Diazirine-based DNA photo-cross-linking probes for the study of protein-DNA interactions

Article abstract of DOI:10.1002/anie.200703625

(Figure Presented) Small modification, large effect: Diazirine can be installed quickly and simply in the major or minor groove of DNA for efficient photo-cross-linking to proteins (see picture). This method should be suitable for mapping out protein-DNA interactions, in particular those that may be sensitive to steric hindrance.

Full text of DOI:10.1002/anie.200703625

Communications
DOI: 10.1002/anie.200703625
Protein–DNA Interactions
Diazirine-Based DNA Photo-Cross-Linking Probes for the Study of
Protein–DNA Interactions**
Uddhav Kumar Shigdel, Junliang Zhang, and Chuan He*
Protein–DNA interactions occur in fundamental life process-
es, such as replication, transcription, DNA modification, and
DNA repair. Chemical and photochemical cross-linking have
been used extensively in probing protein–DNA interac-
tions.[1–3] Chemical cross-linking methods enable the trapping
and characterization of various forms of protein–DNA
complexes that are labile in the absence of covalent link-
ages.[2] Photo-cross-linking has been utilized widely to map
out protein residues involved in protein–DNA interactions
and to trap/identify proteins that interact with DNA.[1,3]
To obtain enough material for characterization, it is
essential to use photo-cross-linkers that provide high yields of
cross-linking. Various photoactive groups have been intro-
duced into DNA for cross-linking studies;[1,3] however, most
of these probes suffer from low cross-linking efficiency as a
result of either low reactivity or photodecomposition, and this
poor cross-linking efficiency makes biochemical studies
tedious and sometimes unreliable. Aryl azides and benzo-
phenone can be tethered to DNA or RNA through thiol-
modified DNA or RNA backbones. Such probes have been
utilized to obtain information on protein–DNA and protein–
Scheme 1. A) Incorporation of diazirine with a C2 (n=1) or C3 (n=2)
RNA interactions.[3c,d] However, the size of these groups may
linker into the major (through the deprotection of O4-triazolyl-dU-
interfere with binding that is sensitive to steric hindrance.
We envisaged the possibility of incorporating the diazirine
photophore into DNA as a photo-cross-linking group. Under
UV irradiation, diazirine eliminates a molecule of N2 to form
a reactive carbene intermediate (Scheme 1).[1,4] This carbene
species can cross-link readily with nearby protein residues
with high efficiency. The use of diazirine has several
advantages: 1) The photo-generated carbene intermediate
has high photo-cross-linking efficiency; 2) diazirine has
superb chemical stability prior to photolysis and photolyzes
rapidly at wavelengths beyond those at which most biological
macromolecules absorb UV light; 3) the introduction of the
small diazirine unit reduces potential steric hindrance; 4) the
method is nonspecific and does not require the presence of
substituted DNA) or minor groove of DNA (through the deprotection
of 2-F-dI-substituted DNA) by using the corresponding diazirine
amines. B) The diazirine-modifed DNA can be photoactivated to
generate a carbene intermediate for cross-linking to DNA-binding
proteins. DBU=1,8-diazabicyclo[5.4.0]undec-7-ene.
specific protein residues for cross-linking. Aryl trifluorome-
thyldiazirine moieties have been attached to DNA bases;[5]
however, the large size of the modification still leads to the
steric problem that we wish to address.
