KR20110055247A - Real-time dna sequencing method using multi-photon excitation - Google Patents

Real-time dna sequencing method using multi-photon excitation Download PDF

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KR20110055247A
KR20110055247A KR1020090112190A KR20090112190A KR20110055247A KR 20110055247 A KR20110055247 A KR 20110055247A KR 1020090112190 A KR1020090112190 A KR 1020090112190A KR 20090112190 A KR20090112190 A KR 20090112190A KR 20110055247 A KR20110055247 A KR 20110055247A
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waveguide
dna
excitation light
fluorescence
dna sequencing
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KR1020090112190A
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Korean (ko)
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조성호
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삼성전자주식회사
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    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869Methods for sequencing
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/52Use of compounds or compositions for colorimetric, spectrophotometric or fluorometric investigation, e.g. use of reagent paper and including single- and multilayer analytical elements
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2521/00Reaction characterised by the enzymatic activity
    • C12Q2521/10Nucleotidyl transfering
    • C12Q2521/101DNA polymerase
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2563/00Nucleic acid detection characterized by the use of physical, structural and functional properties
    • C12Q2563/107Nucleic acid detection characterized by the use of physical, structural and functional properties fluorescence

Abstract

PURPOSE: A real-time DNA sequencing method using multi-photon excitation is provided to block excitation light through a transmission line and to easily supply fluorescence-labeled DNA. CONSTITUTION: A method for real-time DNA sequencing using multi-photon excitation comprises: a step of conjugating DNA polymerase(130) on a synthesis region on a transmission line(110) mounted in a substrate(100); a step of providing DNA template strain or fluorescence-labeled DNA base; a step of irradiating multi-photon excitation light to the synthesis region; and a step of detecting emitted fluorescence using a light detector(140).

Description

Real-time DNA sequencing method using multi-photon excitation

A real-time DNA sequencing method using multi-photon excitation.

A zero-mode waveguide is a metal hole formed by forming a cylindrical hole of several tens of nanometers in diameter on a transparent glass plate, which is called a metal waveguide. A DNA polymerase is attached to the bottom of the metal waveguide, and four DNA bases labeled with a strand of DNA template and fluorescent materials of different colors are introduced through the entrance of the metal waveguide. When the illumination light is exposed to a metal waveguide at the bottom of the substrate, fluorescence occurs when the DNA polymerase binds the complementary DNA base to the DNA base of the DNA template strand. This fluorescence is detected by the metal waveguide and the scanning device located below the glass substrate.

Provides a real-time DNA sequencing method using multi-photon excitation.

Attaching a DNA polymerase to the synthesis region on the waveguide provided in the substrate; Supplying a DNA base labeled with a DNA template strand or fluorescent material; Irradiating multi-photon excitation light to the synthesis region; And detecting fluorescence emitted from the fluorescent material excited by the excitation light with a photodetector.

An anti-reflection film may be formed on the waveguide to prevent reflection of the fluorescence.

The multi-photon excitation light may have an absorption peak that is an integer multiple of the excitation wavelength of the fluorescent material.

The multi-photon excitation light is a two-photon excitation light. The two-photon excitation light may include light having an absorption peak at a wavelength corresponding to twice the absorption peak of the fluorescent material.

The synthetic region can be hydrophilic surface treated to attach a DNA polymerase.

The top of the waveguide may be concave to facilitate attachment of the DNA polymerase.

The waveguide may have a tapered structure so that the DNA polymerase is easily attached.

The diameter of the waveguide may be determined to block the excitation light through the waveguide and transmit the fluorescence.

The diameter r of the waveguide may satisfy r = λ c / n (where λ c is a blocking wavelength and satisfies a wavelength of fluorescence <λ c <excitation light, and n is a refractive index of the waveguide).

The cross section of the waveguide may be circular or polygonal.

The fluorescence may be detected by placing the photodetector close to or in contact with the lower portion of the waveguide.

The DNA polymerase can be located on the top surface of the waveguide without being located at the bottom of the waveguide, thereby facilitating the supply of DNA bases labeled with fluorescent material. Since the excitation light is blocked by the waveguide, there is no need for a dichroic filter that separates the excitation light and the fluorescence. In addition, contact and proximity detection of fluorescence emitted from excited fluorescent materials is possible.

