Photoinduced transcription by using temporarily mismatched caged oligonucleotides

Article abstract of DOI:10.1002/anie.200461779

Spatial and temporal control of the function of DNA with light: In oligonucleotides, protected ("caged") thymidine can act as a temporary mismatch in base pairing and, for example, prevent transcription. The photolabile caging group can be removed by ligh

Full text of DOI:10.1002/anie.200461779

Angewandte
Chemie
Bioorganic Chemistry
Photoinduced Transcription by Using
Temporarily Mismatched Caged
Oligonucleotides**
Lenz Krꢀck and Alexander Heckel*
DNA and RNA are responsible for the storage and flow of
information in nature. Additionally, and especially together
with their analogues and derivatives, DNA and RNA can be
used for a multitude of applications, such as regulation of
gene expression (RNA interference,[1a] microRNA,[1b] ribo-
switches,[1c] antisense approach,[1d] DNAzymes[1e]), modula-
tion of protein function (aptamers,[1f] DNA/RNA decoys[1g]),
molecular diagnostics (microarrays[1h]), or as structural or
functional building blocks for nanoscale material.[1i] In all of
these applications the nucleobases play a central role. To
develop a mechanism for the temporal and spatial control of
the DNA or RNA function, we are investigating ways to
temporarily block the recognition properties of the nucleo-
bases. Since light has the advantage of being a highly
orthogonal trigger signal we decided to use photolabile
“protecting” groups for this purpose. The regulation of gene
expression by light, for example, would be a valuable tool for
the analysis of protein function. The strategy of masking the
activity of a biological compound with a photolabile protect-
ing group is called “caging” and, for example, caged neuro-
transmitters or Ca2+-complexing agents have already been
synthesized and investigated.[2] Likewise, in a pioneering
investigation, adenosine triphosphate (ATP) caged with a
photolabile 1-(2-nitrophenyl)ethyl group was used to study
the Na/K-pump in human red blood cell ghosts.[3]
Herein, we report the synthesis of caged thymidine
phosphoramidites and the use of caged oligonucleotides to
control transcription by light. Photolabile protecting groups
have been used before in oligonucleotide synthesis as
temporary protecting groups[4] and photolabile protecting
groups in the 2’-position in RNA can also inhibit ribozyme
action[4b,5] but they do not prevent Watson–Crick base pairing.
Also, nucleoside analogues and derivatives have been made
which induce DNA strand breaks upon irradiation.[6]
The exocyclic O4 position of thymidine was chosen for the
attachment of the photolabile group (caging group;
Scheme 1). The O4-substituted derivatives of thymidine are
conveniently accessible by the reaction of the suitably
protected precursor 1 with triisopropylbenzenesulfonyl chlo-