Our strategy was to use the convertible nucleoside
method[6] to introduce diazirine units into the major and
minor grooves of DNA. Diazirine amines with two- and three-
carbon-atom linkers (C2: n = 1, C3: n = 2 in Scheme 1) were
synthesized by modifying a reported procedure.[4] Oligonu-
cleotides with O4-triazolyl-dU-CE phosphoramidite or 2-F-
dI-CE phosphoramidite incorporated at specific positions
were prepared by solid-phase synthesis, and the diazirine
amines were introduced by postsynthetic modification/depro-
tection (Scheme 1).[6] The single-stranded DNA ssDNA-1 and
ssDNA-6 were made with the modifications C* and G*,
respectively (Figure 1). C* stands for an N4-modified cytosine
[*] U. K. Shigdel, Dr. J. Zhang,[+] Prof. C. He
Department of Chemistry, University of Chicago
5735 South Ellis Avenue Chicago, IL 60637 (USA)
Fax: (+1)773-702-0805
E-mail: chuanhe@uchicago.edu
[+] Current address:
Department of Chemistry
East China NormalUniversity, Shanghai (P.R. China)
[**] This research was supported by the W. M. Keck Foundation, the
Arnold and Mabel Beckman Foundation, the Camille & Henry
Dreyfus Foundation, the Research Corporation, and a Concept
Award from the U.S. Army MedicalResearch Office.
residue, whereas G* indicates
a modification at the
N2 position of guanosine. ssDNA-1 was annealed with com-
plementary strands to give the double-stranded DNA probes
dsDNA-2, dsDNA-3, and dsDNA-4 with G, A, or T opposite
the diazirine-modified C* residue, respectively (Figure 1).
Supporting information for this article is available on the WWW
under http://www.angewandte.org or from the author.
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As carbenes can cross-link indiscriminately with organic
groups nearby, we also investigated whether the carbene
generated from diazirine would cause any interstrand cross-
linking in dsDNA. We did not observe any products of
interstrand cross-linking with the various major-groove and
minor-groove probes that we tested (data not shown). In
analogy with the model presented for disulfide-tethered
dsDNA, the diazirine moiety on dsDNA may also point
away from the DNA helix and thus generate no products of
interstrand cross-linking.[6b,d]
To showcase the utility of these DNA probes, we
subjected them to photo-cross-linking with DNA-binding
proteins. E. coli DNA adenine methyltransferase (EcoDam)
methylates the N6 position of adenine in GATC sequences.
Structural information on how this protein interacts with the
sequence-specific DNA was limited until a recent structural
report.[9a] We were interested in how this protein interacts
with DNA, and in particular in its sequence-nonspecific
DNA-binding mode. We expressed and purified EcoDam and
studied its photo-cross-linking to various DNA probes con-
taining a diazirine moiety in either the major or the minor
groove of duplex DNA. We mixed EcoDam (1 equiv) with
various DNA probes (3 equiv) on ice for 16 h before
irradiating the samples with a mercury lamp for 10 min. The
samples were then analyzed on Coomassie Blue stained SDS-
PAGE gel. The appearance of a low-mobility band indicated
the formation of cross-linked products. To our delight, very
good yields (20–50%) of cross-linking were observed with
most of the DNA probes (notably with probes 1, 2, 3, 6, 10,
and 11; Figure 2). To ensure maximum cross-linking, all
experiments were performed with 3 equivalents of DNA and
1 equivalent of EcoDam. However, the use of an excess of the
DNA probe may not be necessary (Figure 2A; compare
lanes 2, 4, and 7). A UV irradiation time of 10 min was found
to be optimal for the initiation of cross-linking (Figure 2A,
compare lanes 6, 7, and 8).
We surveyed a range of the probes shown in Figure 1 to
test their versatility. In the first group of probes tested, the
diazirine-containing base was positioned opposite an abasic
site or in a matched or mismatched base pair. Probes 2, 3, 10,
and 11 gave the best results with cross-linking yields of
approximately 40–50% (Figure 2A, lane 7; Figure 2C, lane 6;
Figure 2D, lanes 10, 12, 14, and 16). If the reaction mixture
was preincubated with a 10-fold excess of unmodified
dsDNA, no significant cross-linking was observed between
EcoDam and one of the best probes, dsDNA-10 (Figure 2A,
lane 10). This DNA probe does not contain the sequence
recognized by EcoDam and can be titrated away with the
excess unmodified DNA, thus further demonstrating that the
protein–DNA interaction is critical for photo-cross-linking.
