Micro-flowers changing to nano-bundle aggregates by translocation of the sugar moiety in Janus TA nucleosides

Article abstract of DOI:10.1039/c3cc41383g

We designed and synthesized the Janus-type TA nucleosides (1-3) by using a transglycosylation protocol. Surprisingly, the subtle translocation of the ribose from N8 to N1 by about 230 pm in space leads to the formation of entirely different shaped superstructures, micro-flowers for J-AT and nano-bundles for J-TA.

Full text of DOI:10.1039/c3cc41383g

Joint research work from the Laboratory of
Ethnopharmacology, West China Hospital and the
State Key Laboratory of Oral Diseases, West China
Hospital of Stomatology, Sichuan University
As featured in:
Micro-flowers changing to nano-bundle aggregates by
translocation of the sugar moiety in Janus TA nucleosides
The Janus-type TA nucleosides were designed and synthesized. The
translocation of the ribose from N8 to N1 leads to the formation of
entirely different superstructural morphologies, micro-flowers for
J-AT and nano-bundles for J-TA.
See Wen Huang, Qianming Chen,
Yang He et al.,
Chem. Commun., 2013, 49, 3742.
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Micro-flowers changing to nano-bundle aggregates by
translocation of the sugar moiety in Janus TA
nucleosides†
Cite this: Chem. Commun., 2013,
49, 3742
Received 18th January 2013,
Accepted 4th March 2013
ab
a
Hang Zhao,z Shiliang He,z Mingli Yang,c Xiurong Guo,a Guang Xin,a
Chaoyang Zhang,b Ling Ye,b Liangyin Chu,b Zhihua Xing,a Wen Huang,*a
Qianming Chen*b and Yang He*a
DOI: 10.1039/c3cc41383g
www.rsc.org/chemcomm
We designed and synthesized the Janus-type TA nucleosides (1–3)
by using a transglycosylation protocol. Surprisingly, the subtle
translocation of the ribose from N8 to N1 by about 230 pm in
space leads to the formation of entirely different shaped super-
structures, micro-flowers for J-AT and nano-bundles for J-TA.
Scheme 1 The structures of bidentate J-AT and J-TA nucleosides. The arrows of D
Since the establishment of supramolecular chemistry,1 non-covalent
interactions have been extensively employed to construct complex
represent the hydrogen donors; the arrows of A represent the hydrogen acceptors.
architectures in nanotechnology.2 One of the major challenges in this thymidine because its ribose is connected to the N8 atom which
field is to create predictable and controllable structures by molecular is on the adenine ring, different from the natural nucleosides.
self-assembly.3 To accomplish this, inorganic or organic molecules, Hence, after many tries we finally synthesized, through transglyco-
synthetic polymers and biopolymers (peptides, DNA, RNA) have been sylation reaction, the desired bidentate Janus-type TA nucleosides
investigated over the past decades.4 Due to their unique comple- (J-TA, 1–3) which have the same geometrical arrangements as the
mentarities, equipped with solid-phase synthetic methods and an natural ones with the sugar residues attached to the N1 atom on
enzymatic toolkit, oligonucleotides (DNA or RNA) have become one of the thymine ring (Scheme 1). Although compounds J-AT and J-TA
the most versatile candidates for creating various programmable and (1) have the identical two-faced H-bond arrays and the same sugar
manageable superstructures.4f,g,5 As the building blocks of DNA/RNA, counterparts, the subtle translocation of the ribose from N8 to N1
nucleosides have also been exploited for this purpose.6 Besides by about 230 pm in space leads to the formation of entirely
canonical purines and pyrimidines, other heterocycles have also been different shaped superstructures, micro-flowers for J-AT and
developed to form supramolecular structures which have been widely nano-bundles for J-TA (1–3), which we would like to report herein.
applied in the field of nanomaterials.7,8
For the synthesis of compound 1, initially, the Vorbrueggen
To expand further, the Janus-type tridentate GC (J-GC) and glycosylation reaction was adopted.9d,10 But, various conditions all
bidentate AT and HC nucleosides were designed and synthesized led to the formation of compound 6 instead of compound 8
by our group.9 We found that the J-GC ribonucleoside can form (Scheme S1, ESI†). The reason for the glycosylation reaction regio-
nano-bundles and the Janus-type AT ribonucleoside (J-AT) can selectivity is that N8 of key intermediate 5 is more active than N1, as
form flower-like superstructures in DMF solution.9c However, the illustrated by its larger f value of Fukui functions (Fig. S1, ESI†),
J-AT ribonucleoside is not a perfect mimic of adenosine or which are descriptors of chemical reactivity computed using density
functional theory (DFT). To overcome this problem, we also tried a
a Laboratory of Ethnopharmacology, Institute for Nanobiomedical Technology and
different route: construction of the second pyrimidine ring from
monocyclic pyrimidine nucleoside 10 (Scheme S2, ESI†). Unfortu-
nately, the target compound 8 was not formed probably because the
Membrane Biology, Regenerative Medicine Research Center, West China Hospital,
West China Medical School, Sichuan University, Chengdu 610041, China.
