JP5582557B2 - Pyrimidine nucleoside compounds and uses thereof - Google Patents

Description

  The present invention relates to a novel pyrimidine nucleoside compound, and more particularly to a novel pyrimidine nucleoside compound that can be reversibly isomerized by light irradiation.

  Nucleic acids have various functions by taking higher order structures. Therefore, if the higher-order structure of a nucleic acid can be controlled by an external stimulus such as light, the function of the nucleic acid can be easily controlled, which is considered to have great significance in the fields of biology and medicine.

  As an attempt to control the structure of a nucleic acid, a technique for introducing a photo-responsive substituent into a nucleic acid has been developed. As such a technique, for example, caged nucleic acids in which a photolabile group is introduced into a nucleobase have been proposed (Non-Patent Documents 1 to 5). According to this, the structure of the nucleic acid can be changed by light irradiation.

  In addition, a technique has been proposed in which azobenzene that undergoes EZ isomerization reaction by light irradiation is introduced into the backbone or sugar of a nucleic acid (Non-Patent Documents 6 to 9). According to this, ON / OFF of activity can be reversibly controlled by the difference in influence on the nucleic acid higher order structure in EZ isomerization of azobenzene.

Furthermore, a method for introducing styrene into the base moiety of deoxyguanosine has been proposed (Non-patent Document 10). According to this, EZ isomerization reaction of an ethylenic double bond part can be caused by light irradiation, and a change in higher order structure can be caused. In addition, repeated photoisomerization is possible.
X. Tang, J. Swaminathan, AM Gewirtz, and IJ Dmochowski, Nucleic Acids Res. 2008, 36, 559-569. S. Shah, S. Rangarajan, and SH Friedman, Angew. Chem. Int. Ed. 2005, 44, 1329-1332. L. Krock, and A. Heckel, Angew. Chem. Int. Ed. 2005, 44, 471-473. C. Hobarter, and SK Silverman, Angew. Chem. Int. Ed. 2005, 44, 7305-7309. H. Lusic, DD Young, MO Lively, and A. Deiters, Org. Lett. 2007, 9, 1903-1906. H. Asanuma, D. Matsunaga, and M. Komiyama, Nucleic Acids Symposium Series. 2005, 49, 35-36. D. Matsunaga, H. Asanuma, and M. Komiyama, J. Am. Chem. Soc. 2004, 126, 11452-11453. MZ Liu, H. Asanuma, and M. Komiyama, J. Am. Chem. Soc. 2006, 128, 1009-1015. S. Keiper, and JS Vyle, Angew. Chem. Int. Ed. 2006, 45, 3306-3309. S. Ogasawara, I. Saito, and M. Maeda, Tetrahedron Lett. 2008, 49, 2479-2482.

  However, the above-mentioned caged nucleic acid has a problem that its photoreaction is irreversible and can be controlled only once and in one direction. Moreover, fluorescence cannot be controlled.

  On the other hand, in a nucleic acid in which azobenzene is introduced into a nucleic acid backbone or sugar, a photoreaction can occur reversibly. Therefore, ON / OFF of activity can be reversibly controlled. However, by introducing bulky azobenzene, there is a problem that the higher-order structure of the nucleic acid is distorted in both the E-form and the Z-form, and the activity is lowered. This becomes more prominent when a plurality of azobenzenes are introduced. However, since a plurality of azobenzenes are required to control the nucleic acid higher order structure, a dilemma occurs. Moreover, fluorescence cannot be controlled like caged nucleic acid.

8-Styryl-2′-deoxyguanosine (hereinafter referred to as ^8ST G) described in Non-Patent Document 10 is a photoisomerizable nucleoside. According to this, it is considered that a photoisomerizable nucleic acid that avoids the problems in the caged nucleic acid and the azobenzene-introduced nucleic acid can be provided.

  By the way, since a higher order structure can be formed only with a base, it is desirable to cause isomerization in the base part from the viewpoint of higher order structure control. Moreover, when the site | part modified is a base part, it is preferable at the point which does not inhibit double helix structure formation of DNA, and higher-order structure formation (for example, ribozyme and aptamer) of RNA. Therefore, development of further nucleosides capable of photoisomerization at the base moiety is desired.

  Therefore, the present invention has been made in view of the above problems, and an object thereof is to provide a novel nucleoside compound that can be reversibly isomerized by light irradiation.

  As a result of diligent investigations by the inventors to solve the above-mentioned problems, a novel compound capable of reversibly isomerizing with light by introducing an aryl group or heteroaryl group via an ethylenic double bond at the 5-position of a pyrimidine nucleoside. The inventors have found that a nucleoside can be obtained and have completed the present invention.

  That is, the pyrimidine nucleoside compound according to the present invention is a pyrimidine nucleoside compound in which a group represented by the following general formula (1) is bonded to the 5-position carbon atom of the pyrimidine nucleus in order to solve the above-mentioned problems. .

(In General Formula (1), A represents an aryl group or a heteroaryl group, the aryl group and the heteroaryl group may have a substituent, and * 1 represents a carbon atom at the 5-position of the pyrimidine nucleus; Represents the bonding position of.
The pyrimidine nucleoside compound according to the present invention is preferably a uridine derivative.

  In the pyrimidine nucleoside compound according to the present invention, A is preferably an aryl group or a heteroaryl group having 10 to 20 ring atoms.

  In the pyrimidine nucleoside compound according to the present invention, A is preferably a pyrenyl group or a 9H-fluorenyl group.

  In addition, the isomerization method according to the present invention is a method of isomerizing the pyrimidine nucleoside compound by irradiating the pyrimidine nucleoside compound with light.

  Moreover, the method for changing the optical characteristics according to the present invention is a method for changing the optical characteristics of the pyrimidine nucleoside compound by irradiating the pyrimidine nucleoside compound with light.

  The polynucleotide according to the present invention is a polynucleotide containing a base derived from the pyrimidine nucleoside compound.

  Moreover, the method for changing the thermal stability according to the present invention is a method for changing the thermal stability of the polynucleotide by irradiating the polynucleotide with light.

  An optical switching device material according to the present invention is an optical switching device material containing at least one of the pyrimidine nucleoside compound and the polynucleotide.

