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Nucleotide compositions for inhibiting non-target regions in biological DNA samples and their applications

A target area and composition technology, which is applied in the determination/inspection of microorganisms, biochemical equipment and methods, etc., can solve the problems of not allowing doctors to make more drug decisions, false positives, etc., and achieve fast hybridization and specificity high effect

Active Publication Date: 2021-08-31
CARRIER GENE TECH SUZHOU CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0004] With the increasing refinement and precision of technology and analysis methods, people will inevitably require a way to identify the target area more finely, so as to reduce the roughness of obtaining target information, reduce the cost of obtaining target information, and even require Target information can be more accurately identified at the setting stage. For example, in the field of cancer target drug therapy, there is a one-to-one correspondence between drugs and target information. Even if other irrelevant DNA information is obtained, it will not allow doctors to make more decisions. Patients cannot benefit more from drug decision-making, because the types and scope of application of drugs are very clear and limited, which requires detection technology to tend to obtain more specific and clear data rather than broader data. It can be seen that, On the same drug target, for example, at the position of EGFR 2390, in addition to the reference sequence information G, there can also be three variations of A / T / C, and these three variations, only G>C and G>A The change has the meaning of guiding treatment, and the information of G>T has no medical value at present. However, some detection methods for this position, such as the Taqman probe method, can only identify the mutation of this G, but cannot Confirm which one is G>C, G>A and G>T, which will easily cause false positive results

Method used

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  • Nucleotide compositions for inhibiting non-target regions in biological DNA samples and their applications
  • Nucleotide compositions for inhibiting non-target regions in biological DNA samples and their applications
  • Nucleotide compositions for inhibiting non-target regions in biological DNA samples and their applications

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0038] Example 1: Calculation of the Gibbs free energy of a nucleotide sequence

[0039] Although the calculation of Gibbs free energy is a public knowledge, in order to better support the content disclosed in the present invention, we will show the calculation process of Gibbs free energy here, as well as the implementation in excel, the present invention discloses The Gibbs free energies in the content of are all calculated by this calculation process.

[0040] 1. First of all, we chose the two-base estimation model, which is described in detail in the literature of the SantaLucia, J. team, such as "Thermodynamic parameters for expanded nearest-neighbor model for formation for formation" published in Biochemistry in 1998 of RNA duplexes with Watson-Crick pairs", in brief, involves the following formula:

[0041] a) ΔS1=ΔS0+0.368*log(Salinity);

[0042] b) ΔG1=ΔH0-Temp*ΔS1 / 1000;

[0043] 2. ΔH0 and ΔS0 are empirical constants obtained through research by SantaLucia, J. et ...

Embodiment 2

[0058] Example 2: Suppressing and eliminating PKD1 pseudogenes by using space-occupying methods to improve the detection of PKD1 true gene regions

[0059] 1. The PKD1 gene has 7 pseudogenes with a homology of about 95%. In order to better obtain the information of the true PKD1 gene, we designed a set of nucleosides for PKD1 exon 7, 17, 23, 28 and other positions Acid chain composition, as shown in the following table, wherein the nucleotide sequence I sequence is designed at the place where the PKD1 true and false genes have sequence differences, and biotin, nucleotide chain II and nucleosides are modified on the nucleotide chain I The ratio of acid chain I is 1:10; the nucleotide chain I completely matches the pseudogene, after hybridization, the biotin-labeled nucleotide chain is combined with avidin magnetic beads, and the pseudogene is also captured , and finally detect and verify the ratio of the true gene of PKD1 in the supernatant by common PCR method (which does not ...

Embodiment 3

[0083] Embodiment 3: Comparison of the inhibitory effect of different ratios of nucleotide chain I and nucleotide chain II on pseudogenes

[0084] The specific process is the same as Example 2, the difference is that the ratios of nucleotide chain I and nucleotide chain II are different, and the results also show that the inhibitory effect on pseudogenes is different, such as Figure 7 As shown in the sanger results at the position of exon 11, the ratio of the number of molecules of nucleotide chain II: nucleotide chain I is: concentration condition a=1:10, concentration condition b=1:30.

[0085]

[0086] The analysis of Sanger sequencing results is as follows: Figure 7 As shown, the PCR product of the experimental group is marked as the amplification product of the system that suppresses the pseudogene, and the PCR product of the control group is marked as the amplification product of the system that does not suppress the pseudogene.

[0087] From the comparison of conc...

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Abstract

The invention relates to a nucleotide composition for inhibiting a non-target region in a biological DNA sample and its application. The nucleotide chain composition of the present invention specifically binds to a non-target region so that the non-target region is not amplified non-specifically. increase, recognition, capture, etc.; or, the nucleotide chain composition specifically binds to the target region, further causing the non-target region to be degraded or eliminated, so that the non-target region is not non-specifically amplified, recognized, captured, etc. . The nucleotide chain composition for inhibiting non-target regions in biological DNA samples disclosed by the present invention has the advantages of fast hybridization speed, high specificity, single base difference recognition, etc., and is especially suitable for the removal of heterogeneous chromatin and highly homologous region information Molecular detection fields such as detection and identification of true and false genetic information.

Description

technical field [0001] The invention belongs to the technical field of gene detection, and in particular relates to a nucleotide composition for inhibiting non-target regions in biological DNA samples and an application thereof. Background technique [0002] With the development of science and technology, researchers are increasingly aware that biological DNA samples are usually a complex sample, for example, saliva samples, we all know that there are many bacteria in the mouth, as well as food residues, from When extracting DNA from saliva samples, about 10% of the DNA is not of human origin; for another example, blood samples were considered sterile under natural conditions, and the extracted DNA was naturally of human origin, but , with the development of detection technology and the deepening of analytical understanding, it is now found that some of the free DNA in human blood samples comes from bacteria or other microorganisms; even pure human genomic DNA, there will be...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/6848C12Q1/6869
CPCC12Q1/6848C12Q1/6869C12Q2537/159C12Q2549/125C12Q2535/101
Inventor 罗俊峰汪进平徐雪宋萍陈曦
Owner CARRIER GENE TECH SUZHOU CO LTD
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