E-mail: heyangqx@scu.edu.cn, huangwen@scu.edu.cn
b State Key Laboratory of Oral Diseases, West China Hospital of Stomatology,
Sichuan University, No. 14, Section 3, Renminnan Road, Chengdu,
Sichuan 610041, China. E-mail: qmchen@scu.edu.cn
c Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, China
† Electronic supplementary information (ESI) available: Full experimental details
for all compounds, VT-NMR, molecular modelling and microscopy preparations
and experiments. See DOI: 10.1039/c3cc41383g
sugar exerts certain steric hindrance in the ring closure process.
The transglycosylation reaction11 has not yet been utilized in the
field of pyrimido[4,5-d]pyrimidine nucleoside synthesis. Here, we
investigated the feasibility of this translocation reaction to synthe-
size compound 1 (Scheme 2). The benzoylated 69d was treated with
HMDS and xylene to afford the silylated intermediate 7. Next,
compound 7 was rearranged to afford compound 8. For this step,
‡ These authors contributed equally to this study.
c
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As reported for Janus-type derivatives before,7h,9d the variable tem-
1
perature HNMR (VT NMR) showed that the intermolecular and
intramolecular hydrogen bonds exist for the self-assembly of these
new J-TA nucleoside systems in DMSO (Fig. S11–S13, ESI†).
There are two possible ways to maintain the bidentate hydrogen
bonding arrays for the normal adenosine and thymine base pair: the
Watson–Crick base pair or the reverse Watson–Crick base pair; they
will lead to the formation of either antiparallel-stranded or parallel-
stranded DNA/RNA.12 These two base pair motifs have little energy
difference according to theoretical calculation (B1.3 kJ molꢀ1).13
For currently studied pyrimido[4,5-d]pyrimidine, DFT calculations
predicted a rather small energy difference between these two motifs
(B0.85 kJ molꢀ1, Fig. S14, ESI†). If the Watson–Crick base pair is
adopted a rosette structure will be formed; on the other hand if the
reverse Watson–Crick base pair is adopted a linear tape structure
will be formed (Scheme S4, ESI†). To see which one is dominant for
compounds 1–3 in water, SEM, TM-AFM and TEM were carried out.
Compounds 1–3 and J-AT were dissolved in water (0.2 mg mLꢀ1),
heated and cooled at room temperature for 48 h. Characterization of
J-AT nucleosides using SEM showed that it can form micro-flower
superstructures in water; the thickness of the flower leaves was
about 120 nm (Fig. 1A and Fig. S15, ESI†), which is similar to the
previous observation in DMF.9c There is no finer structure for this
micro-flower observed under TEM. Considering their same base pair
motifs, it is very interesting to investigate whether or not nucleosides
(1–3) will form superstructures similar to Janus-type TA in water. As
a matter of fact, completely different superstructures were found for
them. When observed using SEM, these compounds formed nano-
bundles; the length of the nano-bundles is about 20 mm; these
nanobundles interweave to form three-dimensional networks whose
overall shape is quite similar to that of collagens (Fig. 1B and
Fig. S16–S18, ESI†).14 When these samples were observed under
TM-AFM, the same nanobundles were detected as well
(Fig. S19–S21, ESI†). Then, the finer structure of these nano-bundles
was revealed by TEM which indicated that these nanobundles
consisted of nanotubes with an outer diameter of B4 nm (Fig. 1C
and Fig. S22–S24, ESI†). As reported for GC derivatives,15 these
nanotubes self-assemble through hierarchical non-covalent inter-
actions. Firstly, a six-membered supermacrocycle was constructed by
H-bonding through Watson–Crick base pairs. Indeed, DFT calcula-
tions revealed that the pattern of hexameric macrocyclic form of J-TA
nucleosides is about 43.05 kJ molꢀ1 more stable than the corres-
ponding linear arrangement formed by reverse Watson–Crick base
Scheme 2 Synthesis of the J-TA nucleoside (1): R = TMS; (i) and (ii) steps;9d (iii)
HMDS, xylene, reflux; (iv) dry acetonitrile, TMSOTf, 75 1C, 2 h, 51%; (v) 0.5 M
NaOMe, reflux, 82%.
diverse Friedel–Crafts catalysts (SnCl4, TMSOTf), reaction solvents
(ClCH2CH2Cl, CH3CN, and mixture solvents), reaction times (1 h,
2 h, 6 h, 1 d and 3 d) and reaction temperatures (25 1C, 50 1C, 75 1C
and 100 1C) have been tested and finally the conditions of dry
acetonitrile, TMSOTf, 75 1C, 2 h were proved to be the best choice.