  As described above, the pyrimidine nucleoside compound according to the present invention is a compound in which the group represented by the general formula (1) is bonded to the carbon atom at the 5-position of the pyrimidine nucleus. Therefore, it is possible to provide a new nucleoside compound capable of reversibly switching the structure and optical properties by light.

  Hereinafter, although embodiment of this invention is described, this invention is not limited to this.

[Pyrimidine nucleoside compound]
The pyrimidine nucleoside compound according to the present invention is a pyrimidine nucleoside compound in which a group represented by the following general formula (1) is bonded to the carbon atom at the 5-position of the pyrimidine nucleus.

(In General Formula (1), A represents an aryl group or a heteroaryl group, the aryl group and the heteroaryl group may have a substituent, and * 1 represents a carbon atom at the 5-position of the pyrimidine nucleus; Represents the bonding position of.
The group represented by the general formula (1) can reversibly cause EZ isomerization of the ethylenic double bond portion by two kinds of light having different wavelengths. Therefore, by introducing the above group, a nucleoside compound capable of reversibly changing the structure by light irradiation can be obtained.

  Hereinafter, the pyrimidine nucleoside compound of the present invention will be described in more detail.

  In the present specification, when a certain functional group or atom may have a substituent, the type of substituent, the number thereof, and the substitution position are not particularly limited. Specific examples of the substituent include a halogen atom ( For example, fluorine atom, chlorine atom, bromine atom and iodine atom, preferably bromine atom), aryl group (preferably substituted or unsubstituted aryl group having 6 to 30 carbon atoms, such as phenyl group, tolyl group, xylyl group, mesityl group , Biphenylyl group, naphthyl group, anthryl group, phenanthryl group, fluorenyl group and pyrenyl group), an alkyl group (preferably a substituted or unsubstituted alkyl group having 1 to 20 carbon atoms, for example, methyl group, ethyl group, propyl group, isopropyl group) Group, n-butyl group, sec-butyl group, tert-butyl group, n-pentyl group, neopentyl group, hex Group, heptyl group, octyl group, nonyl group, decyl group, undecyl group, dodecyl group, cyclopentyl group, cyclohexyl group, benzyl group, phenethyl group, diphenylmethyl group and a trityl group). In addition, “carbon number” for a certain group means the carbon number of a portion not containing this substituent for a group having a substituent.

  In this specification, the “pyrimidine nucleoside compound” is a glycoside compound containing a pyrimidine nucleus in which a pyrimidine base and a reducing group of a sugar are bonded by a glycosidic bond.

  Further, in this specification, the “pyrimidine nucleus” refers to a structure represented by the following general formula (2) or (3).

(In the above general formulas (2) and (3), Z ₁ represents an amino group or a protecting group thereof, and * 2 represents a bonding position with a sugar.)
Examples of the protecting group for Z ₁ include triazole, dimethylformamidine, diisobutylformamidine, acetyl group, isobutyl group, benzoyl group, 9-fluorenylmethyloxycarbonyl group (Fmoc), and tert-butoxycarbonyl group (Boc). Can be mentioned.

  In the pyrimidine nucleoside compound of the present invention, the group represented by the general formula (1) is bonded to the 5-position carbon atom of the pyrimidine nucleus. The pyrimidine nucleoside compound becomes either E-form or Z-form by isomerization of the ethylenic double bond part. Specifically, in the case of a pyrimidine nucleoside compound having a structure of the above general formula (3) as the pyrimidine nucleus, for example, it becomes one of the following E-form or Z-form.

(In the above, A and * 2 are synonymous with A and * 2 in the general formulas (1) to (3), respectively.)
The aryl group represented by A in the general formula (1) may be monocyclic or condensed cyclic, and the aryl group may have a substituent. Examples of such aryl groups include phenyl groups; naphthyl groups, as-indacenyl groups, s-indacenyl groups, acenaphthylenyl groups, 9H-fluorenyl groups, phenanthryl groups, anthryl groups, fluoranthenyl groups, acephenanthrylenyls. Aryl groups having 10 to 20 ring atoms such as a group, an aseantrirenyl group, a triphenylenyl group, a pyrenyl group, a chrycenyl group, a tetraphenyl group, a naphthacenyl group and a perylenyl group; Although the aryl group of several 21-30 etc. can be mentioned, it is not limited to these. The aryl group is preferably an aryl group having 10 to 20 ring atoms and a phenyl group having a substituent. As the phenyl group having a substituent, a phenyl group having an electron donating group or an electron withdrawing group such as a nitro group, a diethylamino group, a dimethylamino group, a trifluoromethyl group, a methoxy group, a carbonyl group and a halogen as a substituent. Is mentioned. Among these, as the aryl group, an aryl group having 10 to 20 ring atoms is more preferable, and a naphthyl group, 9H-fluorenyl group, and pyrenyl group are more preferable.

  Examples of the heteroaryl group represented by A in the general formula (1) include a heteroaryl group containing one or more heteroatoms selected from the group consisting of a nitrogen atom, an oxygen atom and a sulfur atom as a ring constituent atom. And may be either monocyclic or condensed cyclic. Moreover, the heteroaryl group may have a substituent. Examples of such heteroaryl groups include monocyclic heteroaryl groups having 5 or 6 ring atoms containing a nitrogen atom as a heteroatom such as pyrrolyl and imidazolyl groups; rings containing a nitrogen atom as a heteroatom such as an indolyl group Condensed cyclic heteroaryl group having 7 to 9 atoms; isoquinolinyl group, 2,7-naphthyridinyl group, 2,6-naphthyridinyl group, 1,6-naphthyridinyl group, 1,5-naphthyridinyl group, quinoxalinyl group, quinazolinyl group , Cinnolinyl group, 9H-carbazolyl group, 9H-β-carbolinyl group, phenanthridinyl group, 1H-perimidinyl group, 4,7-phenanthrolinyl group, 3,8-phenanthrolinyl group and 2,9 -For phenanthrolinyl group such as phenanthrolinyl group, phenazinyl group, and tebenidinyl group The 10H- Kindoriniru of the group, and the like, such as heteroaryl group ring members 10 to 20 containing a nitrogen atom as a hetero atom, but is not limited thereto. The heteroaryl group is preferably a heteroaryl group having 10 to 20 ring atoms. Among these, the heteroaryl group is more preferably a substituted or unsubstituted 9H-carbazolyl group, and more preferably an unsubstituted 9H-carbazolyl group.

