Team:NUDT CHINA/Model

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Abstract

This model is created to evaluate the effectiveness of initial design, and offers guidelines on how the system can (or must) be improved. (You can go to <a href="https://2016.igem.org/Team:NUDT_CHINA/Design">PROJECT. page</a> to see more

Introduction

We create mathematical models of two aspects of our project, a RCA model and a signal detection model.

Assumption and Justification

About model

1. MiRNA is not degraded throughout the reaction process.

2. The two fusion proteins of dCas9 and split-HRP fragments have the same ability to combine with the stem-loop structure, and only when two different proteins next to each other, can they have the ability to catalyze substrate and produce signal.

3. The number of stem-loop structures in each RCA product is equal under a certain reaction time.

4. The enzymatic activity remains unchanged with time under the premise of excessive amount of enzymes or a short-time reaction.

About the data

1. The data we obtain from wet-lab experiment are reliable.

2. All the results are trustworthy in the process of statistical processing and data calculation.

Model

Notations

Symbol	Definition
x	<a name="OLE_LINK7"></a><a name="OLE_LINK6"></a>The concentration of miRNA (pM)
C₁	The concentration of initiated probe (Abbreviated to iprobe)
k₁	<a name="OLE_LINK8"></a>A constant representing the scale factor
K_m	One of the characteristic constants of phi29 DNA polymerase
V_max	One of the characteristic constants of phi29 DNA polymerase
k₂	A constant representing the scale factor
V	The initial speed of RCA
<a name="OLE_LINK9"></a>n₁	The moles of RCA product
n₂	<a name="OLE_LINK10"></a>The number of stem-loop structures in each RCA product
n	The total amount of <a name="OLE_LINK23"></a><a name="OLE_LINK22"></a>stem-loop structures
N	<a name="OLE_LINK41"></a><a name="OLE_LINK16"></a>The molecule number of the fusion protein of dCas9 and split-HRP fragments
k₃	A constant representing the scale factor
y₁	The fluorescence intensity of DNA-dye-complex (RFU)
N₁	The molecule number of the fusion protein of dCas9 and split-HRP fragments in the solution
N₂	<a name="OLE_LINK45"></a>The molecule number of the fusion protein of dCas9 and split-HRP fragments binding with stem-loop structure
k₄	A constant representing the scale factor
k₅	A constant representing the scale factor
ρ	Signal to noise ratio(Abbreviated to SNR)
I	The molecule number of formed intact HRP proteins
I₁	The molecule number of formed intact HRP proteins in the solution
I₂	<a name="OLE_LINK43"></a>The molecule number of formed intact HRP proteins through binding with stem-loop structure
t	Reaction time
y₂	The signal intensity (OD₄₅₀)

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Figure 1. Schematic diagram

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Team:NUDT CHINA/Model

Contents

Model

Development of A Novel Blood-MicroRNA Handy Detection System with CRISPR

Abstract

Introduction

Assumption and Justification

About model

About the data

Model

Notations