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Research Paper
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Acta Biochim Biophys Sin 2005,37:593-600 |
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doi:10.1111/j.1745-7270.2005.00084.x |
RecQ Helicase-catalyzed DNA
Unwinding Detected by Fluorescence Resonance Energy Transfer
Xing-Dong ZHANG,
Shuo-Xing DOU, Ping XIE, Peng-Ye WANG*,
and Xu Guang XI1
Laboratory of Soft Matter Physics,
Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,
Chinese Academy of Sciences, Beijing 100080, China;
1 Laboratoire de Biotechnologies et
Pharmacologie Généique Appliquée CNRS UMR 8113, Ecole Normale Supérieure de
Cachan, 61 Avenue du Président Wilson, 94235 Cachan cedex, France
Received:
March 17, 2005
Accepted:
May 23, 2005
This
work was supported by the grants from the National Natural Science Foundation
of China (No. 60025516 and No. 10334100), the Innovation Project of the Chinese
Academy of Sciences, and the Centre National de
Abbreviations:
FRET, fluorescence resonance energy transfer; H, hexachlorofluorescein; F,
fluorescein; dsDNA, double-stranded DNA; ssDNA, single-stranded DNA; DTT,
dithiothreitol
*Corresponding author: Tel, 86-10-82649568; Fax, 86-10-82640224;
E-mail, [email protected]
Abstract A
fluorometric assay was used to study the DNA unwinding kinetics induced by
Escherichia coli RecQ helicase. This assay was based on fluorescence
resonance energy transfer and carried out on stopped-flow, in which DNA
unwinding was monitored by fluorescence emission enhancement of fluorescein
resulting from helicase-catalyzed DNA unwinding. By this method, we determined
the DNA unwinding rate of RecQ at different enzyme concentrations. We also
studied the dependences of DNA unwinding magnitude and rate on magnesium ion
concentration. We showed that this method could be used to determine the
polarity of DNA unwinding. This assay should greatly facilitate further study
of the mechanism for RecQ-catalyzed DNA unwinding.
Key words helicase; DNA
unwinding; kinetics; stopped-flow; fluorescence resonance energy transfer
(FRET)
DNA and RNA helicases
are unwinding enzymes that can couple nucleotide triphosphate (usually ATP)
binding and hydrolysis to catalyze breakage of the hydrogen bonds between
complementary strands of double-stranded DNA (dsDNA), thus providing
single-stranded DNA (ssDNA) templates required for almost all aspects of
nucleic acid metabolic pathways [16]. These enzymes seem to be ubiquitous in
both prokaryotic and eukaryotic cells as they have been found in diverse
species from bacteria to human [7-13]. It has
been reported widely, since this type of enzyme was originally described and
recognized by Hoffmann-Berling in Escherichia coli almost 30 years ago,
that DNA helicases play essential roles in a variety of biological processes
such as DNA replication, repair, recombination and transcription [14,15], and
defects in DNA helicases can cause genomic instability. It has been shown that
one class of DNA helicases, the RecQ family, plays an important role in
maintenance of genome stability [1618]. We now know that several human diseases
such as Bloom's syndrome, Werner's syndrome and Rothmund-Thomson
syndrome, all of which can lead to cancer, are caused by defection of RecQ
helicase [1922]. The RecQ family helicases BLM and WRN are mutated in Bloom's
syndrome and Werner's syndrome, respectively, and RecQ4 is defective in
Rothmund-Thomson syndrome. Recently, the DNA unwinding mechanism of RecQ
helicases has gained wide interest owing to their role in inherited diseases,
as well as in aging.
To better understand how
helicases unwind the duplex nucleic acids, many continuous fluorometric assays
have been developed to study their detailed kinetic unwinding mechanisms. Up to
now, various types of helicases have been studied by fluorescence methods, such
as PcrA [23], RecBCD [24,25], Dda [26,27], Rep [28,29], Werner's syndrome
protein as well as RecQ [30,31]. Recently, we have used a fluorescence
polarization assay in the biochemical characterization of RecQ helicase and
this method provided much valuable kinetic information for elucidating the
unwinding mechanism of E. coli RecQ in real time [3234]. In particular,
this fluorescence assay can simultaneously monitor DNA binding and helicase-catalyzed
DNA unwinding.
Fluorescence resonance
energy transfer (FRET) assay is an adaptation of similar spectrophotometric
experiments performed with several other helicases such as WRN and Rep [28,30].
