J. Biomedical Science and Engineering, 2010, 3, 496-500
doi:10.4236/jbise.2010.35069 Published Online May 2010 (http://www.SciRP.org/journal/jbise/
JBiSE
).
Published Online May 2010 in SciRes. http://www.scirp.org/journal/jbise
A stage-scanning laser confocal microscope and protocol for
DNA methylation sequencing
Vaithilingam Vaishnavi, Litty Varghese, Baquir Mohammed Jaffar Ali
Life Sciences Division, AU-KBC Research Centre, Anna University, Chennai, India.
Received 25 September 2009; revised 20 October 2009; accepted 25 October 2009.
ABSTRACT
Recent understanding of the role of epigenetic regu-
lation in health and disease has necessitated the de-
velopment of newer and efficient methods to map the
methylation pattern of target gene. In this article we
report construction of a stage-scanning laser confocal
microscope (SLCM) and associated protocol that de-
termines the methylation status of target gene. We
have adapted restricted Sanger’s sequencing where
fluorescine labeled primers and dideoxy guanine
fraction alone are used for target amplification and
termination at cytosine positions. Amplified ssDNA
bands are separated in 6% denaturing PAGE and
scanned using SLCM to sequence the positions of
methylated cytosines. We demonstrate that our me-
thodology can detect < 100 femtomoles of DNA, and
resolve the position of cytosine within ± 2 nucleotide.
In a calibration run using a designer DNA of 99 bases,
our methodology had resolved all the 11 cytosine po-
sitions of the DNA. We have further demonstrated
the utility of apparatus by mapping methylation sta-
tus in the Exon-1 region of a gene, E-Cadherin, in the
plasma DNA sample of a healthy subject. We believe
our approach constitute a low cost alternative to
conventional DNA sequencers and can help develop
methylation based DNA biomarkers for the diagnosis
of disease and in therapeutics.
Keywords: Scanning Confocal Microscope; Fluorescence
Detection; Methylation; Bisulfite Sequencing; DNA
Sequencer
1. INTRODUCTION
Cytosine methylation is required for mammalian devel-
opment [1]. Alterations of CpG island DNA hypermethy-
lation and chromatin modification have been widely do-
cumented in human cancers [2,3] and various other dis-
eases [4,5]. Disease-specific DNA methylation altera-
tions present in tissues and plasma samples can serve as
diagnostic markers for risk assessment, progression,
early detection, treatment prediction and monitoring [6].
Therefore determination of methylation status of target
gene is becoming increasingly important in diagnosis
and treatment. Most laboratories use high performance
liquid chromatography (HPLC) for the detection of 5-
methylcytosine residues [7]. However, HPLC requires
large amount of DNA and significant experimental ex-
perience to obtain reproducible results. Both points are
impedimental to the large-scale analysis of clinical sam-
ples [8]. Bisulfite genomic sequencing provides an effi-
cient method for detecting individual 5-methyl cytosine
(5-MeC) residues in genomic DNA [9]. Analysis of cy-
tosine methylation from the bisulfite- treated and
PCR-amplified DNA can be determined by either clon-
ing or sequencing individual molecules or by direct PCR
sequencing [10]. In cloning approach, it often requires
sequencing of 50-100 individual clones to provide an
accurate estimate of methylation in the population of
molecules. Whereas in sequencing, standard sequencing
is performed using DNA sequencers.
In most situations, methylation status of promoter is
taken as indicator to decide gene is expressed or re-
pressed. It is determined by methylation-specific PCR
(MSP) which detects the presence of methylated DNA in
CpG islands of the promoter [11]. In MSP, primers are
designed to bind specifically to bisulfite converted me-
thylated or unmethylated DNA, leading to specific am-
plification. Advantage of this technique is its high rela-
tive sensitivity, ease of design, and low complexity of
the reaction, but it is limited to determining the methyla-
tion status only in the primer binding region. Therefore,
a new strategy is required to know complete methylation
status of target gene.
Complete information of methylation status can usu-
ally be derived from sequencing the DNA. The current
state-of-the-art technology for high-throughput DNA
sequencing utilizes capillary array DNA sequencers with
laser-induced fluorescence detection [12-15]. In the case
of methylation mapping of the genome, it is redundant to

V. Vaishnavi et al. / J. Biomedical Science and Engineering 3 (2010) 496-500 497
sequence the bisulfite converted DNA when sequence
information of the genome is already known. Any ap-
proach which can by-pass the complete sequencing re-
quirement can be more efficient, faster and resource
conserving.