  In the present specification, the “number of ring-constituting atoms” represents the number of atoms constituting the ring without considering the substituent. In the case of an aryl group, the number of ring-constituting atoms is the number of carbon atoms constituting the ring, for example, 16 for a pyrenyl group. In the case of a heteroaryl group, the number of ring-constituting atoms is the total number of carbon atoms and heteroatoms constituting the ring, for example 10 for a quinoxalinyl group.

  The bonding position with the ethylenic double bond in the aryl group and heteroaryl group is not particularly limited, and may be appropriately determined depending on the group used, the synthesis method, and the like. In the examples described later, they are 2-9H-fluorenyl and 2-pyrenyl. Moreover, when it is a naphthyl group, 2-naphthyl is preferable.

  When A in the general formula (1) is an aryl group having 10 to 20 ring atoms, a phenyl group having a substituent, or a heteroaryl group having 10 to 20 ring atoms, E → Z isomerization In both the Z and E isomerizations, light having a longer wavelength than that in the case where A is a phenyl group having no substituent (for example, light having a wavelength exemplified in the isomerization method described later) is used. Can cause isomerization reaction. Specifically, Z → E isomerization can be performed using light of 290 nm or more. Therefore, in this case, damage to the pyrimidine nucleoside compound due to light and damage to the oligonucleotide containing the base derived from the pyrimidine nucleoside compound of the present invention (for example, formation of a pyrimidine dimer) can be reduced, and a more stable pyrimidine nucleoside can be obtained. Compounds and oligonucleotides can be provided. Moreover, since the bulk is increased as compared with a phenyl group having no substituent, the three-dimensional structure of an oligonucleotide incorporating a base derived from the compound can be controlled more effectively.

  The structure of the sugar moiety to which the pyrimidine nucleus to which the group represented by the general formula (1) is bonded is glycosidically bonded is not particularly limited, and examples thereof include sugar moieties contained in known nucleoside compounds, More specifically, sugar moieties contained in the general formulas (4) and (5) described later can be exemplified.

  As a preferred embodiment of the pyrimidine nucleoside compound of the present invention, a uridine derivative represented by the following general formula (4) in which a group represented by the general formula (1) is bonded to the carbon atom at the 5-position of the pyrimidine nucleus, And cytidine derivatives represented by the following general formula (5). The following general formulas (4) and (5) show the E form, but the pyrimidine nucleoside compound of the present invention is not limited to the E form and may be a Z form.

(In the above general formulas (4) and (5), R ₁ and R ₂ are each independently a hydroxyl group or a protecting group thereof, a reactive group that can be introduced for the production of an oligonucleotide, or a self-organization of a nucleoside derivative. R ₃ represents a hydrogen atom, a hydroxyl group or a protecting group thereof, a reactive group that can be introduced for the production of an oligonucleotide, or a self-assembly of a nucleoside derivative. R ₄ represents an amino group or a protecting group thereof, and A has the same meaning as A in the general formulas (1) to (3).
Examples of the protecting group for R _{1 to} R ₃ include isobutyl, tert-butyldimethylsilyl (TBDMS), triisopropylsilyloxymethyl (TOM), and dimethoxytrityl (DMTr). Examples of the reactive group include 2-cyanoethyl-N, N, N ′, N′-tetraisopropyl phosphoramidite. The details of the above atomic group are described in K. Araki, I. Yoshikawa, Top. Curr. Chem., 2005, 256, 133-165. Specific examples of the atomic group include an acyl chain and an ester chain. Two or more of R _{1 to} R ₃ may be linked to form a ring. Examples of the protecting group for R ₄ include triazole, dimethylformamidine, diisobutylformamidine, acetyl group, isobutyl group, benzoyl group, 9-fluorenylmethyloxycarbonyl group (Fmoc), and tert-butoxycarbonyl group (Boc). Can be mentioned.

  Specific examples of the uridine derivative represented by the general formula (4) include compounds represented by the following general formulas (4-1) and (4-2). Further, specific examples of the cytidine derivative represented by the general formula (5) include compounds represented by the following general formulas (5-1) and (5-2).

(In the above formula, A has the same meaning as A described above.)
The method for synthesizing the pyrimidine nucleoside compound of the present invention is not particularly limited. For example, the 5-position halogen atom of a pyrimidine nucleoside derivative in which the 5-position carbon atom is halogenated (hereinafter also referred to as “halogenated nucleoside derivative”). Is substituted with a vinyl group, and hydrogen of the vinyl group is substituted with an aryl group or a heteroaryl group, a pyrimidine nucleoside compound to which a group represented by the general formula (1) is bonded can be obtained.

  Specifically, 5-iodouridine (IDU) obtained by protecting 5′-OH with DMTr was reacted with tributylvinyltin at 110 ° C. in the presence of a palladium catalyst to replace the 5-position of the pyrimidine nucleus with a vinyl group. -Get vinyluridine (Still coupling). Next, the obtained 5-vinyluridine is reacted with 2-bromopyrene at 115 ° C. in the presence of a palladium catalyst to obtain 5-pyrenylvinyluridine in which the hydrogen of the vinyl group is substituted with pyrene (Heck) reaction).

  The details of the synthesis reaction of the pyrimidine nucleoside compound according to the present invention can be referred to the examples described later. In addition, the raw materials and reagents used for the reaction can be synthesized by known methods, and some are available as commercial products. After the synthesis reaction, the target substance can be obtained by performing purification by a known method as necessary. Whether the target substance has been obtained can be confirmed by identification methods such as NMR and mass spectrometry. The pyrimidine nucleoside compound described above may form a salt depending on the type of functional group and substituent, and may form a hydrate or solvate in a free state or a salt state. This state is also included in the scope of the present invention.

  The pyrimidine nucleoside compound of the present invention can reversibly control the structural change (isomerization). Further, the structure can be changed by turning on / off the light source, and the structure control is easy. It is also expected that it can be used for nucleic acid synthesis by using an appropriate polymerase.