In this method, the dsDNA substrate was typically labeled with fluorescein (F,
donor) at the 3' end and with hexachlorofluorescein (H, acceptor) at the
opposing 5' end. The overlap between the fluorescence emission spectrum
of fluorescein and the excitation spectrum of hexachlorofluorescein results in
an energy transfer from fluorescein to hexachlorofluorescein, which quenches
the fluorescein emission in the duplex. If the dsDNA is unwound or the
complementary strands are separated by helicases, fluorescein and hexachlorofluorescein
are no longer in close proximity so the energy transfer is disrupted, resulting
in an enhancement of fluorescence emission from the fluorescein. One of the
advantages of this assay is that it can non-invasively measure the real-time
kinetics in a millisecond time range and allow DNA unwinding activity to be
monitored continuously at DNA concentrations as low as 2 nM. By the FRET
method, we have determined the DNA unwinding rate of RecQ at different enzyme
concentrations under multi-turnover conditions. The observed unwinding rate at
saturating enzyme concentration is about 3 bp/s, which is consistent with that
measured by using fluorescence polarization assay [32]. We also studied the
dependences of both unwinding magnitude and unwinding rate on magnesium ion
concentration and obtained results that are significantly different from those
reported previously [31].
In this study, we used
the stopped-flow rapid chemical kinetics method to observe the RecQ-catalyzed
unwinding of dsDNA continuously and in real time based on FRET assay.
Materials and Methods
Reagents and buffers
All chemicals were of
reagent grade and all solutions were prepared in high quality de-ionized water
from a Milli-Q water purification system (Millipore Corporation, France) that has
a resistivity greater than
RecQ protein preparation
His6-tagged E. coli RecQ
helicase was expressed from pET-15b expression plasmid in E. coli strain
BL21(DE3) as previously described [33] and was quantified
spectrophotometrically at 280 nm using an extinction coefficient of 3.0´104 cm-1∙M -1. The purified E. coli RecQ protein was
stored in buffer B (
Oligonucleotide reaction
substrates
All oligonucleotide
types used in this research are listed in Table 1. Single-stranded
oligonucleotides, with or without fluorescent label, were purchased from SBS
GeneTech Company, Limited (Beijing, China), and all synthetic oligonucleotides
were purified by denaturing polyacrylamide gel electrophoresis before storage
in
Steady-state
fluorescence spectrum measurement
Steady-state
fluorescence spectra were measured using an F-4500 fluorescence
spectrophotometer (
Stopped-flow
fluorescence measurement
The stopped-flow
fluorescence experiments were carried out using a Bio-Logic SFM-400 mixer with
a
Kinetics data analysis
The kinetics data of DNA
unwinding were fitted to Equation 1.
Eq. 1
in which, F(t)
is the fluorescence signal given in the fraction of duplex unwound; A
and kobs correspond to
the amplitude and the observed rate constant of DNA unwinding, respectively, t
is the DNA unwinding time.
Results and Discussion
Purity of the RecQ
helicase
The RecQ helicase was
overexpressed and purified from E. coli [33]. Gel electrophoresis of the
protein in denaturing conditions gave a single band corresponding to a
molecular mass of about 70 kDa (Fig. 1). This is consistent with the
value determined from the amino acid sequence (68,290 Da). The purity and the
molecular mass of the protein were further confirmed by electrospray mass
spectrometry, which shows that the purity exceeds 95%.
Monitoring dsDNA
unwinding with FRET
The principle of the
method is schematically shown in Fig. 2. The upper strand of the duplex
was labeled with hexachlorofluorescein at the 5' end, whereas the
complementary strand was labeled with fluorescein at the 3' end. The
fluorescence emission spectrum of 3'-fluorescein-labeled ssDNA and the
excitation and emission spectra of 5'-hexachlorofluorescein-labeled ssDNA
are shown in Fig. 3(A). It can be seen there is a large spectrum overlap
between the fluorescein emission and hexachlorofluorescein excitation spectra.
After annealing and formation of dsDNA, when the fluorescein and
hexachlorofluorescein are in close proximity, FRET will occur between the two
fluorescent molecules. Fluorescence emission of fluorescein (525 nm) becomes
reduced and that of hexachlorofluorescein (556 nm) enhanced [Fig. 3(B)].