In this communication, we report the customized in-
strument and protocol for fluorescence detection of DNA
bands, reporting methylation status in a target gene. An
automated stage-scanning laser confocal microscope
(SLCM) has been constructed and calibrated using fluo-
rescently labeled oligo DNA of known lengths. Avoiding
detail sequencing of the target gene and thus eliminating
the use of DNA sequencer has remained a major objec-
tive in our endeavor. In addition, our novel approach in
the protocol enabled mapping the methylation status of
the target gene in detail that can match sequencing of the
gene.
2. METHODS
2.1. Sample Preparations for Bisulfite
Sequencing
2.1.1. DNA Extraction and Sodium Bisulphite
Conversion
Genomic DNA from human blood plasma was isolated
from 1 mL of serum collected from a normal subject
using standard phenol/chloroform method and resus-
pended in 100 µL of water [16]. About 1 µg of DNA was
denatured by NaOH followed by treatment with sodium
bisulfite to convert all unmethylated cytosine to uracil
[17]. Bisulfite treated DNA samples were purified using
the Wizard DNA clean-up system (Promega Corp. USA),
followed by NaOH treatment and ethanol precipitation.
Finally it is resuspended in 20 µl of water.
2.1.2. Amplification of Target DNA
Following two DNA templates were designed and syn-
thesized for calibration of the instrument. Template A:
5’CGA TCG TAT TCG GCG TTT GTT TTC GTTCGG
CGT TTT CGG TTA GTT ATG GGT TTT TGG AGT
CGT AGT TTT TCG GCG TTG TTG TTG TTG TTG
TAG GTA TTT3’ containing 11 CpG spots, and Tem-
plate B: 5'CGA TAG TAT TAG GCG TTT GTT TTA
GTT AGG AGT CTT GGT TAG TTA TGG GTT TTT
GGA GTC GTA GTT TTT CGG GTT GTT GTT GTT
GTT GTA GGT ATT T3’ containing 5 CpG spots, mim-
icking methylated cytosine positions. Using MethPrimer
[18] primer without CpG dinucleotides and devoid of
regions with poly T ≥ 9 is designed to amplify ssDNA
Templates A and B, and target in Exon-1 region of
E-cadherin. The resulting primer synthesized with Fluo-
rescein label (6-FAM) at 5’ is given by: Flu-5’ AAA
TAC CTA CAA CAA CAA CAA CAA C3’ (Ocimum
Biosolutions, Hyderabad). Restricted Sanger’s sequenc-
ing reaction specifically developed for this [19] was
performed using SILVER SEQUENCETM DNA se-
quencing system (Promega Corp. USA) on these tem-
plates. In that dideoxy guanine fraction alone is used so
as to terminate the amplicons at all cytosine positions
which corresponds to methylated cytosines. The opti-
mized thermal cycling condition giving best results were
as follows: 95℃ for 2 min, 35 cycles of 95℃ for 30 sec,
42℃ for 30 sec and 72℃ for 60 sec.
2.1.3. Electrophoresis Separation
Control ssDNA templates of various sizes containing
Fluorescine tag at 5’ end, and the bisulfite PCR products
were separated on 6% denaturing PAGE in 89 mM Tris,
89 mM boric acid, 2 mM ethylenediamine tetra acetic
acid (EDTA) at field strength of 10 V/cm for various
time interval. Before loading the sample into the gel, an
aliquot of the PCR mixture prepared above was added to
2 µL of glycerol and heated at 95℃ for 3 min to dena-
ture the amplicons. Concentration of control ssDNA
templates were gradually decreased in different lanes to
determine lowest possible concentration that can be de-
tected and resolved by the apparatus.
2.2. Stage-Scanning Laser Confocal Microscope
(SLCM)
The optical layout of the SLCM setup is schematically
represented in Figure 1. The apparatus is built around
the Nikon TE2000 microscope frame. The sample
stage consists of a motorized XY translator having 100
mm displacement in each axis (Model: DPM Transla-
tor with Micro Position Controller, Holmarc, India). A
custom built stage plate with 90 mm by 90 mm square
slot constitute platform for gel scan. The 473 nm
DPSS laser, CW/100 mW (Model: Ceil, Laser Quan-
tum, UK) is used for fluorescence excitation. The laser
Figure 1. Optical lay-out of stage-scanning laser confocal
microscope. OBJ: Objective lens; SF: Spatial filter; DM:
Dichroic mirror; M1 and M2: Visible reflecting mirrors; BE:
5x beam expander; ND: Neutral density filter; F: Emission
filter; L: convex lens; I: Iris; PMT: Photomultiplier Tube;
LB: laser beam; CV: confocal volume; CS; confocal volume
section; SW: Sample well; AG: acrylamide gel.