Next, we tested probes that contain G* adjacent to the
abasic site (probes 12–15, Figure 1). We chose G* because the
minor-groove modification led to the best cross-linking yield
among the DNA probes that contain an abasic site. We
observed moderate cross-linking of EcoDam with probes 12,
13, and 14 with both C2 and C3 linkers, whereas minimal cross-
linking was observed when probe 15 was used (Figure 2B,C).
The minor-groove modification in probes 7 and 8 also
generated cross-linked products with EcoDam, although not
Figure 1. DNA sequences used in the photo-cross-linking studies.
The annealing of a complementary strand with an abasic site
opposite the C* residue gave dsDNA-5. DNA probes 7–15
were prepared with the minor-groove modification G*.
Complementary strands were annealed to ssDNA-6 to yield
dsDNA-7 and dsDNA-8 with C or A opposite G*, respec-
tively (Figure 1). DNA probes 9–11 were prepared by
annealing ssDNA-6 to complementary strands containing an
abasic site. DNA probes 12–15 were prepared with G*
positioned in matched or mismatched base pairs adjacent to
an abasic site (Figure 1). The abasic site and mismatched
DNA base pairs were chosen because of their preferences in
interacting with some known base-flipping proteins.[2a,d,7]
To determine whether the diazirine-tethered duplex DNA
was any different from the analogous alkylamine- or disul-
fide-tethered dsDNA, we measured the melting temperatures
(Tm) of the modified duplex oligonucleotides by using a
differential scanning calorimeter.[8] The Tm values of dsDNA-
2 and dsDNA-7 with the C2 linker were determined to be 55.0
and 61.28C, respectively (see the Supporting Information).
The differences in the Tm values of the diazirine-tethered
DNA and normal DNA correlate with the differences
observed previously between the Tm values of normal
dsDNA and those of alkylamine- or disulfide-tethered
dsDNA.[6b,d] Thus, as expected, the diazirine tether does not
introduce additional destabilization relative to that observed
with simple alkylamine tethers.
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and 3 are excellent for photo-cross-
linking reactions between a protein
and DNA. These DNA probes
appear to react with DNA-binding
residues on the surface of EcoDam,
as comparable photo-cross-linking
yields were observed with matched
and mismatched probes. EcoDam
methylates adenine in a sequence-
specific manner.[9] It must scan the
DNA base pairs in its search for a
specific sequence. The close con-
tacts with DNA base pairs may
account for cross-linking with dia-
zirine moities on matched DNA
probes. The structural characteriza-
tion of this “nonspecific” interac-
tion, which we can now trap in high
yields, would provide valuable
information about how EcoDam
binds to nonspecific DNA.
We also studied human O6-
alkylguanine-DNA alkyltransferase
(hAGT), a protein that searches
DNA base damage sequence-non-
specifically.[10] When hAGT was
incubated with our DNA probes,
very good yields of cross-linked
products were observed (Fig-
ure 3A, lanes 5, 7, 9–11, and 13;
Figure 3B, lanes 6 and 10). Experi-
ments with dsDNA-3 and hAGT in
various ratios indicated that almost
all of the hAGT in solution was
consumed with 3 equivalents of
DNA (Figure 3A, compare lanes 5,
7, and 10). An optimal UV irradi-
ation time of 10 min was deter-
Figure 2. SDS-PAGE analysis of the photo-cross-linking reactions between E. coli DNA adenine
methyltransferase (EcoDam; 0.3 nmol) and various DNA probes (0.9 nmol). C2 and C3 are the
lengths of the carbon tethers between the diazirine ring and N2 of guanosine or N4 of cytosine.
A) The photo-cross-linking between probe 10 and EcoDam was studied for its dependence on the
irradiation time with UV light and on the DNA equivalence. A 10-fold excess of a competing
unmodified DNA molecule with the same sequence as that of probe 10 was used in the experiments
shown in lanes 9 and 10. No cross-linking was observed in these two experiments. B–D) Different
probes were tested for cross-linking to EcoDam with and without UV irradiation.
mined from
a time-dependence
study (Figure 3A, compare lanes 9,
10, and 11).
