CN109336921A - DNA base analogs, uses and methods for synthesizing the same - Google Patents
DNA base analogs, uses and methods for synthesizing the same Download PDFInfo
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- C07H21/04—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
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Abstract
The present invention relates to a kind of DNA base analog, purposes and its synthetic method, the DNA base analog structural formula is as follows:The DNA base analog can use DNA synthesizer insertion modification into DNA sequence dna.Using the variation of azobenzene group (green light and blue light) cis-trans isomerism in visible-range in insertion sequence, carry out without invasive, reversibly regulating DNA hybridization, and then regulate and control the biologicallies such as relevant enzymatic activity.The present invention has synthetic method simple, and the time is short, at low cost, it is seen that the advantages that regulation and its high-efficient light regulation of cis-trans-isomer are carried out in optical range is with a wide range of applications in terms of regulating and controlling some biology enzymes.
Description
Technical field
The present invention relates to a kind of DNA base analog, purposes and its synthetic methods.
Background technique
Azobenzene compound is a kind of compound of a kind of azo group both ends connection phenyl.The azobenzene being not decorated point
Son has very strong π-π * transition in UV light region, and weaker n- π * transition is shown in visible light region.Azobenzene chemical combination
Object has trans- (trans) and cis- (cis) two kinds of isomers, wherein transisomer has planar structure, and cis-isomer
With nonplanar structure.In general, transisomer is stablized relatively, under the conditions of ultraviolet light, can be changed into cis-
Isomers；Conversely, the cis-isomer of thermodynamic instability in turn translates into stable under radiation of visible light or heating condition
Transisomer.It is the hot spot of bioanalysis research using the optics performance of control of this cis-trans-isomer of azobenzene molecule.
There is azobenzene molecule very big conjugated π system and a large amount of electron cloud to accumulate.Azobenzene molecule is embedded into
After in DNA chain, by the electron cloud sedimentation of electron cloud on phenyl ring and DNA base, enable the DNA for being embedded with azobenzene
Hybridized well with its complementary DNA.When exposed to ultraviolet light, azobenzene molecule occurs from transisomer to cis-
The transformation of isomers, the variation on this configuration of azobenzene molecule destroy the noncovalent interaction of azobenzene molecule and base, break
Hybridization between bad DNA base finally makes the DNA chain unwinding of hybridization.And when using visible light illumination, azobenzene molecule
It is changed into transisomer from cis-isomer again, again double-stranded DNA is hybridized.This control by striation part
System, may be implemented the hybridization and unwinding of DNA.Compared to other control methods, this control methods have it is simple and fast, when space division
Resolution is high, and the advantages that Non-Invasive.Nuclease correlated response system is regulated and controled for light, there is very extensive application prospect.
But conventional azobenzene molecule is since the condition that light regulates and controls needs ultraviolet light as light source, and ultraviolet light is for life
Objects system has very big injury, not only make protein denaturation but also will lead to nucleic acid break etc..
Summary of the invention
The DNA base analog that there is visible light regulation cis-trans isomerism the object of the present invention is to provide one and its synthesis side
Method.Wherein, the DNA base analog structural formula is as follows,
Synthesized DNA base analog conveniently and efficiently can be embedded into DNA chain using DNA synthesizer in the present invention
In, after green light (515~535nm) irradiation, cis-isomer is generated, destroys DNA hybridization；And using blue light (445~
After 465nm) irradiating, it is returned to transisomer conformation, restores DNA hybridization.The azobenzene DNA base analog that the present invention designs
Any position in DNA chain can be embedded into, and by the design of insertion azobenzene molecule number and embedded location, come optimally
It realizes in visible light region to the light regulating effect of DNA hybridization, and then effective light tune is carried out to relevant biologically
Control.