In the case of dsDNA unwinding studied, the situation is reversed, that is,
fluorescence emission of fluorescein (525 nm) becomes enhanced and that of
hexachlorofluorescein (556 nm) reduced.
To determine whether the
enhancement of fluorescein emission at 525 nm will be detected as a result of
dsDNA unwinding by RecQ, we performed fluorescence measurement under unwinding
reaction conditions before and after initiation of the unwinding activity. RecQ
protein was pre-incubated with fluorescent-labeled dsDNA substrate in unwinding
buffer at 25 ºC, and the emission spectrum was measured. After the addition of
ATP, the emission spectrum measurement was performed (Fig. 4). The
observed enhancement of fluorescein emission at 525 nm is consistent with a
loss of FRET after the dsDNA substrate was unwound by RecQ.
Kinetics of
RecQ-catalyzed DNA unwinding
Using the stopped-flow
fluorescence technique, we studied the kinetic process of RecQ-catalyzed dsDNA
unwinding by monitoring the fluorescence emission enhancement of fluorescein at
525 nm. We performed the experiments at a fixed dsDNA concentration and varying
helicase concentration. The dsDNA substrate and RecQ helicase were mixed and
incubated at 25 ºC for 5 min in unwinding buffer A in syringe 1 and the
unwinding reaction was initiated by rapid mixing with ATP from syringe 4. The
results are given in Fig. 5, where the concentration of
fluorescein-labeled dsDNA is fixed at 2 nM and the kinetic trace at each RecQ
concentration was obtained from an average of three measurements. The unwinding
amplitude (the fraction of duplex unwound) and the observed rate constant were
determined by fitting the experimental results with Equation 1. They are
summarized in Table 2 and shown in Fig. 6. It can be seen that
the unwinding amplitude and unwinding rate increase with increasing [RecQ]. The
unwinding amplitude starts to saturate at [RecQ]=40 nM while the unwinding rate
starts to saturate at slightly higher [RecQ], indicating that dsDNA substrates
are completely saturated by RecQ molecules. The maximum unwinding rate is approximately
3 bp/s, which is consistent with previous experimental results [32].
Effect of Mg2+ and ATP on
unwinding activity
We studied the effect of
Mg2+ and ATP on RecQ helicase activity. It
has been shown that magnesium ions are required for the helicase activity of
RecQ and other helicases [31,35,36]. It was reported that the helicase activity
of RecQ is unexpectedly optimal at a free Mg2+ concentration of
It should be noted that
in our previous work [32], a residual DNA unwinding activity was observed
without magnesium, but no background unwinding was observed in our present
experiments. One possible reason is that the trapping of Mg2+ by EDTA disturbs the stability of
DNA-RecQ complexes and leads to a decrease of the measured anisotropy [32]. In
the present experiments, there would be no change of fluorescence signal as
long as the two strands of dsDNA are not separated.
It is well established
that ATP hydrolysis is required for dsDNA unwinding by RecQ helicase [32,35].
As shown in Fig. 8, DNA unwinding was not observed before the addition
of ATP to initiate the unwinding reaction by RecQ helicase. As a comparison, we
performed another experiment that the unwinding reaction was triggered by the
addition of
Using the
ATPase-deficient mutant, RecQ(K
Polarity of DNA
unwinding by RecQ
Because DNA helicases
are involved in the initiation of replication [5], they may display specific
polarity when they translocate on either the leading (3'®5' polarity) or
lagging (5'®3'
polarity) strand. It is now generally believed that the observed polarity
requirement of helicases is a consequence of a directional bias in
translocation on the ssDNA template (i.e. 3'®5' or 5'®3'). The polarity
of unwinding by DNA helicases can usually be determined using a DNA substrate consisting
of a linear ssDNA template flanking the duplex region at one end. Similar to
many other helicases [37], RecQ requires an ssDNA overhanging adjacent to the
duplex for initiating unwinding activity. We have used fluorescence
polarization assay to determine that the unwinding polarity of RecQ is 3'®5'. Native gel
electrophoresis and autoradiography helicase assay also gave the same results
[35,36]. In our present study, we used two types of dsDNA substrates: one
containing a 3'-ssDNA tail (substrate I) and the other containing a 5'-ssDNA
tail (substrate III). In accordance with previous studies, dsDNA with a 5'-ssDNA
tail is not recognized or unwound by RecQ (Fig. 9). Thus RecQ has a DNA
unwinding activity characteristic of a DNA helicase with a 3'®5' polarity. We
also used a blunt-ended dsDNA (substrate II) to detect the helicase activity of
RecQ. No fluorescence enhancement was detected after addition of ATP as the
concentration of RecQ reached 50 nM (data not shown). This assay could be
widely applied to the determination of unwinding polarity of different
helicases, regardless of monopolar or bipolar helicases, provided that a
suitable, non-inhibitory fluorescent dye is selected to label duplex DNA
substrates [26-28].
