CN116092575A - Discrimination method of G-DNA structure based on GMNS rule - Google Patents

Abstract

The invention discloses a G-DNA structure discrimination method based on GMNS rule, belonging to the technical field of biological analysis, comprising the following steps: (1) numbering a DNA sequence; (2) screening for characteristic fragments; (3) analyzing G base characteristics; (4) counting GM structural units; (5) discrimination of G-DNA Structure. The invention establishes the G-DNA structure discrimination method which is applicable to short-chain DNA and based on G base distribution characteristics, and is beneficial to realizing simple and rapid analysis of the G-DNA structure.

Description

Discrimination method of G-DNA structure based on GMNS rule

technical field

The invention belongs to the technical field of biological analysis, in particular to a G-DNA structure discrimination method based on the GMNS rule.

Background technique

With the in-depth study of nucleic acid, it is found that the DNA structure has the characteristics of diversity, such as single-stranded DNA, double-stranded DNA, hairpin DNA, I-DNA, G-DNA, DNA trimer, etc. The diversity of DNA structure is small The interaction between molecules and DNA provides a rich mode of action, provides a more suitable target site for specific recognition or capture of small molecules, and provides a basis for research on the interaction between DNA and small molecules. Therefore, it is of great significance to carry out the analysis of DNA structure, especially the three-dimensional structure.

Facts have shown that although there are only four types of DNA bases: adenine, guanine, cytosine, and thymine, the DNA sequences composed of them vary in thousands of ways. How to determine the three-dimensional structure of DNA is the first problem to be solved. At present, it is relatively easy to distinguish single-stranded DNA, double-stranded DNA, and hairpin DNA, mainly based on whether the DNA molecules and DNA molecules can be connected by hydrogen bonds to form complementary base pairing. However, for G-DNA (G quadruplex DNA), there is currently no directly available discrimination method, and it can only be analyzed by means of experimental results and instrumental characterization, such as ultraviolet-visible spectroscopy, infrared spectroscopy, and circular dichroism spectroscopy. wait. Therefore, for any given DNA sequence, whether it can be formed in G-DNA, or whether a specific structural unit with what base, base sequence, and structural characteristics can form I-DNA or G-DNA, cannot be determined at present. Judgment result.

G-DNA has been widely used in the fields of physiological functions, biomedicine, food safety analysis, and environmental protection. Therefore, exploring the laws, revealing the essence, and proposing a method for discriminating the G-DNA structure are crucial to the study of the combination of small molecules and DNA molecules. It is of great significance in terms of mode, mode of action and pathogenic mechanism.

Contents of the invention

The invention discloses a method for discriminating the G-DNA structure based on the GMNS rule, which can judge whether it is a G-DNA structure only according to the DNA sequence without experiment, and is simple and convenient.

In order to achieve the above object, the present invention adopts the following technical solutions:

The G-DNA structure discrimination method based on the GMNS rule comprises the following steps:

(1) Numbered DNA sequence

Number the bases B of a given DNA fragment starting from either end: B ₁ , B ₂ , B ₃ , B ₄ ...;

(2) Screening of characteristic fragments

Take the G-rich base fragment in the given DNA fragment, and calibrate the first base G as the effective base G _x , where x is the number of the first base G in the given DNA fragment; from G _x base Start counting until the number of G _x+n bases ends, select B _xy to B _x+n+z as effective characteristic fragments of G-DNA; 35≥n≥9, 10≥y≥0, 10≥z≥0 ;

(3) Analysis of G base characteristics

Analyze the G structural unit consisting of several consecutive G bases in the effective characteristic fragment, where the G structural units with different base numbers are marked as GM, and M is the number of G bases in the G structural unit, such as M1, M2, M3 , M4...;

(4) Counting GM structural units

Calculate the number N of each GM structural unit separately;

(5) G-DNA structure discrimination

Mark and calculate the number of bases S between adjacent G structural units;

M≥2, N≥1, 8≥S≥1, and there are structural repeating units in the effective characteristic fragments, it is judged as G-DNA structure;

There are structural repeating units in the effective characteristic fragment, which means that in the effective characteristic fragment:

For a G structural unit, at least 4 non-consecutive repeats;

Or for a combined structure formed by at least two G structural units, there are at least 2 non-continuous repeats; the above-mentioned "non-continuous" means that there are other bases other than G between adjacent G structural units.

Furthermore, the G-base-rich fragment refers to the concentrated part of G bases in a given DNA fragment, especially refers to the part of the base sequence of the structural repeating unit.

Further, the number of effective characteristic fragment bases does not exceed 36.

Further, any end is the 3' end and/or the 5' end.

Further, the proportion of G bases in the effective characteristic fragments is 10%-80%.

Further, G bases account for 35% to 80% of the effective characteristic fragments.

Further, 35≥n≥16, 4≥y≥0, 4≥z≥0.

Further, 5≥M≥2, 12≥N≥3, 4≥S≥1.

Within the further defined range of M, N, S, the determined G-DNA structure is more stable.

Further, a routine program language can be used to write a program for discriminating G-DNA structure according to the above-mentioned method to form a discriminating G-DNA structure for use in modules or systems.