Preferably, the synthetic route of DNA base analog of the invention is preferably as follows:
Synthetic DNA base analogue on the basis of tetramethoxy phenylazobenzoic acid analog.Utilize dicyclohexyl carbon two
D- Soviet Union ammonia alcohol on imines (DCC) and 1- hydroxy benzo triazole (HOBt) catalysis amide reaction forming, forms intermediate product AZO-
02；On the basis of intermediate product AZO-02,4-4 '-dimethoxytrityl chloromethanes is introduced, is with pyridine and methylene chloride
Solvent obtains intermediate product AZO-03 under the catalytic action of 4-dimethylaminopyridine (DMAP).In the base of intermediate product AZO-03
On plinth, 2- cyanoethyl N, N- diisopropyl chloro phosphoramidite are introduced.With N, N- diisopropyl ethyl amine is alkali and catalyst, two
Chloromethanes is solvent, under anhydrous and oxygen-free reaction condition, obtains final product AZO-04.Its synthetic route is as follows:
Preferably, step 1 introduces the ammonia alcohol conduct of raw material D- Soviet Union on the basis of phenylazobenzoic acid analog (AZO-01)
Skeleton, there are two the intermediate products of hydroxyl for anamorphic zone.Using N, N'- dicyclohexylcarbodiimide (DCC) and 1- hydroxy benzo three
The condensation of nitrogen azoles (HOBt) forms amido bond, obtains intermediate product AZO-02.
Preferably, step 1 includes: AZO-01, D- Soviet Union ammonia alcohol, dicyclohexylcarbodiimide, I-hydroxybenzotriazole and 4-
Dimethylamino naphthyridine is mixed with the ratio of molar ratio 1-5:1-5:1-5:1-5:0.1-1, and suitable anhydrous THF is added thereto
And methanol, reaction is stirred at room temperature overnight；After reaction, it is filtered to remove precipitating, obtains AZO-02.
Preferably, step 2 introduces 4,4 '-dimethoxytrityl chlorine of raw material on the basis of intermediate product AZO-02
Methane under the catalytic action of 4-dimethylaminopyridine (DMAP), obtains intermediate product AZO- using pyridine and methylene chloride as solvent
03。
Preferably, step 2 includes: that AZO-02 and 4-dimethylaminopyridine are mixed with the ratio of molar ratio 1:0.01-0.1,
After container removes air, the pyridine of 1-10 times of volume is added；Obtain the first solution；
Compared with AZO-2, molar ratio be 1-2 4,4'- dimethoxytrityl chlorine in another container, pump drainage remove
Air adds 1-10 times of volumes methylene chloride, obtains the second solution；Second solution is added drop-wise to the first solution dropwise later
In, it is protected from light and reaction is stirred at room temperature overnight；After reaction, it is extracted with water and ethyl acetate, retains organic phase and with drying,
Organic solvent is then removed, product AZO-03 is obtained.
Preferably, step 3 introduces raw material 2- cyanoethyl N, N- diisopropyl chlorine on the basis of intermediate product AZO-03
For phosphoramidite；With N, N- diisopropyl ethyl amine is alkali and catalyst, and methylene chloride is solvent, in anhydrous and oxygen-free reaction condition
Under, obtain final product AZO-04.
Preferably, in step 3: AZO-03 being added in a container, 1-20 times of volume dichloromethane is added under nitrogen protection
Alkane；Under the conditions of ice-water bath, the N of 2-10 times of molar ratio, the 2- of N- diisopropyl ethyl amine and 0.5-2 times of molar ratio is added dropwise
Cyanoethyl N, N- diisopropyl chloro phosphoramidite reacts 2~4h in ice bath, obtains AZO-4.
The invention has the following advantages that
1, synthesis material is cheap, step simple possible；
2, after molecule is embedded into DNA chain, azobenzene can regulate and control its cis-trans-isomer by green light and blue light,
And then DNA hybridization and unwinding are regulated and controled；Without using purple light, injury of the purple light to biosystem is avoided.