Conclusion
The fluorometric
stopped-flow assay based on FRET has been proven to be a powerful method for
the study of DNA unwinding characteristics of helicases such as Rep protein and
WRN helicase [28,30]. Similar fluorescence assays have been widely used to
study other helicases [38-40]. In this work, we
showed that this stopped-flow FRET assay gave some results which are consistent
with those obtained from other assays [31,32,35]. To study the kinetic
mechanisms of DNA unwinding by RecQ helicase, this stopped-flow FRET assay is
ideal because it can provide continuous kinetics data in the millisecond to
second time range. In addition, as demonstrated in the present work, this
fluorescence assay is extremely sensitive, allowing DNA unwinding to be
monitored continuously and in real time at dsDNA concentrations as low as 2 nM.
This assay can be further used to study the rapid kinetic mechanism by which
RecQ helicase unwinds duplex DNA. For example, it is known that RecQ functions
as a monomer [33], but is there any functional interaction of RecQ molecules
during DNA unwinding, as in the case of hepatitis C virus helicase [41]?
Combined with traditional electrophoresis assay and single-molecular helicase
assay [33,42], this fluorometric stopped-flow assay may enable us to find
answers to such important questions.
References
1 West SC. DNA
helicases: New breeds of translocating motors and molecular pumps. Cell 1996,
86: 177-180
2 Marians KJ. Helicase structures: A
new twist on DNA unwinding. Structure 1997, 5: 1129-1134
3 Hall MC, Matson SW. Helicase
motifs: The engine that powers DNA unwinding. Mol Microbiol 1999, 34: 867-877
4 Tuteja N, Tuteja R. Unraveling DNA
helicases: Motif, structure, mechanism and function. Eur J Biochem 2004, 271:
1849-1863
5 Matson SW, Bean DW, George JW. DNA
helicases: Enzymes with essential roles in all aspects of DNA metabolism.
Bioessays 1994, 16: 13-22
6 Lohman TM, Bjornson KP. Mechanisms
of helicase-catalyzed DNA unwinding. Annu Rev Biochem 1996, 65: 169-214
7 Gangloff S, McDonald JP, Bendixen
C, Arthur L, Rothstein R. The yeast type I topoisomerase Top3 interacts with
Sgs1, a DNA helicase homolog: A potential eukaryotic reverse gyrase. Mol Cell
Biol 1994, 14: 8391-8398
8 Stewart E, Chapman CR, Al-Khodairy
F, Carr AM, Enoch T. rqh1+, a
fission yeast gene related to the Bloom's and Werner's syndrome genes, is
required for reversible S phase arrest. EMBO J 1997, 16: 2682-2692
9 Cogoni C, Macino G.
Posttranscriptional gene silencing in Neurospora by a RecQ DNA helicase.
Science 1999, 286: 2342-2344
10 Kusano K, Berres ME, Engels, WR.
Evolution of the RECQ family of helicases: A Drosophila homolog, Dmblm,
is similar to the human bloom syndrome gene. Genetics 1999, 151: 1027-1039
11 Puranam KL, Blackshear PJ. Cloning and
characterization of RECQL, a potential human homologue of the Escherichia
coli DNA helicase RecQ. J Biol Chem 1994, 269: 29838-29845
12 Kitao S, Shimamoto A, Goto M, Miller RW,
13 Matson SW, Tabor S,
14 Abdel-Monem M, Durwald H,
Hoffmann-Berling H. Enzymic unwinding of DNA. 2. Chain separation by an
ATP-dependent DNA unwinding enzyme. Eur J Biochem 1976, 65: 441-449
15 Matson SW, Kaiser-Rogers KA. DNA
helicases. Annu Rev Biochem 1990, 59: 289-329
16 Chakraverty RK, Hickson ID. Defending
genome integrity during DNA replication: A proposed role for RecQ family
helicases. Bioessays 1999, 21: 286-294
17 Hanada K, Ukita T, Kohno Y, Saito K, Kato
JI, Ikeda H. RecQ DNA helicase is a suppressor of illegitimate recombination in
Escherichia coli. Proc Natl Acad Sci
18 Cobb JA, Bjergbaek L, Gasser SM. RecQ
helicases: At the heart of genetic stability. FEBS Lett 2002, 529: 43-48
19 Crabbe L, Verdun RE, Haggblom CI, Karlseder
J. Defective telomere lagging strand synthesis in cells lacking WRN helicase
activity. Science 2004, 306: 1951-1953
20 Zhang AH, Xi XG. Molecular cloning of a
splicing variant of human RECQL helicase. Biochem Biophys Res Commun 2002, 298:
789-792
21 Bjergbaek L, Cobb JA, Gasser SM. RecQ
helicases and genome stability: Lessons from model organisms and human disease.