  Introducing a photoresponsive group to the base moiety has little influence on the entire molecular structure, and thus it is considered that the activity can be controlled while maintaining the function of the nucleic acid. Since the polynucleotide comprising a base derived from the pyrimidine nucleoside compound of the present invention has a modified base part, the effect of the above modification on the formation of a double helix structure of DNA and the formation of higher-order structures such as RNA ribozymes and aptamers. Can be performed well without receiving. In the pyrimidine nucleoside compound of the present invention, since a photoresponsive group is introduced at the 5-position of the pyrimidine nucleus, hydrogen bonding with a complementary strand is not inhibited in the polynucleotide. In particular, when a B-type double helix is controlled, the steric hindrance with the backbone can be almost eliminated in the E body.

  The pyrimidine nucleoside compound of the present invention can be easily introduced into a polynucleotide by a nucleic acid amplification technique such as PCR or RCA for the same reason. In addition, a polynucleotide containing a base derived from the pyrimidine nucleoside compound of the present invention can be synthesized using a nucleotide derived from the pyrimidine nucleoside compound of the present invention by a known nucleic acid synthesis technique.

[Isomerization method and method of changing optical properties]
Furthermore, the present invention provides a method for isomerizing the compound by irradiating the pyrimidine nucleoside compound of the present invention with light, and changes the optical properties of the compound by irradiating the pyrimidine nucleoside compound of the present invention with light. Regarding the method.

  As described above, the pyrimidine nucleoside compound of the present invention can reversibly cause EZ isomerization of the ethylenic double bond portion of the group represented by the general formula (1). Since the pyrimidine nucleoside compound of the present invention has high stability in both E-form and Z-form, isomerization does not proceed unless irradiated with light, and isomerization (E → Z isomerization and Z → E isomerism) occurs by light irradiation. Control). E → Z isomerization can occur by irradiating the E form with ultraviolet light or visible light (for example, light having a wavelength of 350 to 500 nm). Z → E isomerization can be caused by irradiating Z-form with light having a shorter wavelength than the light used for E → Z isomerization (for example, a wavelength of 290 to 350 nm). Both E → Z photoisomerization and Z → E photoisomerization can proceed easily at room temperature. The isomerization conditions such as the light irradiation time for isomerization, the light source used and the intensity of the irradiation light may be set as appropriate. Regarding the isomerization conditions, the examples described later can also be referred to.

  The pyrimidine nucleoside compound of the present invention differs in optical characteristics such as absorption spectrum, fluorescence intensity, and quantum yield between E-form and Z-form. Therefore, the photophysical properties of the pyrimidine nucleoside compound of the present invention can be changed by isomerization by light irradiation. Furthermore, since photoisomerization can occur reversibly, the light characteristics of the compound can be reversibly changed by repeatedly irradiating the pyrimidine nucleoside compound of the present invention with light of different wavelengths. The light irradiation conditions for changing the light characteristics are as described above.

[Method of changing thermal stability]
Furthermore, the present invention relates to a method for changing the thermal stability of the polynucleotide by irradiating the polynucleotide of the present invention with light.

Since the polynucleotide of the present invention contains a base derived from the aforementioned pyrimidine nucleoside compound, it contains a pyrimidine nucleus to which a group represented by the general formula (1) is bonded via an ethylenic double bond. Therefore, EZ isomerization of this ethylenic double bond can be reversibly caused by light irradiation. The polynucleotide of the present invention differs in thermal stability such as melting temperature ( _Tm value) between E-form and Z-form.

  Therefore, the thermal stability of the polynucleotide of the present invention can be changed by isomerization by light irradiation. Furthermore, the change in thermal stability due to light irradiation can occur reversibly. The light irradiation conditions for changing the thermal stability are the same as the light irradiation conditions for isomerizing the pyrimidine nucleoside compound.

  In the present specification, the polynucleotide is in the E form (Z form), which is represented by the general formula (1) when the polynucleotide contains one base derived from the above-described pyrimidine nucleoside compound. It shall refer to a polynucleotide in which the positional relationship between the group and the pyrimidine nucleus to which the group is bonded is E-form (Z-form). Moreover, in this embodiment, although the polynucleotide containing one base derived from the above-mentioned pyrimidine nucleoside compound is described, the number of bases derived from the above-mentioned pyrimidine nucleoside compound contained in the polynucleotide of the present invention. Is not limited to one base.

[Optical switching device materials]
Furthermore, the present invention relates to an optical switching device material comprising at least one of the pyrimidine nucleoside compound of the present invention and a polynucleotide derived from the pyrimidine nucleoside compound.

  The optical switching type device material of the present invention comprises at least one of the pyrimidine nucleoside compound of the present invention and one or more of the above polynucleotides. The optical switching device material of the present invention can also contain other components commonly used in electronic devices.

  In the present invention, the “light switching type” refers to a property capable of switching functions and structures by light irradiation. As described above, the pyrimidine nucleoside compound of the present invention can be reversibly isomerized by light irradiation to change the structure, and the optical characteristics can be changed accordingly. By utilizing this property, for example, by switching the state of the E body to ON or 1 of the bit in the digital signal and setting the state of the Z body to OFF or 0 of the bit in the digital signal, electronic devices such as switching elements and storage elements can be obtained. Can be formed. In particular, the optical switching device material of the present invention is suitable as an optical switch of an optically driven nanodevice.

  Examples will be shown below, and the embodiments of the present invention will be described in more detail. Of course, the present invention is not limited to the following examples, and it goes without saying that various aspects are possible in detail. Further, the present invention is not limited to the above-described embodiments, and various modifications can be made within the scope shown in the claims, and the present invention is also applied to the embodiments obtained by appropriately combining the disclosed technical means. It is included in the technical scope of the invention. Moreover, all the literatures described in this specification are used as reference.

  The following examples will be described with reference to the following schematic scheme 1.