Scheme 1. Synthesis of the photoactivatable caged phosphoramidites
3a–e as well the caged nucleosides Tcaꢀe. Reaction conditions:
a) 1. iPr3C6H2SO2Cl, DMAP, Et3N; 2. respective alcohol, Et3N; b) NH3/
MeOH (quant.); c) DMTrCl, pyridine; d) CEOP(Cl)NiPr2, DIEA.
DMAP=N,N-dimethyl-aminopyridine, DMTr=dimethoxytrityl, DIEA=
diisopropylethylamine, CE=(2-cyanoethyl), Bn=benzyl.
ride and then with the respective alcohols of the caging groups
(!2a–e). As photolabile protecting groups the commonly
used 2-nitrobenzyl group and its faster deprotecting a-
methyl-substituted derivative as well as the 2-nitrophenethyl
group and its a-methyl-substituted derivative were chosen.
The 2-nitrophenethyl group has been used by Pfleiderer
et al.[7] and has the advantage of not forming a nitroso
compound upon deprotection[8], a property that is important
for cellular and in vivo studies. The benzylated derivative 2e
and its subsequent derivatives were also included in these
studies as control compounds which are not deprotected by
light. Deacetylation and DMTr-protection of the 5’-position
afforded the protected 3’-OH-free intermediates which were
converted under standard conditions into the phosphorami-
dites 3a–e.
To investigate the duplex-destabilizing effect of the caged
thymidine monomers Tcaꢀe (Scheme 1; c = caged) they were
included in 25-mer-oligodeoxynucleotides in the positions
indicated in Table 1 and thermal denaturation experiments
were performed using dA25 as the counter strand. As the
results in Table 1 show, the introduction of just one caged
nucleotide leads to a significant reduction in the melting
temperature (up to 58C). This effect can be increased if more
Table 1: Results of thermal denaturation experiments of the given
oligonucleotides with dA25 as counter strand.[a]
[*] L. Krꢀck, Dr. A. Heckel
X
5’-T8TTTTXTTTTT8–3’ 5’-T8TTTXXXTTTT8-3’ 5’-T8XTTTXTTTXT8-3’
Rheinische Friedrich-Wilhelms-Universitꢁt Bonn
Kekulꢂ-Institut fꢃr Organische Chemie und Biochemie
Gerhard-Domagk-Strasse 1, 53121 Bonn (Germany)
Fax: (+49)228-73-5388
Tca 50.3 (51.1)
Tcb 48.6 (53.2)
Tcc 48.9 (53.0)
Tcd 48.5 (54.0)
Tec
47.3 (46.9)
44.2 (51.1)
44.9 (51.7)
44.5 (52.7)
41.2 (44.3)
32.3 (51.9)
34.7 (51.8)
32.3 (53.2)
33.8 (34.2)
E-mail: heckel@uni-bonn.de
[**] This work was funded by a Liebig-Fellowship of the “Verband der
Chemischen Industrie” (VCI (Germany)) for A.H.
[a] Melting temperatures in8C before and (in parenthesis) after irradi-
ation of the sample at 366 nm for 30 min (error ca. 0.78C). With
unmodified T25 a melting temperature of 53.8 (54.0)8C was obtained.
Supporting information for this article is available on the WWW
under http://www.angewandte.org or from the author.
Angew. Chem. Int. Ed. 2005, 44, 471 –473
DOI: 10.1002/anie.200461779
ꢀ 2005 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
471

