (Figure 1).
The strategy is general and could be used to generate a variety of
nylon-based materials, or to direct the assembly of other organic
polymers.
Initial synthetic protocols attempted 2′-OH alkylation of a
protected ribonucleoside, but this approach was inefficient for
hindered electrophiles.12 However, 2′-deoxy-2′-mercaptouridine13
was alkylated with 1a and 1b to afford 2′-S-alkylated nucleosides
exclusively (Scheme 1). Tritylation and phosphitylation of 2b
afforded the modified phosphoramidite 4b. Two extra steps were
taken to replace the stable phthalimidyl groups in 3a with DNA
synthesizer-friendly trifluoroacetyl groups.14 Phosphitylation of the
resulting nucleoside 3e afforded amino-modified phosphoramidite
4e. Monoamino and carboxyl-modified phosphoramidites 4d and
4f were prepared by similar methods. The respective nucleotidyl
groups are shown in deprotected form in Figure 2.
and amino groups, respectively; p1 and p2 are their respective protecting
groups. Black vertical chains with alternate “P” represent a nucleic acid
backbone; the red vertical chain represents the nylon backbone; the violet
horizontal lines (right) represent “rungs” on the ladder oligomer.
Scheme 1. Synthesis of 2′-Deoxy-2′-alkylthiouridine
Phosphoramiditesa
a Reagents and conditions: (i) RI (1a, 1b) or RBr (1c, 1d), DIEA/
CH3CN, rt, 10 h; (ii) DMTrCl/pyridine, rt, 2 h; (iii) NH2NH2/CH3OH, reflux,
3 h; (iv) CF3CO2Et/CH3OH, rt 16 h; (v) ClP(NiPr2)(OCH2CH2CN)/CH2Cl2,
TEA, DMAP, rt, 30 min. (a: R ) CH2CH(CH2CH2NPhth)2; b: R )
CH2CH(CH2CH2CO2Bn)2; c: R ) (CH2)4NPhth; d: R ) (CH2)4CO2Et;
e: R ) CH2CH(CH2CH2NHCOCF3)2; f: R ) (CH2)4NHCOCF3).
Figure 2. Structures of 2′-modified nucleotidyl units.
strands from the CPG support. The conventional concentrated
ammonium hydroxide treatment could not be used due to aminolysis
between NH3 and the ester moieties.15 Deprotection with prevention
of the Michael addition between acrylonitrile and deprotected
amines16 was accomplished by including 10% piperidine in metha-
nolic NaOH. To prevent acetate ions (from hydrolysis of the 5′-
acetyl groups of the capped failure strands) from competing as
alternative coupling partners, they were eliminated by triple ethanol
precipitation prior to being subjected to amide-coupling conditions.
The concurrent deprotection of amino and carboxyl groups and the
removal of ODNs from CPG support was therefore achieved with
this customized protocol. The ODNs were characterized by MALDI-
TOF mass spectrometry17 (Table 1).
Modified phosphoramidites were incorporated into 16-mer ODNs
through conventional ODN synthesis. The sequences are shown in
Table 1. Methanolic NaOH was used to deprotect and remove the
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J. AM. CHEM. SOC. 2003, 125, 10178-10179
10.1021/ja035186r CCC: $25.00 © 2003 American Chemical Society

C O M M U N I C A T I O N S
Table 1. Sequences and MALDI-TOF MS Characterization of Synthetic ODNs
1a. This research has been supported by Grants GM-29554 from
NIGMS, N00014-98-1-0093 from ONR, CHE-0079702, DMI-
0210844, EIA-0086015, DMR-01138790, and CTS-0103002 from
NSF, F30602-01-2-0561 from DARPA/AFSOR, and the NYU
Technology Transfer Fund.
Supporting Information Available: Synthesis and characterization
of compounds 2-4 and all the ODNs (PDF). This material is available
free of charge via the Internet at http://pubs.acs.org.
References
Figure 3. Chemical structures of DNA/nylon conjugates.
(1) (a) Pearson, H. Nature 2003, 421, 312. (b) Dennis, C. Nature 2002, 418,
122. (c) Couzin, J. Science 2002, 298, 2296.
(2) Uhlmann, E.; Peyman, A. Chem. ReV. 1990, 90, 543.
(3) Nielsen, P. E. Acc. Chem. Res. 1999, 32, 624.
(4) Barawkar, D. A.; Bruice, T. C. J. Am. Chem. Soc. 1999, 121, 10418.
(5) (a) Vester, B.; Lundberg, L. B.; Sørensen, M. D.; Babu, B. R.; Douthwaite,
S.; Wengel, J. J. Am. Chem. Soc. 2002, 124, 13682. (b) Demidov, V. V.
Trends Biotechnol. 2003, 21, 4.
(6) (a) Santoro, S. W.; Joyce, G. F.; Sakthivel, K.; Gramatikova, S.; Barbas,
C. F., III. J. Am. Chem. Soc. 2000, 122, 2433. (b) Thum, O.; Ja¨ger, S.;
Famulok, M. Angew. Chem., Int. Ed. 2001, 40, 3990. (c) Lermer, L.;
Roupioz, Y.; Ting, R.; Perrin, D. M. J. Am. Chem. Soc. 2002, 124, 9960.