3, it can according to need any one position for being embedded into DNA sequence dna using DNA synthesizer；
4, the azobenzene of the method for the present invention insertion, R can be-H ,-OCH3,-CH3,-SCH3Deng not influencing it to insertion
The light regulating effect of DNA.
Detailed description of the invention
Fig. 1 is final product AZO-04's1H NMR spectra.
Fig. 2 is final product AZO-04's31P NMR spectra.In Fig. 2,147ppm and 148ppm are
The characteristic peak of phosphoramidite, 14ppm are the characteristic peak of by-product.
Fig. 3 is the DNA HPLC purification result for being modified with azobenzene base analogue.Wherein, 260nm absorption peak is 1. indicated,
2. indicating 490nm (azobenzene molecule) absorption peak.
Fig. 4 is to be modified with the DNA of azobenzene base analogue by green light (515-535nm, the 25mW/ of different time
cm2) irradiation HPLC characterization result.Wherein, 1. -6. indicate irradiation time be followed successively by 0min, 1.5min, 3min, 5min,
10min, 15min, 30min and 60min are calculated by integral area, and cis (%) content gradually increases, to obtain preferably
Green light light application time is 30min.
Fig. 5 be modified with azobenzene base analogue DNA first pass through 30min green light irradiation, then by it is different when
Between blue light (445-465nm, 25mW/cm2) irradiation HPLC characterization result.Wherein, 1. -4. indicate irradiation time be followed successively by
0min, 2.5min, 5min and 7.5min are calculated by integral area, and cis (%) content can be obtained and gradually decrease, to obtain
Preferable blue light light application time is 5min.
Fig. 6 is to be modified with the DNA of azobenzene base analogue to first pass through green light illumination (515-535nm, 25mW/cm2,
30min), the concentration of cisoid conformation gradually decreases after the different time.It is obtained according to the mapping of ln [cis] and time oblique
The apparent conversion rate K that rate, as cisoid conformation are converted to anti conformationobs, then according to τ1/2=ln 2/Kobs, and then obtain
The cis- half-life period τ to trans- conversion1/2=46.2h.
Specific embodiment
With R=OCH3For, synthetic route is as follows
1, synthetic product AZO-02, synthetic route are as follows:
AZO-01 (390mg, 1.0mmol) is added in a round-bottomed flask, D- revives ammonia alcohol (106mg, 1.0mmol), two rings
Hexyl carbodiimide (DCC, 247mg, 1.2mmol), I-hydroxybenzotriazole (HOBT, 162mg, 1.2mmol) and 4- diformazan ammonia
Yl pyridines (DMAP, 24mg, 0.2mmol), and suitable anhydrous tetrahydro furan and methanol are added thereto, it is stirred at room temperature and reacted
Night.After reaction, it is filtered to remove precipitating, crude product is isolated and purified with silica gel chromatographic column again, and nuclear-magnetism and mass spectrum carry out table
Sign.1H NMR(500MHz,CDCl3) δ=6.97 (s, 2H), 6.20 (s, 2H), 4.24 (m, 2H), 4.22 (m, 2H), 3.88 (s,
3H),3.86(s,6H),3.72(s,6H),1.23(d,3H).ESI-MS Calculated for C22H30N3O8:464.2([M+
H]+),found:464.8。
2, synthetic product AZO-03, synthetic route are as follows:
Be added in a round-bottomed flask AZO-02 (463mg, 1.0mmol) and 4-dimethylaminopyridine (DMAP, 6.1mg,
0.05mmol) pump drainage removes air, and 2mL pyridine (pyridine) then is added thereto.By 4,4'- dimethoxytrityl
Chlorine (DMT-Cl, 339mg, 1.0mmol) is weighed in another small round-bottomed flask, and pump drainage removes air, adds 2mL dichloro
Methane (DCM).DMT-Cl solution is added drop-wise to dropwise in AZO-02 solution later, is protected from light and reaction is stirred at room temperature overnight.Reaction knot
Shu Hou is extracted with water and ethyl acetate, is retained organic phase and is used anhydrous Na2SO4It is dry, organic solvent is then removed, it is thick to produce
Product are isolated and purified with silica gel chromatographic column again, and nuclear-magnetism and mass spectrum are characterized.1H NMR(500MHz,CDCl3) δ=7.40 (m,
2H),7.29(m,5H),7.19(m,2H),7.11(s,2H),6.89(d,1H),6.80(m,4H),6.22(s,2H),4.20(m,
1H),3.86(m,15H),3.76(d,6H),3.55(dd,1H),3.35(dd,1H),3.22(d,1H),1.21(d,3H).ESI-
MS Calculated for C43H47N3O10:766.3([M+H]+),found:766.3。
3, synthetic product AZO-04, synthetic route are as follows:
AZO-03 (765mg, 1.0mmol) is added in a round-bottomed flask, 5mL methylene chloride is added under nitrogen protection.