Low cross-linking was observed
when the DNA probe 2 with either
as efficiently as probes 1, 2, 3, 6, 10, and 11 (data not shown),
but the best yields (ca. 50%) were observed with probes 10
and 11. Base-flipping proteins, such as EcoDam, are known to
recognize unstable sites in a specific manner,[7] which may
account for the higher yields of cross-linking observed for
probes 10 and 11. When the single-stranded DNA probes 1
and 6 were used, we observed 1:2 protein–DNA complexes on
the gel as well as the 1:1 protein–DNA complexes (Fig-
ure 2D). These additional complexes might arise from the
binding of a small fraction of EcoDam to two ssDNA
molecules simultaneously. Our results show that one can
identify several DNA probes that cross-link efficiently with
the target protein from a quick screen (see the Supporting
Information).
a C2 or a C3 linker was used (Figure 3A, lane 3; Figure 3B,
lane 8), whereas the mismatched probe 3 with a C2 or C3
linker gave the photo-cross-linked product in very good yield
(50–75%; Figure 3A,B, lane 10). The DNA probe 4, with a
C*:T mismatch, underwent less cross-linking than that
observed with probe 3 (C*:A; Figure 3B). The use of
ssDNA-1 with a C2 or C3 linker led to little cross-linking
(Figure 3B, lanes 2 and 4). When a 10-fold excess of
unmodified, mismatched dsDNA was added to the reaction
mixture, less of the covalently linked complex was formed
(Figure 3A, lane 13), which indicates that hAGT can be
titrated away from dsDNA-3 with mismatched dsDNA. We
observed minimal photo-cross-linking of hAGTwith dsDNA-
5 and other DNA probes containing minor-groove modifica-
tions (results not shown), most likely as a result of a lack of
contact of the tethered diazirine with the protein.[10b,c] Overall,
Given that a nonspecific sequence was used in the study
with EcoDam, the results of the experiments with probes 2
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Keywords: cross-linking · diazirine · DNA probes ·
.
photochemistry · proteins
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Figure 3. SDS-PAGE analysis of the photo-cross-linking reactions
between human AGT (0.3 nmol) and DNA probes 1–4 (0.9 nmol). C2
and C3 are the lengths of the carbon tethers between the diazirine ring
and N4 of cytosine. A) Comparison of the photo-cross-linking effi-
ciency of matched (probe 2) and mismatched probes (probe 3) with
hAGT. Lanes 12 and 13 show the extent of competition from a 10-fold
excess of an unmodified mismatched DNA with the same sequence as
that of probe 3. B) Photo-cross-linking with different DNA probes and
tether lengths.
the most efficient cross-linking with hAGTwas observed with
dsDNA-3 with a C2 linker.
In summary, we have described a simple and quick
method for the incorporation of diazirine into the major and
minor grooves of DNA for efficient photo-cross-linking to
proteins. Good to excellent yields of cross-linking with two
different proteins were observed for the resulting DNA
probes with small diazirine modifications. This method
appears to be suitable for mapping out protein–DNA
interactions, in particular those that may be sensitive to
steric hindrance. The high cross-linking efficiency observed in
several cases would allow direct purification of the photo-
cross-linked products for structural characterization. Alter-
natively, protein residues engaged in photo-cross-linking can
be identified readily by mass spectrometry and mutated to
Cys residues in preparation for chemical disulfide cross-
linking with disulfide-tethered oligonucleotides. The resulting
disulfide-linked complex can be subjected to structural
studies. Furthermore, the relatively high cross-linking effi-
ciency of these diazirine-based probes makes them promising
tools for the covalent trapping of proteins from cell extracts.
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Received: August 9, 2007
Published online: November 12, 2007
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