498 V. Vaishnavi et al. / J. Biomedical Science and Engineering 3 (2010) 496-500
beam is expanded to fill the back-focal plane of the 20
X objective (Nikon). A rectangular slit is introduced as
a spatial filter to section the confocal volume to a thin
rectangular confocal volume-section. It is aligned par-
allel to the DNA bands so as to efficiently excite fluo-
rescine tagged to the DNA and minimize the back-
ground noise in emission signal. The emission is col-
lected through an iris acting as a confocal spatial filter
at left port of the microscope. The photomultiplier tube
(Hamamatsu H7468) serves as the detector.
2.3. Data Acquisition and Control
XY-Stage and PMT are controlled through RS232 inter-
face. Linear scan is made at a speed of 0.9 mm/s and
fluorescence signal is acquired by PMT set at 550 V, 100
ms integration with 0.01 ms dead time interval. Typical
scan of the full length gel is about 80 mm for ~ 89 sec,
giving ~11data points per mm scan. The laser power at the
back-focal plane of the objective is ~3.5 mW.
2.4. Resolution and Sensitivity
Ability to resolve ssDNA bands is determined by re-
solving 20 to 43 bases oligo DNA for lower lengths and
73 and 76 bases oligo DNA for longer length. Sensitivity
of detection is determined by linear dilution of control
ssDNA templates. The optimized scanning and detection
protocol given in the above section was followed th-
roughout the measurement of sensitivity & resolution as
well as for mapping the methylation pattern in ssDNA
templates and target gene in human genomic DNA.
3. RESULT AND DISCUSSION
3.1. Characterization of SLCM
3.1.1. Sensitivity
Figure 2(a) demonstrates the ability of the apparatus to
resolve less than 100 femtomole of fluorescine tagged
DNA. The quantity of ssDNA detected is less than typi-
cal amount of DNA available in sequencing PCR prod-
ucts in laboratory conditions. Further, perusal of instru-
ment parameters for SLCM suggests that there is more
room to improve the fluorescence detection which may
bring down the sensitivity level even further.
3.1.2. Resolution
Following the same parameters for detection, Figure 2(b)
gives the resolution of four short length oligos differing
in two bases. In Figure 2(c), resolution of three base
differences in longer length oligo is demonstrated. To
further demonstrate the ability to resolve multiple bands,
ssDNA ladder of eight bands is scanned and given in
Figure 2(d). Scrutiny of DNA band separation in Figure
2 suggests that the ability to resolve further is limited by
short mobility of bands. In the current configuration, we
have practical limitation of 80 mm scan of the sample
which limits the maximum distance over which ssDNA
bands can run. In other words, longer scan length will be
in a position to resolve the bands to single base resolu-
tion. Since methyl sequences can occur at minimum of
two bases difference, we have not further explored the
ability of the instrument to resolve better.
3.2. Methylation Mapping in Genomic DNA
Efficient, unbiased PCR amplification from methylated
and unmethylated genomic DNA is essential for any
PCR amplification-dependent method designed to detect
methylation following bisulphite conversion. Amplicons
generated from methylated genomic DNA remains CpG
rich relative to the amplicons from unmethylated ge-
nomic DNA, and are often amplified less efficiently.
Amplicons from bisulphite-converted genomic DNA
typically have homopolymer stretches of 9 or more Ts
(As), resulting in poor (or no) amplification. A broad-
ened signal have been observed during electrophoresis
for these amplicons due to enzyme “slippage” causing n
+ 1 and n – 1 sequences [20]. By selecting amplicons
containing no more than 5 consecutive Ts (or As), our
PCR was almost always successful. Achieving these two
requirements–avoiding homopolymer stretches and de-
signing a primer in a non-CpG region often restricts
primer selection to a single possibility for any amplicons
within CpG Island.
Following specifically developed restricted Sanger’s
sequencing protocol [19], two ssDNA templates having
known numbers of cytosines were subjected for methyl
sequencing. Figure 3(a) gives resolution of all eleven
positions present in the ssDNA Template-A, and Figure
3(b) gives all the five positions present the in ssDNA
Template-B. In Figure 4(a), methyl sequencing results on
the bisulfite treated human genomic DNA at DNA target
Figure 2. Demonstrates sensitivity and resolution of SCLM. (a)
Detection of 100 femtomoles of ssDNA of 43bases; (b) Resolu-
tion of oligos of length 20, 23, 25 and 43 bases; (c) Resolution
of oligos of length 72 and 76 bases; (d) Resolution of set of 8
ssDNA Templates length varying from 26 bases to 99 bases.