(7) (a) Scho¨ning, K.-U.; Scholz, P.; Guntha, S.; Wu, X.; Krishnamurthy, R.;
Eschenmoser, A. Science 2000, 290, 1347. (b) Chaput, J. C.; Ichida, J.
K.; Szostak, J. W. J. Am. Chem. Soc. 2003, 125, 856.
Figure 4. MALDI-TOF MS of 5 (a), and the coupled product 5C (b).
(8) Seeman, N. C. Trends Biotechnol. 1999, 17, 437.
(9) Seeman, N. C. Nature 2003, 421, 427.
(10) Winfree, E.; Liu, F.; Wenzler, L. A.; Seeman, N. C. Nature 1998, 394,
539.
(11) Li, X.; Zhan, Z.-Y. J.; Knipe, R.; Lynn, D. G. J. Am. Chem. Soc. 2002,
124, 746.
(12) Zhu, L.; dos Santos, O.; Seeman, N. C.; Canary, J. W. Nucleotides
Nucleosides Nucleic Acids 2002, 21, 723.
(13) (a) Divakar, K. J.; Mottoh, A.; Reese, C. B.; Sanghvi, Y. S. J. Chem.
Soc., Perkin Trans. 1 1990, 969. (b) Ozaki, H.; Momiyama, S.; Yokotsuka,
K.; Sawai, H. Tetrahedron Lett. 2001, 42, 677.
(14) Telser, J.; Cruickshank, K. A.; Morrison, L. E.; Netzel, T. L. J. Am. Chem.
Soc. 1989, 111, 6966.
(15) Berthod, T.; Pe´tillot, Y.; Guy, A.; Cadet, J.; Molko, D. J. Org. Chem.
1996, 61, 6075.
(16) Avino, A. M.; Eritja, R. Nucleosides Nucleotides 1994, 13, 2059.
(17) (a) Pieles, U. Zu¨rcher, W.; Scha¨r, M.; Moser, H. E. Nucleic Acid Res.
1993, 21, 3191. (b). Li, Y. C. L.; Cheng, S.-W.; Chan, T.-W. D. Rapid
Commun. Mass Spectrom. 1998, 12, 993.
(18) (a) Kunishima, M.; Kawachi, C.; Hioki, K.; Terao, K.; Tani, S. Tetrahedron
2001, 57, 1551. (b) Liu, D. R.; Gartner, Z. J.; Kanan, M. W. Angew.
Chem., Int. Ed. 2002, 41, 1796.
(19) (a) Schmidt, J. G.; Christensen, L.; Nielsen, P. E.; Orgel, L. E. Nucleic
Acids Res. 1997, 25, 4792. (b) Seitz, O.; Mattes, A. Angew. Chem., Int.
Ed. 2001, 40, 3178.
(20) (a) Sarracino, D.; Richert, C. Bioorg. Med. Chem. Lett. 1996, 6, 2543.
(b) Berggren, W. T.; Takova, T.; Olson, M. C.; Eis, P. S.; Kwiatkowski,
R. W.; Smith, L. M. Anal. Chem. 2002, 74, 1745.
(21) These estimates are lower limits, as small amounts of sodium in the spectra
obscure and artificially inflate the starting material peak.
(22) In 5C, a less likely topological isomer is possible under these reaction
conditions. Control experiments were performed to study the distance
dependence of the coupling reaction between amino and carboxyl groups
separated by a spacer. Strands 5′-(dT)xUC(dT)nUN(dT)y (x + n + y ) 14,
n ) 0, 1, 2, 3, 6, 10) were subjected to amide-bond promoting conditions.
It was found that the coupling yield was highly dependent upon the length
of the spacer (dT)n. When n g 2, the yield was less than 50%; when n )
6 or 10, coupled products were barely detectable. Therefore, the amide
bonds were biased to form between amino and carboxyl groups on adjacent
nucleotidyl residues.
ODN 1 was first subjected to amide-coupling conditions. Both
condensing agents DMT-MM18 and EDC19 proved effective in
promoting the intrastrand amide-forming reaction between UN and
UC under various buffer conditions. DMT-MM was preferred, as
it did not leave residual covalent adducts. The yield of the coupling
reaction was estimated by MALDI-TOF analysis.20 The yield of
ODN 1C from 1 was estimated to be more than 95%, whereas the
yield of 2C with three amide bonds was 78%, which also put the
single amide-bond forming yield over 95%.21 A control coupling
reaction using an ODN with regular T residues replacing UC in 2
showed no mass loss.
Isomers 3 and 4 were treated under coupling conditions to afford
ODNs with two amide bonds closing two fused 21-member rings
containing both a phosphodiester backbone and the newly formed
aliphatic carboxamide structure, as characterized by MALDI-TOF
MS (Table 1). The condensation of ODN 5 yielded three amide
bonds to form 5c (Figures 3 and 4) with three fused 21-member
rings.22 Structures of several of the product strands are indicated
in Figure 3. The linear polyamide backbone is essentially Nylon-
5,7.
The foregoing results should be extensible using additional bases
to more complex systems in which the self-assembling properties
of DNA can be exploited. Aside from obvious applications in the
antisense and gene therapy areas, we anticipate significant utility
in nanotechnology.
Acknowledgment. We thank Loraine Foley for performing
ODN synthesis and Osvaldo dos Santos for synthesizing compound
JA035186R
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