Composition for measuring the binding affinity between nucleic acid and test substance, and use thereof
a technology of which is applied in the field of composition for measuring can solve the problems of inability to achieve high accuracy and easy measurement of the binding affinity between nucleic acid and test substance, and the range of examinable substances as test substances is limited, and the method is likely to be affected by fluorescence. achieve the effect of high accuracy and easy measurement of the binding affinity
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example 1
Synthesis of X2S
[0177]X2S was synthesized through the following synthetic pathway:
[0178]Specifically, 2,7-dihydroxyxanthone was first synthesized from xanthone as described in (i) Sergio H. Szajnman, Wen Yan, Brian N. Bailey, Roberto Docampo, Eleonora Elhalem, Juan B. Rodriguez., J. Med. Chem. 2000, 43, 1826-1840. and (ii) Tamara C. S. Pace, Sarah L. Monahan, Andrew I. MacRae, Monica Kaila, Cornelia Bohne., Photochemistry and Photobiology, 2006, 82:78-87.
[0179]Next, 2,7-dihydroxyxanthone (0.13 mmol, 30.0 mg) was dissolved in 7 ml of dry tetrahydrofuran (THF). Then, triphenylphosphine (86.3 mg, 0.33 mmol, 2.5 eq.) and diethyl azodicarboxylate (40% toluene solution, 143 mg, 150 μl, 0.33 mmol, 2.5 eq.) were added to the mixture. The resultant solution was stirred at room temperature for 15 minutes. After that, 2-amino-1-ethanol protected by an N-Boc group (53 mg, 50 μl, 0.33 mmol) was further added to the solution, which was then stirred at room temperature for 24 hours.
[0180]Subsequen...
example 2
Evaluation of Binding Between X2S and RNA
[0183]Next, binding between X2S and RNAs was evaluated. The RNAs used in the present example had the structure illustrated in FIG. 2. FIG. 2 is a diagram schematically illustrating the structure of the RNAs used in the present example. The RNAs used in the present example had sequences shown in SEQ ID NOs: 1 through 3.
[0184]The symbol N in FIG. 2 represents either a base out of A, U, C, and G, or no base. Thus, in a case where a particular RNA as in FIG. 2 has N representing a base out of A, U, C, and G, the RNA is an RNA formed by hybridization of an RNA having the base sequence shown in SEQ ID NO: 1 with a single strand RNA having the base sequence shown in SEQ ID NO: 2. On the other hand, in a case where a particular RNA as in FIG. 2 has N representing no base, the RNA is an RNA formed by hybridization of an RNA having the base sequence shown in SEQ ID NO: 1 with an RNA having the base sequence shown in SEQ ID NO: 3.
[0185]According to the ...
example 3
Evaluation of Binding between X1S and RNA
[0189]Binding between X1S and RNAs was evaluated by a method identical to the method described in Example 2, except that X1S was used instead of X2S. A result is shown in FIG. 5. FIG. 5 is a graph illustrating the result of the evaluation of binding between X1S and RNAs. The horizontal axis represents the fluorescence wavelength, whereas the vertical axis represents the fluorescence intensity.
[0190]FIG. 5 verifies that X1S as well as X2S binds to RNAs regardless of whether the bulge structure is present. A detected decrease in the fluorescence intensity was small as compared to the case of X2S.
[0191]The following describes how X1S used in the present example was synthesized. The synthesis of X1S was performed through the following synthetic pathway:
[0192]In this synthetic pathway for X1S, a compound 3 was synthesized (reaction i) from compounds 1 and 2 by a method described in Org. Lett. 2005, Vol 7, No. 19, 4273-4275.
[0193]In a subsequent re...
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| Property | Measurement | Unit |
|---|---|---|
| Fluorescence | aaaaa | aaaaa |
| Affinity | aaaaa | aaaaa |
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