Swiss Med Wkly 2002, 132: 433-442
22 Shen JC,
23 Dillingham MS, Wigley DB, Webb MR. Direct
measurement of single-stranded DNA translocation by PcrA helicase using the
fluorescent base analogue 2-aminopurine. Biochemistry 2002, 41, 643-651
24 Roman LJ, Kowalczykowski SC.
Characterization of the helicase activity of the E. coli RecBCD enzyme
using a novel helicase assay. Biochemistry 1989, 28: 2863-2873
25 Eggleston AK, Rahim NA, Kowalczykowski
SC. A helicase assay based on the displacement of fluorescent, nucleic
acid-binding ligands. Nucleic Acids Res 1996, 24: 1179-1186
26 Houston P, Kodadek T. Spectrophotometric
assay for enzyme-mediated unwinding of double-stranded DNA. Proc Natl Acad Sci
27 Raney KD, Sowers LC, Millar DP, Benkovic
SJ. A fluorescence-based assay for monitoring helicase activity. Proc Natl Acad
Sci
28 Bjornson KP, Amaratunga M,
30 Choudhary S, Sommers JA, Brosh RM Jr.
Biochemical and kinetic characterization of the DNA helicase and exonuclease
activities of Werner syndrome protein. J Biol Chem 2004, 279: 34603-34613
31 Harmon FG, Kowalczykowski SC. Biochemical
characterization of the DNA helicase activity of the Escherichia coli
RecQ helicase. J Biol Chem 2001, 276: 232-243
32 Xu HQ, Zhang AH, Auclair C, Xi XG. Simultaneously monitoring DNA binding and helicase-catalyzed DNA unwinding by fluorescence polarization. Nucleic Acids Res 2003, 31: e70
33 Xu HQ, Deprez E, Zhang AH, Tauc P,
Ladjimi MM, Brochon JC, Auclair C et al. The Escherichia coli
RecQ helicase functions as a monomer. J Biol Chem 2003, 278: 34925-34933
34 Dou SX, Wang PY, Xu HQ, Xi XG. The DNA
binding properties of the Escherichia coli RecQ helicase. J Biol Chem
2004, 279: 6354-6363
35 Umezu K, Nakayama K, Nakayama H. Escherichia
coli RecQ protein is a DNA helicase. Proc Natl Acad Sci
36 Matson SW. Escherichia coli
helicase II (uvrD gene product) translocates unidirectionally in a 3' to
5' direction. J Biol Chem 1986, 261: 10169-10175
37 Bennett RJ, Keck JL, Wang JC. Binding
specificity determines polarity of DNA unwinding by the Sgs1 protein of S.
cerevisiae. J Mol Biol 1999, 289: 235-248
38 Lucius AL, Wong CJ, Lohman TM.
Fluorescence stopped-flow studies of single turnover kinetics of E. coli
RecBCD helicase-catalyzed DNA unwinding. J Mol Biol 2004, 339: 731-750
39 Stavropoulos DJ, Bradshaw PS, Li X, Pasic
I, Truong K, Ikura M, Ungrin M et al. The Bloom syndrome helicase BLM
interacts with TRF
40 Boguszewska-Chachulska AM, Krawczyk M,
Stankiewicz A, Gozdek A, Haenni AL, Strokovskaya L. Direct fluorometric measurement
of hepatitis C virus helicase activity. FEBS Lett 2004, 567: 253-258
41 Levin MK, Wang YH, Patel SS. The functional interaction of the hepatitis C virus helicase molecules is responsible for unwinding processivity. J Biol Chem 2004, 279: 26005-