Hereinafter, exemplary embodiments of the present invention will be described in detail with reference to the accompanying drawings. However, the examples exemplified below are not intended to limit the scope of the present invention, but are provided to fully explain the present invention to those skilled in the art. In the drawings, like reference numerals refer to like elements, and the size of each element in the drawings may be exaggerated for clarity and convenience of description.

Referring to FIG. 1, the disclosed DNA sequencing apparatus includes a substrate 100, one or more waveguides 110 penetrating through the substrate 100, and a photodetector 140 under the waveguide 110. As the substrate 100, a metal, a semiconductor, or a dielectric such as a polymer or glass may be used. The synthesis region 125 to which the DNA polymerase 130 is attached is provided on the upper surface of the waveguide 110. The one or more synthetic regions 125 are spaced apart from each other, and may correspond to the one or more waveguides 110 one-to-one. Although not shown in the figure, one or more composite regions 125 may be arranged in two dimensions, such as a matrix. For example, the synthesis region 125 may have a diameter of several hundred nm when its cross section is circular, which is just one example, and the cross section of the synthesis region 125 may be a polygon such as a rectangle or a pentagon. Synthetic region 125 may be hydrophilic surface treated to facilitate attachment of DNA polymerase 130.

In the disclosed composite region 125, an anti-reflection film 120 may be provided. Therefore, the surface of the anti-reflection film 120 becomes the compound region 125 itself. The anti-reflection film 120 prevents the reflection of the fluorescence emitted from the fluorescent material labeling the DNA base. The anti-reflection film 120 may be disposed to cover the end of the waveguide 110 exposed to the substrate 100. The anti-reflection film 120 may be formed of a material having affinity for the DNA polymerase 130, a DNA base labeled with a fluorescent substance, or a liquid in which they are dispersed so that the DNA polymerase 130 may be attached well. The anti-reflection film 120 is not an essential component and may be omitted. When the anti-reflection film 120 is omitted, the surface of the synthesis region 125 may be surface treated to have affinity for the DNA polymerase 130, the DNA base labeled with the fluorescent substance, or the liquid in which they are dispersed. For example, when the substrate 100 is formed of a hydrophobic material such as silicon (Si), the synthetic region 125 may be locally oxidized to be surface treated to be hydrophilic.

One or more waveguides 110 are formed through the substrate 100. One end of the waveguide 110 is placed on the side to which the DNA polymerase 130 of the substrate 100 is attached, and the other end of the waveguide 110 is the surface to which the DNA polymerase 130 of the substrate 100 is attached. On the back side of the One end region of the waveguide 110 lying on the side of the substrate 100 to which the DNA polymerase 130 is attached may correspond to the synthetic region 125 to which the DNA polymerase 130 may be easily attached. The upper portion of the waveguide 110 may be made concave to facilitate attachment of the DNA polymerase 130. In addition, the waveguide 110 may be tapered to facilitate attachment of the DNA polymerase 130.

The at least one waveguide 110 may be formed of a material that transmits fluorescence emitted from the excited fluorescent material and blocks excitation light that excites the fluorescent material, and a cross section may be circular or polygonal. The shape of this cross section may correspond to the shape of the composite region 125. As the waveguide 110, a material having a pass band of a wavelength band of fluorescence may be used. For example, the semiconductor, polymer or dielectric material of the transparent material may be dyed with a dye belonging to the wavelength range of fluorescence, or the pigment, which belongs to the wavelength range of fluorescence, may be formed on the transparent semiconductor, polymer or dielectric material. . Such dyes or pigments used in the waveguide 110 are well known in the field of display technology or optics, and thus detailed descriptions thereof will be omitted.

When sequencing DNA using a zero-mode waveguide, the DNA polymerase should be located at the bottom of the waveguide hole, and the circulation of the solution moves the DNA base labeled with fluorescent material to the bottom of the waveguide hole where the DNA polymerase is located. There was a difficulty.