Subsequently, the target compound 1 was obtained as a white
powder by removing the benzoyl groups from compound 8.
For the synthesis of 20-deoxyribonucleosides (2 and 3), the same
transglycosylation reaction was adopted (Scheme S3, ESI†). However,
the anomeric mixture of 13a (b) and 13b (a) was difficult to separate
by FC or recrystallization. After the toluoyl groups were removed it
was also impossible to separate the a and b isomers. In order to get
the pure anomeric 20-deoxynucleosides, the 4,4-dimethoxytrityl
(DMT) group was employed. When the DMT group was introduced
into the 50-OH group, compounds 14a and 14b could be separated
by FC successfully. Afterwards, the DMT groups of 14a and 14b were
removed and the target compounds 2 (b) and 3 (a) were obtained.
The Nuclear Overhauser Effect (NOE) gave unambiguous evidence
concerning the configuration of the anomeric center: 10-H of 2
produced a strong NOE at 20-Ha and 20-Hb while 10-H of 3 showed an
NOE at 20-Ha, and 30-H simultaneously (Fig. S2 and S3, ESI†).
The structures of compounds 1–3 were characterized using NMR
and HRMS. The coupling interaction between the C7 atom of the AT
base and the 10-H atom of the sugar provided the evidence that the
sugar was attached to the N1 atom of the thymine ring (Fig. S4–S9,
ESI†). The UV spectroscopy of compounds 1–3 showed a blue
shift of 23 nm compared with J-AT, which was an additional
indication of their different isomeric form (Fig. S10, ESI†).
Fig. 1 Imaging of micro-flowers and nano-bundles by (A) SEM micrograph of J-AT; (B) SEM image of sample 1; (C) TEM image of compound 1.
c
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Guiping Yuan of the Analysis and Testing Center of Sichuan
University for helping us to process variable temperature NMR
and TEM images.
Notes and references
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pairs (Fig. 2A and Fig. S25, ESI†). Secondly, these six-membered
rings stacked layer by layer to form rosette nanotubes (Fig. 2B
and C). The calculations at the ff03 force-field level were performed
for the stacking up to n = 12 layers, showing that the stacking leads
to extra stability for the rosette nanotubes (Fig. 2D and Fig. S26,
ESI†) and the elongation of these nanotubes is energetically favour-
able. Previously, the GC base derivatives were reported by Fenniri
and coworkers to form B10% nanobundles by nanotubes. Here we
have found that nearly 100% of nanotubes associate to form higher
ordered nano-bundles. The difference is obviously due to the
presence of sugars attached to the base, which will introduce
additional hydrogen bonds between adjacent nanotubes. The
hollow structure of nanotubes together with the densely packed
nano-bundle networks formed by nucleosides 1–3 may have potential
to be used for drug delivery systems and biomaterial engineering.
In summary, we have developed a viable route to synthesize the
new pyrimido[4,5-d]pyrimidine Janus-type TA ribonucleoside (1–3) by
transglycosylation reactions. Albeit J-AT and J-TA (1) have the identical
two-faced H-bond arrays and the same sugar counterparts, the subtle
translocation of the ribose from N8 to N1 (by about 230 pm in space)
leads to the formation of drastically different shaped superstructures,
micro-flowers for J-AT and nano-bundles for J-TA (1–3). Previously, we
have shown that the modifications of base moieties can change the
superstructures of these Janus-type nucleosides.9c The current pheno-
menon indicates that not only the base pair but the spatial arrange-
ment of the sugar is also a deterministic factor to direct the three
dimensional superstructure shapes. Based on these findings, we
believe that, by further fine-tuning the structural parameters of these
Janus-type nucleosides such as the functional groups, the torsion
angle of the glycosyl bond (anti- or syn-conformation), the sugar
puckering mode (North- or South-conformation), etc., more beauties
and complexities of the macro-world can be reproduced and find
certain applications in the micro- or nano-world. These experimental
and theoretical studies are currently under intensive investigations
and will be published in the near future.
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We thank the National Natural Science Foundations of China
(document no: 20772087, 81061120531, 30930100), ISTCPC
(2012DFA31370) and the Open Foundation (SKLODSCUKF2012-04)
from the State Key Laboratory of Oral Diseases Sichuan University
for the financial support. We also thank Xiaoyan Wang and
c
3744 Chem. Commun., 2013, 49, 3742--3744
This journal is The Royal Society of Chemistry 2013