Example 1: Synthesis of 5'-O- (4,4'-dimethoxytrityl) -5-iodo-2'-deoxyuridine
2.0 g of 5-iodo-2′-deoxyuridine (Compound 1 in Scheme 1) was placed in a two-necked eggplant type flask and azeotroped three times with pyridine (10 mL). Subsequently, pressure reduction and nitrogen substitution were repeated three times, and the inside of the system was sufficiently substituted with nitrogen. 30 mL of pyridine and 6 mL of triethylamine were added thereto, and 2.10 g of dimethoxytrityl chloride dissolved in pyridine (10 mL) was slowly added dropwise at 0 ° C. Thereafter, the reaction solution was stirred at room temperature for 5 hours. After the reaction, the solvent was removed by an evaporator and then purified by a medium pressure liquid chromatograph. At that time, chloroform / methanol was used as a developing solvent. By collecting the fraction containing the desired product and removing the developing solvent, 2.97 g of 5′-O- (4,4′-dimethoxytrityl) -5-iodo-2′-deoxyuridine (compound in Scheme 1) 2) was obtained as a white powder. The identification results are shown below.
¹ H NMR (CDCl ₃ ) δ: 8.15 (s, 1H), 7.22-7.42 (m, 11H), 6.84 (m, 4H), 6.32 (dd, J = 7.8, 6.4, 1H), 4.55 (m, 1H ), 4.10 (m, 1H), 3.79 (s, 6H), 3.41 (dd, J = 10.7, 2.9, 1H), 3.36 (dd, J = 10.7, 2.9, 1H), 2.51 (ddd, J = 13.7, 5.4, 2.0, 1H), 2.29 (m, 1H). FAB MS (M + H) ⁺ Calculated: 657.12; Found: 657.14.

[Example 2: Synthesis of 5'-O- (4,4'-dimethoxytrityl) -5-vinyl-2'-deoxyuridine]
700 mg of 5′-O- (4,4′-dimethoxytrityl) -5-iodo-2′-deoxyuridine obtained in Example 1 was placed in a two-necked eggplant type flask, and 3 mL of N-methylpyrrolidone was added. After that, the solution was bubbled with argon gas for 10 minutes. Next, 134 mg of tetrakis (triphenylphosphine) palladium and 0.62 mL of tributylvinyltin were added, and the reaction solution was heated to reflux at 110 ° C. for 1 hour. After the reaction, it was purified by medium pressure liquid chromatography. At that time, chloroform / methanol was used as a developing solvent. By collecting the fraction containing the desired product and removing the developing solvent, 176 mg of 5′-O- (4,4′-dimethoxytrityl) -5-vinyl-2′-deoxyuridine (Compound 3 in Scheme 1) Was obtained as a white powder. The identification results are shown below.
¹ H NMR (CDCl ₃ ) δ: 9.09 (s, 1H), 7.68 (s, 1H), 7.39 (d, J = 7.3, 1H) 7.32-7.23 (m, 9H), 6.86-6.81 (m, 4H) , 6.40 (t, J = 7.32, 1H), 4.93 (dd, J = 10.3, 3.4, 1H), 4.56 (s, 1H), 4.10 (d, J = 2.9, 1H), 3.45 (dd, J = 10.7 , 3.4, 1H), 3.37 (dd, J = 10.7, 3.4, 1H), 2.47 (ddd, J = 13.6, 5.4, 2.9, 1H), 2.32-2.26 (m, 1H), 1.81 (s, 1H). ¹³ C NMR (CDCl ₃ ) δ: 161.9, 158.7, 149.6, 144.2, 136.7, 136.1, 135.4, 135.3, 130.0, 128.1, 128.0, 127.5, 127.1, 123.8, 116.4, 113.3, 113.2, 112.8, 86.9, 86.2, 85.0 77.2, 72.1, 63.4, 55.2, 41.1. FAB MS (M + H) ⁺ Calculated: 557.23; Found: 557.19.

[Example 3: Synthesis of 5'-O- (4,4'-dimethoxytrityl) -5-((E) -2- (pyrenyl) vinyl) -2'-deoxyuridine]
141 mg of triphenylphosphine was placed in a two-necked eggplant type flask, and vacuuming and nitrogen substitution were repeated three times to sufficiently purge the system with nitrogen. Thereto were added 10 mL of DMF, 48.5 mg of palladium (II) acetate, and 449 mL of triethylamine, and the mixture was stirred at 60 ° C. for 10 minutes. After confirming that the reaction solution turned wine red, 911 mg of 1-bromopyrene dissolved in DMF (5 mL) and 1.2 g of 5 ′ obtained in Example 2 dissolved in DMF (5 mL) were obtained. -O- (4,4'-dimethoxytrityl) -5-vinyl-2'-deoxyuridine was added in order, and the mixture was heated to reflux at 115 ° C for 1 hour. After the reaction, the catalyst was removed by filtration, and the filtrate was purified by medium pressure liquid chromatography. At that time, chloroform / methanol was used as a developing solvent. By collecting the fraction containing the desired product and removing the developing solvent, 1.04 g of 5′-O- (4,4′-dimethoxytrityl) -5-((E) -2- (pyrenyl) vinyl)- 2′-Deoxyuridine (Compound 4 in Scheme 1) was obtained as an orange oil. The identification results are shown below.
¹ H NMR (CDCl ₃ ) δ: 9.37 (s, 1H), 8.54 (d, J = 16.1, 1H), 8.20 (d, J = 9.8, 1H), 8.12-7.58 (m, 8H), 7.51-7.08 (m, 9H), 6.68 (d, J = 8.8, 1H), 6.53 (dd, J = 7.8, 6.3, 1H), 6.35 (d, J = 16.1, 1H), 4.61 (s, 1H), 4.18 ( s, 1H), 3.64-3.58 (m, 1H), 3.35 (dd, J = 10.7, 2.9, 1H), 2.61-2.56 (m, 1H), 2.47-2.40 (m, 1H). ¹³ C NMR (CDCl ₃ ) δ: 162.6, 162.0, 158.6, 149.5, 144.2, 137.3, 135.3, 135.2, 132.1, 131.4, 130.9, 130.6, 129.9, 128.2, 128.1, 127.7, 127.3, 127.2, 127.1, 125.8, 125.0, 124.9, 124.8, 124.7, 123.5, 123.4, 123.3, 123.1, 86.9, 86.6, 85.4, 77.2, 72.5, 63.5, 54.9, 41.4, 36.5, 31.4. FAB MS (M + H) ⁺ Calculated: 757.29; Found: 757.23.