In the disclosed DNA sequencing method, the DNA polymerase 130 may be attached to the synthesis region 125 provided on the upper surface of the waveguide 110. Therefore, the DNA polymerase 130 can be easily supplied with a DNA template strand or a DNA base labeled with a fluorescent substance. The DNA polymerase 130 is an enzyme that assists in DNA replication and catalyzes DNA synthesis along the DNA template strand. A DNA labeled strand and a base labeled with a fluorescent substance are supplied to the DNA polymerase 130 attached to the synthesis region 125. DNA bases, namely adenine (A), guanine (Guanine, G), cytosine (C), and thymine (T) are labeled with different fluorescent materials. The fluorescent material may be bound to the base of the DNA base, or may be bound to the phosphate group of the DNA base. The DNA polymerase 130 attached to the synthesis region 125 captures a DNA base complementary to the DNA template strand to synthesize a new DNA strand. When the excitation light is irradiated to the synthesis region 125, when the DNA base labeled with the fluorescent material is bound by the DNA polymerase 130, the excited fluorescent material is separated from the DNA base to emit fluorescence. The emitted fluorescence may be detected by the photodetector 140 provided under the waveguide.

The excitation light may use multi-photon excitation. Hereinafter, a case of two-photon excitation will be described as an example. The excitation light of two-photon excitation includes light of a wavelength corresponding to twice the absorption peak of the fluorescent material. In this case, the fluorescent material is hardly excited by the single-photon, but excited by the two-photon because the wavelength of the two-photon coincides with the wavelength of the absorption band of the fluorescent material. In order to excite four different color fluorescent materials, excitation light having four different peak wavelengths is grouped together. Four DNA base-fluorescent material complexes with different absorption bands for two-photon absorb two different photon excitation light and emit four different colors of fluorescence.

Since the excitation light itself is longer than the cutoff wavelength of the waveguide 110, the excitation light cannot pass through the waveguide 110, and the fluorescence is shorter than the cutoff wavelength of the waveguide 110.

Figure 112009071172056-PAT00001

In Equation 1, λ c satisfies a wavelength of fluorescence <λ c <excitation light as a cutoff wavelength of the waveguide 110, n is a refractive index of the waveguide 110, and r is a diameter of the waveguide 110. As shown in Equation 1, the cutoff wavelength of the waveguide 110 is a product of the refractive index and the diameter of the waveguide 110, and when light of longer wavelength is incident into the waveguide 110 in the form of an evanescent wave. Pass through to low depths only. The maximum passing depth of the two-photon excitation light is within several micrometers for about 100 nm longer than the blocking wavelength in visible and near infrared. The fluorescence that has passed through the waveguide 110 may be detected by the photodetector 140, and the DNA base labeled by the fluorescent substance may be determined. Therefore, DNA sequencing is possible by determining four DNA bases A, G, C, and T synthesized by the DNA polymerase 130.

For example, when the blocking wavelength condition of the excitation light is determined to be 800 nm or less longer than the longest wavelength peak among four kinds of fluorescent colors, the excitation light having a wavelength peak of 800 nm or more does not pass through the waveguide 110. If the excitation wavelength peaks of the four kinds of first to fourth fluorescent materials are 450 nm, 500 nm, 550 nm, and 600 nm, respectively, the two-photon excitation light is 900 nm, 1000 nm, 1100 nm, It has an absorption peak at 1200 nm. The wavelength peak of each fluorescence becomes 500 nm, 550 nm, 600 nm, and 650 nm longer than the excitation wavelength peak by stokes shift. In this case, the shortest wavelength peak among the excitation light wavelength peaks is 900 nm. Since the wavelength peak of the excitation light is longer than the blocking wavelength, the excitation light cannot pass through the waveguide 110. In addition, since the longest peak of the wavelength peaks of the four different fluorescence is 650 nm, since all the fluorescence has a wavelength peak shorter than the blocking wavelength, all the fluorescence can pass through the waveguide 110.

Under the condition that the blocking wavelength is 800 nm, when the refractive index (for example, the refractive index is 1 or more) when the material of the waveguide 110 is an oxide, the diameter of the waveguide 110 is about 550 nm or less. If the diameter of the waveguide 110 is too small, even fluorescence cannot pass, so that the fluorescence is not blocked, the diameter of the waveguide 110 is 450 nm or more. When the diameter of the waveguide 110 is 550 nm or less, the passing depth of the evanescent wave of the excitation light is within several micrometers. As such, the diameter of the waveguide 110 may be determined to block excitation light and transmit fluorescence.

Referring to FIG. 4, it is shown how deep the excitation light having four different wavelength peaks can pass into the waveguide 110 in the waveguide 110 having a blocking wavelength of 800 nm. The passing depth d is given by Equation 2 below.