Under the conditions of ice-water bath, N, N- diisopropyl ethyl amine (DIPEA, 516mg, 4mmol) and 2- cyanoethyl N, N- bis- is added dropwise
Isopropyl chloride reacts 2~4h, is isolated and purified with silica gel chromatographic column, core for phosphoramidite (237mg, 1.0mmol) in ice bath
Magnetic and mass spectrum are characterized, such as Fig. 1, and 2.1H NMR(500MHz,CDCl3) δ=7.43 (m, 2H), 7.31 (d, 4H), 7.28 (m,
1H),7.22(m,1H),7.09(s,1H),7.05(s,1H),6.81(m,5H),6.22(s,2H),4.48(m,1H),4.38(m,
1H),3.86(m,8H),3.83(m,6H),3.77(s,6H),3.53(m,4H),1.28(m,6H),1.13(m,12H),1.01
(d,2H).ESI-MS Calculated for C52H65N5O11P:966.4([M+H]+),found:966.7。
4, final product AZO-04 is applied to synthesize in DNA synthesizer.
Design synthesis one has the DNA oligonucleotides of product AZO-04, and sequence is as follows: 5 '-GGT ATC X GCC
TAA-3 ', wherein X is product AZO-04, which is mAZO-DNA.The insertion of product AZO-04 uses conventional
DNA synthesis program, only coupling time extend to 900s.After synthesis, first use methylamine/ammonium hydroxide (v/v, 1/1) by DNA sequence dna
It is cut down from solid phase carrier CPG, then pumps methylamine/ammonium hydroxide, dissolved with 0.1mol/L acetic acid triethylamine (TEAA), after crossing film
It is isolated and purified with HPLC, such as Fig. 3.
5, the HPLC of different time green light illumination regulation characterizes experiment.
By 6 50 μ L, 10 μM of mAZO-DNA (PBS buffer solution: 100mM NaCl, 100mM phosphate, 5mM MgCl2,
PH 7.4) sample, in 25mW/cm2Irradiated respectively under the conditions of the green light (515nm~535nm) of power different time (0,5min,
10min, 15min, 30min, 60min), HPLC analysis and characterization is then carried out respectively, as a result such as Fig. 4.
6, the HPLC of different time blue light illumination regulation characterizes experiment.
By 4 50 μ L, 10 μM of mAZO-DNA (PBS buffer solution: 100mM NaCl, 100mM phosphate, 5mM MgCl2,
PH 7.4) sample, first in 25mW/cm230min is irradiated under the conditions of the green light of power, then by different time (0,2.5min,
5min, 7.5min) blue light (445nm~465nm, 25mW/cm2Power) illumination, HPLC analysis and characterization is then carried out respectively, as a result
Such as Fig. 5.
7, to the azobenzene being embedded into DNA, the calculating of the cis- half-life period to trans- conversion.