[Example 4: Synthesis of 5'-O- (4,4'-dimethoxytrityl) -5-((E) -2- (fluorenyl) vinyl) -2'-deoxyuridine]
141 mg of triphenylphosphine was placed in a two-necked eggplant type flask, and vacuuming and nitrogen substitution were repeated three times to sufficiently purge the system with nitrogen. Thereto were added 10 mL of DMF, 48.5 mg of palladium (II) acetate, and 449 mL of triethylamine, and the mixture was stirred at 60 ° C. for 10 minutes. After confirming that the reaction solution turned wine red, 794 mg of 2-bromofluorene dissolved in DMF (5 mL) and 1.2 g of 5 obtained in Example 2 dissolved in DMF (5 mL) were obtained. '-O- (4,4'-dimethoxytrityl) -5-vinyl-2'-deoxyuridine was added in order, and the mixture was heated to reflux at 115 ° C for 1 hour. After the reaction, the catalyst was removed by filtration, and the filtrate was purified by medium pressure liquid chromatography. At that time, chloroform / methanol was used as a developing solvent. By collecting the fraction containing the desired product and removing the developing solvent, 854 mg of 5′-O- (4,4′-dimethoxytrityl) -5-((E) -2- (fluorenyl) vinyl) -2 ′ -Deoxyuridine (compound 5 in Scheme 1) was obtained as a yellow powder. The identification results are shown below.
¹ H NMR (CDCl ₃ ) δ: 9.33 (s, 1H), 8.03 (s, 1H), 7.70 (d, J = 7.8, 1H), 7.11-7.53 (m, 14H), 6.90-6.96 (m, 2H ), 6.77 (m, 4H), 6.49 (m, 1 H), 6.36 (d, J = 16.1, 1H), 4.57 (s, 1H), 4.15 (m, 1H), 3.59-3.69 (m, 8H) , 3.31 (m, 1H), 2.54 (m, 1H), 2.39 (m, 1H), 1.85 (s, 1H) 13 C NMR (CDCl 3) δ:. 162.1, 158.6, 149.6, 144.3 143.5, 143.2, 141.4 , 141.0, 136.0, 135.8, 135.5, 135.4, 130.6, 129.9, 128.0, 127.2, 126.7, 126.5, 126.4, 125.6, 124.9, 122.7, 119.8, 119.5, 113.3, 113.1, 86.8, 86.5, 85.3, 72.4, 63.5, 55.1 , 41.4, 36.6. FAB MS (M + H) ⁺ Calculated: 757.29; Found: 757.23.

[Example 5: 5'-O- (4,4'-dimethoxytrityl) -3'-O- (2-cyanoethoxy- (N, N-diisopropylamino) -phosphino) -5-((E)- Synthesis of 2- (pyrenyl) vinyl) -2′-deoxyuridine]
620 mg of 5′-O- (4,4′-dimethoxytrityl) -5-((E) -2- (pyrenyl) vinyl) -2′-deoxyuridine obtained in Example 3 was added to a 2-neck eggplant-shaped flask. The pressure reduction and nitrogen substitution were repeated three times to sufficiently purge the system with nitrogen. Thereto was added 5 mL of dichloromethane, 449 mL of 2-cyanoethyltetraisopropylphosphorodiamidite, and 3.95 mL of 0.25M tetrazole dissolved in acetonitrile, and the mixture was stirred at room temperature for 1 hour. After the reaction, the solvent was removed and the product was purified by medium pressure liquid chromatography. At that time, dichloromethane / methanol was used as a developing solvent. By collecting the fraction containing the desired product and removing the developing solvent, 454 mg of 5′-O- (4,4′-dimethoxytrityl) -3′-O- (2-cyanoethoxy- (N, N-diisopropyl) Amino) -phosphino) -5-((E) -2- (pyrenyl) vinyl) -2′-deoxyuridine (Compound 6 in Scheme 1) was obtained as a yellow powder. The identification results are shown below.
FAB MS (M + H) ⁺ Calculated: 957.40; Found: 957.50.

[Example 6: 5'-O- (4,4'-dimethoxytrityl) -3'-O- (2-cyanoethoxy- (N, N-diisopropylamino) -phosphino) -5-((E)- Synthesis of 2- (fluorenyl) vinyl) -2′-deoxyuridine]
620 mg of 5′-O- (4,4′-dimethoxytrityl) -5-((E) -2- (fluorenyl) vinyl) -2′-deoxyuridine obtained in Example 4 was added to a 2-neck eggplant-shaped flask. The pressure reduction and nitrogen substitution were repeated three times to sufficiently purge the system with nitrogen. Thereto were added 5 mL of dichloromethane, 301 mL of 2-cyanoethyltetraisopropylphosphorodiamidite, and 3.79 mL of 0.25M tetrazole dissolved in acetonitrile, and the mixture was stirred at room temperature for 1 hour. After the reaction, the solvent was removed and the product was purified by medium pressure liquid chromatography. At that time, dichloromethane / methanol was used as a developing solvent. By collecting the fraction containing the target product and removing the developing solvent, 512 mg of 5′-O- (4,4′-dimethoxytrityl) -3′-O- (2-cyanoethoxy- (N, N-diisopropyl) Amino) -phosphino) -5-((E) -2- (fluorenyl) vinyl) -2′-deoxyuridine (Compound 7 in Scheme 1) was obtained as a yellow powder. The identification results are shown below.
FAB MS (M + H) ⁺ Calculated: 921.40; Found: 921.12.

Example 7: 5′-O- (4,4′-dimethoxytrityl) -3′-O- (2-cyanoethoxy- (N, N-diisopropylamino) -phosphino) -4- (1,2, Synthesis of 4-triazolyl) -5-((E) -2- (pyrenyl) vinyl) -2′-deoxyuridine]
1.17 g of 1,2,4-triazole was placed in a two-necked eggplant-shaped flask, and vacuuming and nitrogen substitution were repeated three times to sufficiently purge the system with nitrogen. Thereto were added 25 mL acetonitrile, 334 mL sulfolyl chloride, and 2.36 mL triethylamine, and the mixture was stirred at 0 ° C. for 30 minutes. 5′-O- (4,4′-dimethoxytrityl) -3′-O- (2-cyanoethoxy- (N, N-diisopropylamino) -phosphino obtained in Example 5 then dissolved in acetonitrile ) -5-((E) -2- (pyrenyl) vinyl) -2'-deoxyuridine (250 mg) was added, and the mixture was stirred at 0 ° C for 2 hours. After the reaction, the solvent was removed and the product was purified by medium pressure liquid chromatography. At that time, dichloromethane / methanol was used as a developing solvent. By collecting the fraction containing the desired product and removing the developing solvent, 165 mg of 5′-O- (4,4′-dimethoxytrityl) -3′-O- (2-cyanoethoxy- (N, N-diisopropyl) was obtained. Amino) -phosphino) -4- (1,2,4-triazolyl) -5-((E) -2- (pyrenyl) vinyl) -2'-deoxyuridine (Compound 8 in Scheme 1) as a yellow powder Obtained. The identification results are shown below.
FAB MS (M + H) ⁺ Calculated: 1010.44; Found: 1010.63.