Figure 112009071172056-PAT00002

In Equation 2, n is the refractive index of the waveguide 110, λc is the blocking wavelength of the waveguide 110, λ is the wavelength of the excitation light passing through the waveguide 110. Referring to FIG. 4, as the wavelength of the excitation light increases, the excitation light may pass deeply into the waveguide 110, but most of the excitation light may be blocked at a depth of 1 μm or less.

Three-photon excitation has an absorption peak at three times the wavelength of the excitation wavelength peak of the fluorescent material, and four-photon excitation has four times the excitation wavelength peak of the fluorescent material. It has an absorption peak at the wavelength of. In the case of more multi-photon excitation, the same principle has an absorption peak at a wavelength of an integral multiple of the excitation wavelength peak of the fluorescent material. In general, two-photon excitation can be most efficient because the absorption cross section decreases as the photon multiple increases.

The fluorescence is generated by the excitation light, and the downward fluorescence is emitted toward the rear surface of the substrate 100 via the waveguide 110. On the other hand, the excitation light is also directed downward but can pass only a very low depth through the waveguide 110 as described above. Since only the fluorescence is emitted when viewed from the back of the substrate 100, it is possible to determine the type of DNA base synthesized through the fluorescence image seen from the back. When sequencing DNA using a zero-mode waveguide, a dichroic filter is essential, in which excitation light and fluorescence both enter and exit from the waveguide to separate excitation light and fluorescence. According to the disclosed DNA sequencing method, since the excitation light is blocked by the waveguide 110 and only the fluorescence passes through the waveguide 110, a separate dichroic filter is not required.

As described above, the fluorescence emitted from the fluorescent material labeled with the DNA base is emitted to the back of the substrate 100 through the waveguide 110. The fluorescence that has passed through the waveguide 110 may be detected by the photodetector 140, and the photodetector 140 may include an image sensor itself such as a photomultiplier tube (PMT), a charge coupled device (CCD), and a CMOS image sensor (CIS). Or a scanner using such an image sensor. At this time, the fluorescence emitted from the end of the waveguide 110 on the rear side of the substrate 100 is focused at a Rayleigh length. Rayleigh length means the distance from the point where a light beam is condensed and the cross-sectional area becomes the minimum and the cross-sectional area doubles. Accordingly, the photodetector 140 may be disposed to be in contact with the DNA sequencing apparatus as shown in FIG. 1 or may be disposed proximity to a Rayleigh distance as shown in FIG. 2 to improve fluorescence detection efficiency. .

Referring to FIG. 2, one or more waveguides 110 may include a core 113 and a cladding layer 115. The core 113 may be formed of a material that transmits fluorescence emitted from the excited fluorescent material and blocks excitation light that excites the fluorescent material. The cross section of the core 113 may be circular or polygonal. The shape of this cross section may correspond to the shape of the composite region 125. The core 113 may be made of a material having a pass band of the wavelength band of fluorescence. For example, the semiconductor, polymer or dielectric material of the transparent material may be dyed with a dye belonging to the wavelength band of fluorescence, or the pigment, which belongs to the wavelength band of fluorescence, may be formed on the semiconductor, polymer or dielectric material of the transparent material. Such dyes or pigments used in the core 113 are well known in the field of display technology or optics, and thus detailed descriptions thereof will be omitted.

The cladding layer 115 surrounding the core 113 may be formed of a material having a refractive index lower than that of the core 113 so as to totally reflect fluorescence passing through the core 113. For example, the cladding layer 115 may be formed of oxides such as MgO 2 and SiO 2 . In some cases, a dopant may be added to the clad layer 115 to further lower the refractive index of the clad layer 115, or conversely, a dopant may be added to the core to relatively increase the refractive index of the core 113. If the refractive index of the substrate 100 is smaller than the refractive index of the core 113, the cladding layer 115 may be omitted, and the substrate 100 around the core 113 may function as the cladding layer 115. . If both the core 113 and the cladding layer 115 are dielectrics, no blocking wavelength exists, but the size of the core 113 may be determined to maximize fluorescence progress and minimize transmission of excitation light. DNA sequencing method using the DNA sequencing device shown in Figure 2 can determine the nucleotide sequence as described above. Components not described among the components of the DNA sequencing apparatus illustrated in FIG. 2 are substantially the same as corresponding components of the DNA sequencing apparatus illustrated in FIG. 1, and thus redundant descriptions thereof will be omitted.