By 8 50 μ L, 10 μM of mAZO-DNA (PBS buffer solution: 100mM NaCl, 100mM phosphate, 5mM MgCl2,
PH 7.4) sample, in 25mW/cm230min is irradiated under the conditions of the green light of power, then different time points after illumination
HPLC characterization is carried out respectively, by the statistics and calculating of peak area, obtains being embedded into the azobenzene in DNA, it is cis- to trans-
Conversion half-life period, such as Fig. 6.
Claims (10)
1.DNA base analogue, structural formula are as follows:
2. the purposes of DNA base analog as described in claim 1, the regulation for DNA hybridization and unwinding.
3. the application method of DNA base analog as described in claim 1, is irradiated using green light, cis-isomer is generated；It is blue
Light irradiation, returns to transisomer conformation.
The preparation method of 4.DNA base analogue, including following synthesis step:
5. the preparation method of DNA base analog as claimed in claim 4, it is characterised in that:
Step 1 introduces raw material D- Soviet Union's ammonia alcohol as skeleton on the basis of phenylazobenzoic acid analog, and there are two hydroxyls for anamorphic zone
The intermediate product of base；With N, the condensation of N'- dicyclohexylcarbodiimide and 1- hydroxy benzo triazole forms amido bond, obtains
To intermediate product AZO-02.
6. the preparation method of DNA base analog as claimed in claim 4, it is characterised in that: step 1 includes: AZO-01,
D- Soviet Union ammonia alcohol, dicyclohexylcarbodiimide, I-hydroxybenzotriazole and 4-dimethylaminopyridine are with molar ratio 1-5:1-5:1-5:
The ratio of 1-5:0.1-1 mixes, and suitable anhydrous THF and methanol are added thereto, and reaction is stirred at room temperature overnight；Reaction terminates
Afterwards, it is filtered to remove precipitating, obtains AZO-02.
7. the preparation method of DNA base analog as claimed in claim 4, it is characterised in that: step 2, in intermediate product
On the basis of AZO-02,4,4 '-dimethoxytrityl chloromethanes of raw material, using pyridine and methylene chloride as solvent, 4- bis- are introduced
Under the catalytic action of methylamino pyridine, intermediate product AZO-03 is obtained.
8. the preparation method of DNA base analog as claimed in claim 7, it is characterised in that: step 2 include: AZO-02 and
4-dimethylaminopyridine is mixed with the ratio of molar ratio 1:0.01-0.1, and after container removes air, the pyrrole of 1-10 times of volume is added
Pyridine；Obtain the first solution；
In another container relative to 4, the 4'- dimethoxytrityl chlorine that AZO-2 molar ratio is 1-2, pump drainage removes air,
1-10 times of volumes methylene chloride is added, the second solution is obtained；Second solution is added drop-wise to dropwise in the first solution later, is kept away
Light room temperature is stirred to react overnight；After reaction, it is extracted with water and ethyl acetate, retains organic phase and with drying, then
Organic solvent is removed, product AZO-03 is obtained.
9. the preparation method of DNA base analog as claimed in claim 4, it is characterised in that: step 3, in intermediate product
Raw material 2- cyanoethyl N, N- diisopropyl chloro phosphoramidite are introduced on the basis of AZO-03；With N, N- diisopropyl ethyl amine is
Alkali and catalyst, methylene chloride are solvent, under anhydrous and oxygen-free reaction condition, obtain final product AZO-04.
10. the preparation method of DNA base analog as claimed in claim 9, it is characterised in that: in step 3, in a container
1-20 times of volumes methylene chloride is added in middle addition AZO-03 under nitrogen protection；Under the conditions of ice-water bath, it is added dropwise 2-10 times
2- cyanoethyl N, N- the diisopropyl chloro phosphoramidite of the N of molar ratio, N- diisopropyl ethyl amine and 0.5-2 times of molar ratio,
2~4h is reacted in ice bath, obtains AZO-4.
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| CN113248556A (en) * | 2021-05-18 | 2021-08-13 | 武汉科技大学 | Assembly of nucleic acid grafted azobenzene, preparation method and application |
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