[Example 8: Photoisomerization reaction and change in optical properties]
11-mer oligonucleotide (5′-CAGTAXGTCG-3 ′) containing 5- (2- (pyrenyl) vinyl) -2′-deoxyuridine (hereinafter referred to as ^5PV U) and its complementary strand (5′-CGTACACTACTG- 3 ′) A reaction solution (100 mM NaCl, 10 mM phosphate buffer; pH 7.0) was prepared so that each of (SEQ ID NO: 1) was 5 mM to obtain a stock solution (FIG. 1 (a)). X in the oligonucleotide is a base having the structure shown in FIG. 200 mL of the stock solution was transferred to a 1 cm square quartz cell, and irradiated with 430 nm light at room temperature for 4 minutes in the dark to photoisomerize from E form to Z form. At this time, MAX-302 of Asahi Spectroscopy Co., Ltd. was used as the light source, and MX0430 of the same company was used as the filter. FIG. 1 shows the UV / visible light absorption spectrum of each of E body and Z body, and FIG. 2 shows the fluorescence spectrum thereof.

  As shown in FIGS. 2 and 3, it can be seen that both the absorption and fluorescence spectra of the Z body are blue shifted (shifted to the short wavelength side) compared to the E body. This is a typical change in isomerization.

[Example 9: Change in thermal stability of double strand by isomerization]
200 mL from the stock solution in Example 8 was transferred to a 1 cm square quartz cell, irradiated with 430 nm light in the dark at room temperature for 4 minutes, and photoisomerized from E form to Z form. At this time, MAX-302 of Asahi Spectroscopy Co., Ltd. was used as the light source, and MX0430 of the same company was used as the filter. The melting temperature (T _m value) of each of E body and Z body was calculated from the T _m curve (FIG. 3). Value of _{T m} E bodies 29 ° C., value of _{T m} Z isomer is 22.5 ° C., and the difference ([Delta] T _m) was 6.5 ° C.. Thus, photoisomerization can be used to control the thermal stability of the double strand.

  According to the present invention, since a nucleoside capable of causing a reversible change in structure and optical properties by light can be provided, a polynucleotide whose function can be reversibly controlled by light can be produced. Therefore, it can be used in industries such as the biochemical field and the medical field.

It is a figure which shows the oligonucleotide which ^{concerns on} a present Example, (a) has shown the arrangement | sequence of the 11mer oligonucleotide containing ^5PV U of this invention, and the sequence of its complementary strand, (b) is (a) The structure of ^5PV U represented by X in the middle is shown. It is a figure which shows UV / visible absorption spectrum of the oligonucleotide which concerns on a present Example. It is a figure which shows the fluorescence spectrum of the oligonucleotide which concerns on a present Example. It is a figure which shows the _Tm curve of the oligonucleotide which concerns on a present Example.

Claims (8)

A group represented by the following general formula (1) is bonded to a carbon atom at the 5-position of the pyrimidine nucleus represented by the following general formula (2) or (3) , and a nitrogen atom at the 1-position of the pyrimidine nucleus And a pyrimidine nucleoside compound to which a sugar represented by the following general formula (6) is bound.

(In the general formulas (2) and (3), Z ₁ is an amino group, or the amino group is triazole, dimethylformamidine, diisobutylformamidine, acetyl group, isobutyl group, benzoyl group, 9-fluorenylmethyloxycarbonyl. It represents a group protected with a group (Fmoc) or a tert-butoxycarbonyl group (Boc), and * 2 represents a bonding position with a sugar.
In General Formula (1), A represents an aryl group having 10 to 20 ring atoms or a heteroaryl group having 10 to 20 ring atoms, and the aryl group and the heteroaryl group have a substituent. * 1 represents the bonding position with the 5-position carbon atom of the pyrimidine nucleus.
In general formula (6), R ₁ and R ₂ are each independently protected with a hydroxyl group , and the hydroxyl group is protected with isobutyl, tert-butyldimethylsilyl (TBDMS), triisopropylsilyloxymethyl (TOM) or dimethoxytrityl (DMTr). Or a group represented by the following formula (7), wherein R ₃ is a hydrogen atom, a hydroxyl group , and the hydroxyl group is isobutyl, tert-butyldimethylsilyl (TBDMS), triisopropylsilyloxymethyl (TOM) or dimethoxytrityl ( A group protected by DMTr) or a group represented by the following formula (7) :

* 3 represents the bonding position with the nitrogen atom at position 1 of the pyrimidine nucleus. ) The pyrimidine nucleoside compound according to claim 1, wherein the pyrimidine nucleus is a uridine derivative represented by the general formula (2) .   The pyrimidine nucleoside compound according to claim 1 or 2, wherein A is a pyrenyl group or a 9H-fluorenyl group. A group represented by the following general formula (1) is bonded to a carbon atom at the 5-position of the pyrimidine nucleus represented by the following general formula (2) or (3) , and a nitrogen atom at the 1-position of the pyrimidine nucleus Next, the pyrimidine nucleoside compound to which the saccharide represented by the following general formula (6) is bonded is irradiated with light to isomerize the ethylenic double bond part of the group represented by the following general formula (1). A method of performing E → Z isomerization by irradiating light with a wavelength of 350 nm to 500 nm, or irradiating light with a wavelength of 290 nm to 350 nm .