3A to 3D, the types of DNA bases synthesized by the DNA polymerase 130 are determined by detecting the first to fourth fluorescence emitted from the first to fourth fluorescent materials 150, 155, 160 and 165. The steps are shown. Referring to FIG. 3A, the DNA polymerase 130 synthesizes adenine labeled with the first fluorescent substance 150 on a new DNA strand. When the multi-photon excitation light is irradiated to the synthesis region 125, the first fluorescent material is released as the first fluorescent material 150 labeled with adenine is separated from the adenine as soon as the adenine is synthesized on the new DNA strand. The multi-photon excitation light is blocked by the waveguide 110, but the first fluorescence passes through the waveguide 110 and is detected by the photodetector 140. Therefore, it can be determined that the DNA base synthesized through the detected first fluorescence is adenine. 3B to 3D detect the second to fourth fluorescence emitted from the second to fourth fluorescence materials 155, 160 and 165 through the same process, and the DNA base synthesized by the DNA polymerase 130 is represented. The steps for determining guanine, cytosine and thymine, respectively, are shown. Components not described among the components of the DNA sequencing apparatus illustrated in FIGS. 3A to 3D are substantially the same as corresponding components of the DNA sequencing apparatus illustrated in FIG. 1, and thus redundant descriptions thereof will be omitted.

DNA sequencing method using the present invention multi-photon excitation has been described with reference to the embodiment shown in the drawings for clarity, but this is merely illustrative, and those skilled in the art from various modifications and It will be appreciated that other equivalent embodiments are possible. Therefore, the true technical protection scope of the present invention will be defined by the appended claims.

1 shows a DNA sequencing apparatus for use in the disclosed DNA sequencing method.

FIG. 2 shows a DNA sequencing device, in which the cladding layer is further provided in the DNA sequencing device of FIG. 1.

3A to 3D show the detection steps of the first to fourth fluorescence emitted from the first to fourth fluorescence materials separated from adenine, guanine, cytosine, and thymine labeled with fluorescence of different colors, respectively.

Fig. 4 shows the waveguide passage depth of excitation light having four different wavelengths when the blocking wavelength of the waveguide is 800 nm in the case of two-photon excitation.

<Brief description of the major symbols in the drawings>

100: substrate 110: waveguide

115: cladding layer 120: antireflection film

125: synthetic region 130: DNA polymerase

140: photodetector 150: first fluorescent material

155: second fluorescent material 160: third fluorescent material

165: fourth fluorescent material

Claims (11)

Attaching a DNA polymerase to the synthesis region on the waveguide provided in the substrate; Supplying a DNA base labeled with a DNA template strand or fluorescent material; Irradiating multi-photon excitation light to the synthesis region; And DNA sequencing method comprising the step of detecting the fluorescence emitted from the fluorescent material excited by the excitation light with a photodetector. The method of claim 1, Wherein said multi-photon excitation light has an absorption peak that is an integer multiple of the excitation wavelength of said fluorescent material. The method of claim 1, Wherein said multi-photon excitation light is a two-photon excitation light, and said two-photon excitation light comprises light having an absorption peak at a wavelength corresponding to twice the absorption peak of said fluorescent material. The method of claim 1, A DNA sequencing method in which an antireflection film is formed on the waveguide to prevent reflection of the fluorescence. The method of claim 1, The synthesis region is a DNA sequencing method is a hydrophilic surface treatment so that the DNA polymerase can be attached. The method of claim 1, A DNA sequencing method in which the upper portion of the waveguide is concave to facilitate attachment of the DNA polymerase. The method of claim 1, The DNA sequencing method is made of a tapered structure so that the DNA polymerase is easily attached. The method of claim 1, DNA sequencing method for determining the diameter of the waveguide in order to block the excitation light through the waveguide and transmit the fluorescence. The method of claim 8, The diameter r of the waveguide satisfies r = λ c / n (where λ c is the blocking wavelength to satisfy the wavelength of the fluorescence <λ c <the wavelength of the excitation light and n is the refractive index of the waveguide). DNA sequencing method. The method of claim 1, DNA sequencing method wherein the cross section of the waveguide is circular or polygonal. The method of claim 1, DNA sequencing method for detecting the fluorescence by placing the photodetector close to or in contact with the lower portion of the waveguide.
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