Communications
caged nucleotides are included, especially if they are not
scription (Figure 2). An assay was used in which a 68-
nucleotide (nt) antisense strand with a T7-promoter served as
the template. The T7-promoter region was complemented
with the shorter oligonucleotides S1–S6 to for a double strand
cumulated around one position within the oligonucleotide.
Branched caging groups result in a slightly increased destabi-
lization of the duplex compared to their nonbranched
analogues (see for example the entries for the oligomers
containing Tca und Tcb). With the incorporation of only three
caged nucleotides a maximum decrease in melting temper-
ature of 21.58C was obtained. In a second series of experi-
ments the melting temperatures were determined after
irradiation of the samples for 30 min at 366 nm. As can be
seen in Table 1, only the oligonucleotides with the caged Tdc
showed the same melting temperature, after irradiation, as
the unmodified T25 oligomer used as control compound.
These findings suggest that the caged nucleotides can be
thought of as being “temporary mismatches”. Including the
benzylated thymidine Tce in an oligonucleotide leads to a
decrease in melting temperature which remained unchanged
upon irradiation with light.
To study the deprotection kinetics 4 nmol of each of the
oligonucleotides shown in Table 1 was irradiated at 366 nm
and the formation of the resulting uncaged T25 was detected
by HPLC (Figure 1). As can be seen, in the case of the
Figure 2. Relative amounts of transcription product formed after 1 h
with or without initial irradiation (1 h, 366 nm) of the sample before
starting the transcription by addition of the T7 RNA polymerase.
and allow the T7 RNA polymerase to recognize the promoter
region. The amount of transcription product after 1 h of
incubation was determined by phosphorimaging (a-32P-gua-
nosine triphosphate (GTP) was used for body labeling). The
three oligonucleotides S2, S3, and S4 contain, respectively,
three, two, and one caged nucleotide in the T7 promoter
region. Unlike with the control oligonucleotide S1, in the
presence of these unmodified oligonucleotides no transcrip-
tion takes place. This result is not because the two DNA-
strands in the experiment are not associated to one another
since, for example, S4 and the antisense strand show a melting
temperature of 72.08C in the transcription buffer. It must
rather be due to a severe perturbation of the local duplex
structure owing to the caging group which prevents the RNA
polymerase from recognizing the promoter region.[9] After
irradiation of the respective samples (before the addition of
the T7 RNA polymerase) the same amount of transcription
product was formed as in the control reaction with the
uncaged oligomer S1. Transcription could also be triggered by
irradiating the samples containing the intact caged sense
strands after 1 h of incubation with T7 RNA polymerase in
which no product had been formed. The shorter oligomers S5
and S6 behaved similarly.[10] However, the results shown in
Figure 2 demonstrate that it is not necessary to heavily
destabilize the entire duplex to prevent transcription and that
the incorporation of one or two caged nucleotides is quite
enough.
Figure 1. Amount of uncaged oligonucleotide during the photodepro-
tection (366 nm). In every experiment 4 nmol of the caged oligonucleo-
tide was used and the product formation was detected by HPLC.
photodeprotection of the oligomers containing the caged Tbc
the reaction reached a stationary state in which, as well as the
product, an as yet unidentified byproduct was present which
did not react further upon irradiation. In the case of the
oligomers with the caged Tdc however, the deprotection was
not only faster under the irradiation conditions used but the
yield of resulting uncaged oligonucleotide was almost quan-
titative within error limits. The oligomers with the caged Tac
and Tcc were also subjected to this test. However, especially
with several caged nucleotides in the same oligomer, the
deprotection was very slow and the yields were poor. In
conclusion, the caged Tcd showed the best properties with
regard to perturbation of duplex structure and ease of
photodeprotection.
To studying the use of caged photoactivatable nucleotides
in biological systems we tried to temporarily block tran-
472
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Angewandte
Chemie
[9] For a crystal structure of the T7 RNA polymerase with the T7-
Other groups have also studied the regulation of gene
expression by light.[11] However in their approaches entire
plasmids or mRNA strands were subjected to benzylating
conditions in which the photolabile groups were attached
presumably to backbone phosphates. In contrast to the
strategy presented herein, this approach does not lead to a
well-defined product but rather to a statistical distribution of
caged positions and introduces more modifications than
necessary. In the other investigations the full transcriptional
activity could not be restored.
promoter region see: G. M. T. Cheetham, D. Jeruzalmi, T. A.
Steitz, Nature 1999, 399, 80 – 83.
[10] It was confirmed experimentally, in all cases, that the oligonu-
cleotides produced upon irradiation were indeed the expected
ones.
[11] a) W. T. Monroe, M. M. McQuain, M. S. Chang, J. S. Alexander,
F. R. Haselton, J. Biol. Chem. 1999, 274, 20895 – 20900; b) H.
Ando, T. Furuta, R. Y. Tsien, H. Okamoto, Nat. Genet. 2001, 28,
317 – 325.
In conclusion we have demonstrated that caged thymi-
dines can be used as temporary mismatches to inhibit a
function, transcription in this case. They can be introduced in
oligomers at any desired and well-defined position through
their easily accessible phosphoramidites 3a–e. With long-
wavelength UV light (366 nm) the photodeprotection of the
caged Tcd occurs fast, with high yield, and without formation of
nitroso compounds. One or two caged nucleotides at the right
position can be enough to completely inhibit a function.
Received: August 25, 2004
Keywords: DNA · gene expression · oligonucleotides ·
.
photoactivation
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