V. Vaishnavi et al. / J. Biomedical Science and Engineering 3 (2010) 496-500 499
on Exon-1 using methylation insensitive primer is given.
As a control for resolution of DNA bands, three ssDNA
templates of known bases run concurrently on parallel
lane is given in Figure 4(b). In Figure 4(c), band posi-
tion of known control DNA ladder is plotted against the
base number. The data is fit to a polynomial to interpo-
late unknown base information corresponding to position
information. For pedagogical reason all possible CpG
positions within 100 bases are plotted (red diamonds).
From the precise band position of methyl sequenced
DNA in Figure 4(b), and the known corresponding base
information, unknown nucleotide sequence is obtained
through interpolation of fit in Figure 4(c). It is observed
that the target gene had only 30 and 64 base positions
from 3’ end of the primer found to be methylated. It is
noted that only two cytosines are methylated out of 15
available CpG positions. Ability to retrieve all amplicons
in template DNA (Figures 3(a) and 3(b)) suggests that
the target sequence in human genomic DNA is partially
methylated at the CpG islands in the promoter region.
We emphasis that in prototype resolution of DNA bands
in this manner can be software-controlled by inputting
the calibration parameters into the system, giving raise
to instant reading of target DNA band sequence. Infor-
mation on methylation sequence position together with
quantitative gene expression data can shed more light on
the mechanism of epigenetic regulation. More signifi-
cantly, ability of SLCM to obtain quantitative informa-
tion on DNA methylation as well as to track its position
precisely anywhere in the target sequence can open up
many possibilities including development of DNA me-
thylation as biomarkers.
4. CONCLUSIONS
It is demonstrated that a customized SLCM apparatus
can efficiently resolve ssDNA separation in acrylamide
Figure 3. Resolution of methyl sequencing bands in ssDNA
Templates. (a) Separation of methylation bands in ssDNA Tem-
plate-A and; 9b) Separation of bands in ssDNA Template-B.
Figure 4. (a) Methyl sequencing of target gene in human ge-
nomic sample using SLCM. Human genomic DNA amplified
at the target sequence in Exon-1 region of E-cadhrein, mapped
using methyl insensitive in SLCM; (b) Resolution of three
known length ssDNA templates runs concurrently with ge-
nomic DNA as control; (c) Calibration of DNA band separation
distance versus base number. Blue solid circles represents con-
trol ladder of known number of bases. Continuous line is fit to
the data and red diamonds represents possible CpG positions
within the target region.
gel. We have applied this to map the methylation pattern
of target gene. Our SLCM built on low-cost but high
sensitive photon detector enabled discrimination of DNA
bands of less than 100 femtomoles. Perusal of the pa-
rameters of excitation and detection reveal tremendous
scope to engineer the sensitivity and resolution in the
same configuration. We note that the geometry of fluo-
rescence excitation achieved by using a spatial filter is
confocal volume-section instead of volume. It has con-
siderably improved the signal-to-noise. We have also
outlined how the current specification can be improved
with extension of scan length and modification. Further,
XY scan of gel can enable mapping multiple lanes,
thereby sequencing long length of target in a gene or
multiple targets in the same genome. We emphasize that
normally methylation status away from promoter region
or more specifically, away from primer region could not
be obtained in any methods except complete sequencing

500 V. Vaishnavi et al. / J. Biomedical Science and Engineering 3 (2010) 496-500
(1), 119-127.
of the gene. Striking outcome of the approach presented
here is that along with specifically developed methyl
sequencing protocol, simple ways to methyl sequence
the target gene and access information on the status of
methylation away from the promoter region is demon-
strated.
[10] Grigg, G
.W. and Clark, S.J. (1994) Sequencing 5-methy-
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431-436.
[11] Herman, J.G., Graff, J.R., Myohanen, S., Nelkin, B.D. and
Baylin, S.B. (1996) Methylation-specific PCR: A novel
PCR assay for methylation status of CpG islands. Pro-
ceedings of the National Academy of Sciences, 93(18),
9821-9826.
5. ACKNOWLEDGEMENTS
We thank S. Navaneethakrishnan for his help. This work was sup-
ported by Department of Science and Technology, Government of
India Grant No. DST/TSG/PT/2006/63.
[12] Stach, D., et al. (2003) Capillary electrophoretic analysis
of genomic DNA methylation levels. Nucleic Acids Re-
search, 31(2), e2.
JBiSE
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