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Angewandte
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Scheme 1. Synthesis of phosphoramidite 1 for incorporation of D.
Reagents and conditions: a) DMT-Cl, pyridine, room temperature, 6 h,
99%; b) AD-mix-b, tBuOH, H2O, 08C, 24 h, 73%; c) tBDMS-Cl,
imidazole, CH2Cl2, room temperature, 16 h, 74%; d) (2-cyanoethyl)
N,N-diisopropyl chlorophosphoramidite, Me2NEt, CH2Cl2, RT, 45 min,
75%.
generated in four steps from 3-buten-1-ol (2, Scheme 1). First,
the primary hydroxy group was protected as a dimethoxytrityl
ether to give 3. Sharpless asymmetric dihydroxylation of the
alkene using AD-mix-b afforded the vicinal diol 4 in the
desired R configuration.[6] Silylation of the primary hydroxy
group of 4, followed by phosphitylation of the secondary
alcohol 5, yielded the phosphoramidite 1.
Figure 2. a) DNA-catalyzed synthesis of 2’,5’-branched nucleic acids.
b) 8LV13 deoxyribozyme for synthesis of 2’,5’-branched DNA.[8]
c) 9HR17 deoxyribozyme for connecting an RNA adaptor strand to
a DNA scaffold strand.[12] The first four nucleotides of each adaptor
strand form a base-paired (bp) region with the marked nucleotides of
loop B to generate a three-helix junction structure. LG=leaving group.
Upon mixing each of the four standard DNA nucleoside
phosphoramidites with 1, and using these mixtures in solid-
phase synthesis, combinatorial NDS libraries of deoxyribo-
zymes or any other functional DNA can be generated. The
next steps resemble the analysis performed in other interfer-
ence methods recently reported for characterization of func-
tional DNA, including CoMA and dNAIM.[7] First, active and
inactive library members are separated by electrophoresis or
affinity chromatography, for example, based on the reaction
catalyzed by a DNA enzyme of interest, or binding of a ligand
in the case of aptamers (Figure 1c). The readout of the
nucleoside deletion is then initiated by alkaline hydrolysis,
which leads to cleavage of the DNA strands at the deleted
nucleoside positions (i.e. at sites where D was incorporated),
and is followed by PAGE analysis and quantification of the
interference effect (Figure 1d). Missing hydrolysis bands in
the active fraction suggest that nucleosides at these positions
are essential for DNA function and must be retained. On the
other hand, hydrolysis bands that are present in the active
fraction reveal nucleosides that are dispensable for DNA
activity. Shortened DNA sequences are then generated and
functional assays are used to confirm the combinatorial
screening results. Initially positive variations are then com-
bined to look for synergistic improvements of activity, to
optimize the minimal functional sequence.
For our proof-of-concept demonstration of combinatorial
NDS mutagenesis of functional DNA, we chose two deoxy-
ribozymes that catalyze the synthesis of covalently branched
nucleic acids. These DNA enzymes activate the 2’-hydroxy
group of an internal branch-site nucleotide in the scaffold
strand substrate to form a new phosphodiester bond to the 5’-
terminus of the adaptor strand substrate (Figure 2a).[8]
Scaffold and adaptor strand can each be either DNA or
RNA, resulting in four possible combinations (note: a DNA
scaffold strand must have at least one internal ribonucleotide
that serves as a branch site). Deoxyribozymes have been
identified for each of these four combinations to generate
branched nucleic acids for various applications.[9] The most
prominent combination is 2’,5’-branched RNA, which resem-
bles the core structure of lariat RNA, the product generated
after the first step of RNA splicing.[10] RNA-DNA-branching
deoxyriboyzmes have been used to attach DNA constraints to
ribozymes for the regulation of RNA function, and the DNA-
catalyzed synthesis of 2’,5’-branched DNA has been consid-
ered as construction element for DNA nanotechnology.[11]
Herein, we study two deoxyribozymes that connect different
adaptor strands to the branch-site ribonucleotide of DNA
scaffold strands. The 8 LV13 deoxyribozyme uses 5’-adeny-
lated DNA as the adaptor substrate (Figure 2b),[8] and the
9HR17 deoxyribozyme uses 5’-triphosphorylated RNA to
attach an RNA adaptor to the DNA scaffold (Figure 2c).[12]
Both deoxyribozymes were selected in a structural context
that allows for the formation of a three-helix junction
structure and the formation of two single-stranded loop
regions. Loop A contains 33 nt, and loop B has 7 nt, which
together account for the 40 randomized nucleotides in the
DNA library used for in vitro selection.
We demonstrate that combinatorial NDS mutagenesis can
easily distinguish which of these 40 nt are required for the
activity of the deoxyribozyme, and which ones play no
essential role. The first step entailed the synthesis of the
respective DNA libraries, containing statistically distributed
D residues. To adjust the number of nucleoside deletions to
about one D per molecule, we studied the incorporation
efficiency of phosphoramidite 1 in competition with each of
the four standard DNA phosphoramidites (dN). Pentameric
model oligonucleotides were synthesized with different dN:1
ratios. After deprotection, the products were analyzed by
HPLC, and the product ratio was determined by integrating
the peak area of the UV absorbance trace.[13] The desired
incorporation ratio was achieved by using 30% 1 at a phos-
phoramidite concentration of 100 mm, and a coupling time of
four minutes. Using these conditions, deoxyribozyme libraries
were synthesized, for which the phosphoramidite mixtures
were employed only for loops A and B (the binding arms
were synthesized with standard DNA phosphoramidites
only). After deprotection and purification, the DNA libraries
ꢀ 2013 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
Angew. Chem. Int. Ed. 2013, 52, 2995 –2999