(In the general formulas (2) and (3), Z ₁ is an amino group, or the amino group is triazole, dimethylformamidine, diisobutylformamidine, acetyl group, isobutyl group, benzoyl group, 9-fluorenylmethyloxycarbonyl. It represents a group protected with a group (Fmoc) or a tert-butoxycarbonyl group (Boc), and * 2 represents a bonding position with a sugar.
In the general formula (1), A represents an aryl group or a heteroaryl group, the aryl group and the heteroaryl group may have a substituent, and * 1 represents a carbon atom at the 5-position of the pyrimidine nucleus. Represents the bonding position of.
In general formula (6), R ₁ and R ₂ are each independently protected with a hydroxyl group , and the hydroxyl group is protected with isobutyl, tert-butyldimethylsilyl (TBDMS), triisopropylsilyloxymethyl (TOM) or dimethoxytrityl (DMTr). Or a group represented by the following formula (7), wherein R ₃ is a hydrogen atom, a hydroxyl group , and the hydroxyl group is isobutyl, tert-butyldimethylsilyl (TBDMS), triisopropylsilyloxymethyl (TOM) or dimethoxytrityl ( A group protected by DMTr) or a group represented by the following formula (7) :

* 3 represents the bonding position with the nitrogen atom at position 1 of the pyrimidine nucleus. ) A group represented by the following general formula (1) is bonded to a carbon atom at the 5-position of the pyrimidine nucleus represented by the following general formula (2) or (3) , and a nitrogen atom at the 1-position of the pyrimidine nucleus There is a method for changing the optical properties by irradiating light to a pyrimidine nucleoside compound to which a saccharide represented by the following general formula (6) is bonded, wherein the group represented by the following general formula (1): A method in which an ethylenic double bond is subjected to E → Z isomerization with light having a wavelength of 350 nm to 500 nm, or Z → E isomerization with light having a wavelength of 290 nm to 350 nm .

(In the general formulas (2) and (3), Z ₁ is an amino group, or the amino group is triazole, dimethylformamidine, diisobutylformamidine, acetyl group, isobutyl group, benzoyl group, 9-fluorenylmethyloxycarbonyl. It represents a group protected with a group (Fmoc) or a tert-butoxycarbonyl group (Boc), and * 2 represents a bonding position with a sugar.
In General Formula (1), A represents an aryl group having 10 to 20 ring atoms or a heteroaryl group having 10 to 20 ring atoms, and the aryl group and the heteroaryl group have a substituent. * 1 represents the bonding position with the 5-position carbon atom of the pyrimidine nucleus.
In general formula (6), R ₁ and R ₂ are each independently protected with a hydroxyl group , and the hydroxyl group is protected with isobutyl, tert-butyldimethylsilyl (TBDMS), triisopropylsilyloxymethyl (TOM) or dimethoxytrityl (DMTr). Or a group represented by the following formula (7), wherein R ₃ is a hydrogen atom, a hydroxyl group , and the hydroxyl group is isobutyl, tert-butyldimethylsilyl (TBDMS), triisopropylsilyloxymethyl (TOM) or dimethoxytrityl ( A group protected by DMTr) or a group represented by the following formula (7) :

* 3 represents the bonding position with the nitrogen atom at position 1 of the pyrimidine nucleus. )   A polynucleotide comprising a base derived from the pyrimidine nucleoside compound according to claim 3. A group represented by the following general formula (1) is bonded to a carbon atom at the 5-position of the pyrimidine nucleus represented by the following general formula (2) or (3) , and a nitrogen atom at the 1-position of the pyrimidine nucleus And a method of changing the thermal stability by irradiating light to a polynucleotide containing a base derived from a pyrimidine nucleoside compound to which a sugar represented by the following general formula (6) is bound. A method in which the ethylenic double bond part of the group represented by formula (1) is E → Z isomerized with light having a wavelength of 350 nm to 500 nm, or Z → E isomerized with light having a wavelength of 290 nm to 350 nm .

(In the general formulas (2) and (3), Z ₁ is an amino group, or the amino group is triazole, dimethylformamidine, diisobutylformamidine, acetyl group, isobutyl group, benzoyl group, 9-fluorenylmethyloxycarbonyl. It represents a group protected with a group (Fmoc) or a tert-butoxycarbonyl group (Boc), and * 2 represents a bonding position with a sugar.
In General Formula (1), A represents an aryl group having 10 to 20 ring atoms or a heteroaryl group having 10 to 20 ring atoms, and the aryl group and the heteroaryl group have a substituent. * 1 represents the bonding position with the 5-position carbon atom of the pyrimidine nucleus.
In general formula (6), R ₁ and R ₂ are each independently protected with a hydroxyl group , and the hydroxyl group is protected with isobutyl, tert-butyldimethylsilyl (TBDMS), triisopropylsilyloxymethyl (TOM) or dimethoxytrityl (DMTr). Or a group represented by the following formula (7), wherein R ₃ is a hydrogen atom, a hydroxyl group , and the hydroxyl group is isobutyl, tert-butyldimethylsilyl (TBDMS), triisopropylsilyloxymethyl (TOM) or dimethoxytrityl ( A group protected by DMTr) or a group represented by the following formula (7) :

* 3 represents the bonding position with the nitrogen atom at position 1 of the pyrimidine nucleus. ) A group represented by the following general formula (1) is bonded to a carbon atom at the 5-position of the pyrimidine nucleus represented by the following general formula (2) or (3) , and a nitrogen atom at the 1-position of the pyrimidine nucleus An optical switching device material comprising: at least one of a pyrimidine nucleoside compound to which a sugar represented by the following general formula (6) is bound, and a polynucleotide containing a base derived from the pyrimidine nucleoside compound.

(In the general formulas (2) and (3), Z ₁ is an amino group, or the amino group is triazole, dimethylformamidine, diisobutylformamidine, acetyl group, isobutyl group, benzoyl group, 9-fluorenylmethyloxycarbonyl. It represents a group protected with a group (Fmoc) or a tert-butoxycarbonyl group (Boc), and * 2 represents a bonding position with a sugar.
In General Formula (1), A represents an aryl group having 10 to 20 ring atoms or a heteroaryl group having 10 to 20 ring atoms, and the aryl group and the heteroaryl group have a substituent. * 1 represents the bonding position with the 5-position carbon atom of the pyrimidine nucleus.
In general formula (6), R ₁ and R ₂ are each independently protected with a hydroxyl group , and the hydroxyl group is protected with isobutyl, tert-butyldimethylsilyl (TBDMS), triisopropylsilyloxymethyl (TOM) or dimethoxytrityl (DMTr). Or a group represented by the following formula (7), wherein R ₃ is a hydrogen atom, a hydroxyl group , and the hydroxyl group is isobutyl, tert-butyldimethylsilyl (TBDMS), triisopropylsilyloxymethyl (TOM) or dimethoxytrityl ( A group protected by DMTr) or a group represented by the following formula (7) :

* 3 represents the bonding position with the nitrogen atom at position 1 of the pyrimidine nucleus. )

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