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| | <li>Real shape of mRNA is tertiary structure but we consider efficiency of circularization regarding it secondary structure. Because it is too difficult to model basing tertiary structure.</li><br> | | <li>Real shape of mRNA is tertiary structure but we consider efficiency of circularization regarding it secondary structure. Because it is too difficult to model basing tertiary structure.</li><br> |
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| | <h6><font size="5" face="Century"> 【Method of calculation】</font><br></h6> | | <h6><font size="5" face="Century"> 【Method of calculation】</font><br></h6> |
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| | + | <p> We make following two assumptions, and calculate the efficiency of circularization in each phenomenon.</p><br> |
| | + | <p>Ⅰ.In structure of mRNA indicated in fig.1, we assume that stability of all combinations between 3’ and 5’ side of the intron is a correlation with their possibility (possibility of being close to each other). Therefore we assume that stability of these combinations is a correlation with possibility of circularization.</p> |
| | + | <p>Ⅱ.We assume that distance of both splicing sites in structure of RNA indicated in fig.1 is a correlation with possibility of circularization.</p> |
| | + | </font> |
| | + | <h6><font size="4" face="Century"> About phenomenon of Ⅰ</font><br></h6> |
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Revision as of 17:52, 18 September 2015
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PROJECT
MODELING
Efficiency of circularization of mRNA is proportion to probability of meeting 3’ and 5’ side of the intron which is in the both side of mRNA. In this study, we designed complementary sequences near the 5’side of the intron and the 3’side of the intron to improve the efficiency of circularization of mRNA.
If there are complementary sequences, both splicing sites approach and the reaction of circularization is easy to happen because these sequences make hydrogen bands.
Therefore we predict how much efficiency of circularization improved.
The generators used in this study are (1)
[BBa_K1332011]
(2)
[BBa_K1859026]
(3)
[BBa_K1859024]
(4)
[BBa_K1859025]
mRNA transcribed from these generators are the sequences of the following parts.
(1) the 3´side of the intron
[BBa_K1859008]
, RBS
[BBa_B0034]
, RFP
[BBa_K1332002]
, the 5´side of the intron
[BBa_1332009]
(2) the 3´side of the intron
[BBa_K1859015]
, RBS
[BBa_B0034]
, RFP
[BBa_K1332002]
, the 5´side of the intron
[BBa_K1859016]
(3) the 3´side of the intron
[BBa_K1859003]
, RBS
[BBa_B0034]
, RFP
[BBa_K1332002]
, the 5´side of the intron
[BBa_K1859004]
(4) the 3´side of the intron
[BBa_K1859001]
, RBS
[BBa_B0034]
, RFP
[BBa_K1332002]
, the 5´side of the intron
[BBa_K1859006]
(1)It is the sequence of expressing circular mRNA in last year’s study
(2)It has complementary sequences outside the splicing sites.
(3)It has complementary sequences inside the splicing sites.
(4)It has also complementary sequences inside the splicing sites.
(3) and (4) are the reverse of the position of complementary sequences.
(Please look at the experiment page)
バンノの図を貼る4つ
Fig.1 prediction of secondary structure of 4 kinds of mRNA
In figure, black lines show 3’intron, 5’intronM and splicing site.
First, when we consider the circularize efficiency, we have following three assumptions.
We assume that only the shapes that are illustrated in following fig.1 exist in mRNA which is not circularized yet. In the other words, we think that circularization doesn’t happen in other structures which are supposed to exist.
We assume that circular mRNA are only monomers so we assume that dimer and the others are not formed. Therefore we think that circular mRNA is formed by reacting both splicing sites of one molecule of mRNA.
Real shape of mRNA is tertiary structure but we consider efficiency of circularization regarding it secondary structure. Because it is too difficult to model basing tertiary structure.
【Method of calculation】
We make following two assumptions, and calculate the efficiency of circularization in each phenomenon.
Ⅰ.In structure of mRNA indicated in fig.1, we assume that stability of all combinations between 3’ and 5’ side of the intron is a correlation with their possibility (possibility of being close to each other). Therefore we assume that stability of these combinations is a correlation with possibility of circularization.
Ⅱ.We assume that distance of both splicing sites in structure of RNA indicated in fig.1 is a correlation with possibility of circularization.
About phenomenon of Ⅰ
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