The beneficial effects of the present invention are:

1) The GMNS method adopted in the present invention is simple, fast, and improves analysis efficiency;

2) The GMNS method adopted in the present invention is applicable to the rapid discrimination of G-DNA structure;

4) The GMNS method adopted in the present invention can reduce and reduce the experimental cost;

5) The GMNS method adopted in the present invention can provide theoretical support for the research on the interaction mode of G-DNA and small molecules.

In summary, the present invention proposes a GMNS method for quickly discriminating the G-DNA structure, and establishes a G-DNA structure discriminating method suitable for short-chain DNA based on the distribution characteristics of G bases. The verification provides a theoretical basis and a theoretical support for revealing the mechanism of G-DNA and the target interaction. The GMNS method has the characteristics of simplicity, rapidity and high reliability for the three-dimensional structure analysis of short-chain DNA, and is of great significance and value for enriching and perfecting the analysis of DNA structure and the study of the interaction with targets.

Description of drawings

Figure 1 is a schematic diagram of the base numbering of the DNA sequence of Example 1.

Figure 2 is a schematic diagram of the base numbering of the DNA sequence of Example 2.

Detailed ways

The following clearly and completely describes the technical solutions in the embodiments of the present invention. Obviously, the described embodiments are only some of the embodiments of the present invention, but not all of them. Based on the embodiments of the present invention, all other embodiments obtained by persons of ordinary skill in the art without making creative efforts belong to the protection scope of the present invention.

Example 1 Numbering DNA sequence

Given DNA-1, the nucleotide sequence is as follows: 3'-GGGTTGGGCTGGGTGGGGCT-5', SEQ ID NO.1;

The bases are numbered starting from the 3' end, as shown in Figure 1.

Example 2

(1) Numbered DNA sequence

Given DNA-2, the nucleotide sequence is as follows: 3'-CATCTTGGGGTTGGGGTTGGGGTT GGGGTCATCT-5', SEQ ID NO.2;

The bases are numbered from the 3' end, as shown in Figure 2;

Among them, the total number of bases is 34; the number of G bases is 16, and G bases account for 47%. DNA-2 can be directly used as a G base-rich fragment for subsequent analysis.

(2) Screening of characteristic fragments

Starting from the starting end of the numbering, mark the first base G as an effective base Gx, x=7;

Start counting from G _x (G ₇ ) bases to G _x+n (G ₂₈ ) bases, there are 22 bases between G ₇ and G ₂₈ , and the number of base differences n is 21, satisfying 35 ≥n≥9, select B _xy to B _x+n+z (G ₇ -G ₃₀ ) as effective characteristic fragments of G-DNA, y=0, z=2, satisfy 10≥y≥0, 10≥z≥ 0; The effective characteristic fragments have a total of 24 bases, no more than 36, the number of G bases is 16, and G bases account for 67%, which meets 10%-80%.

Example 3

(1) Numbered DNA sequence

Given DNA-3, the nucleotide sequence is as follows: 5'-ATTCAGGGTGGGTGGGTGGGTATT CA-3', SEQ ID NO.3;

Bases are numbered starting from the 5' end;

Among them, the total number of bases is 26; the number of G bases is 12, and G bases account for 46%. DNA-3 can be directly used as a G base-rich fragment for subsequent analysis.

(2) Screening of characteristic fragments

Starting from the starting end of the numbering, mark the first base G as an effective base G _x , x=6;

Start counting from G _x (G ₆ ) bases to G _x+n (G ₂₀ ) bases, there are 15 bases between G ₆ and G ₂₀ , and the number of base differences n is 14, satisfying 35 ≥n≥9, select B _xy to B _x+n+z (G ₆ -G ₂₁ ) as effective characteristic fragments of G-DNA, y=0, z=1, satisfy 10≥y≥0, 10≥z≥ 0; The effective characteristic fragment has a total of 16 bases, no more than 36, the number of G bases is 12, and G bases account for 75%, which meets 10% to 80%.

(3) Analysis of G base characteristics

Analyze the G structural unit consisting of several consecutive G bases in the characteristic fragment, where the G structural units with different base numbers are marked as GM, and M is the number of G bases in the G structural unit:

Including G3(GGG);

(4) Counting GM structural units

Calculate the number N of GM structural units: G3 is 4;

There is a structural repeat unit (GGG) B in the effective characteristic fragment, which meets the requirements for the existence of a structural repeat unit in the effective characteristic fragment: for a G structural unit, at least 4 non-continuous repeats;

(5) G-DNA structure discrimination

Mark and calculate the number S of bases between adjacent G structural units: 1, 1, 1 in sequence;

When M is 3, it meets M≥2; when N is 4, it meets N≥1; when S is 1, it meets 8≥S≥1. If there are structural repeating units in the effective characteristic fragment, it can be identified as G-DNA structure.

Example 4

According to the GMNS method in Example 3, the following DNA sequences are determined respectively:

DNA-4: 5'-AATGGGTAGGGCGGGTTGGGATGAA-3', SEQ ID NO.4;

DNA-5: 5'-AAGGGTTAGGGTTAGGGTTAGGGTTAC-3', SEQ ID NO.5;

DNA-6: 5'-ATTGGGGTTGGGGTTGGGGTTGGGGTTATTA-3', SEQ ID NO.6;

DNA-7: 5'-ATTGGTTGGTTGTTGTTGTTGGGTTACT-3', SEQ ID NO.7;

DNA-8: 5'-AGGGGTTTTGGGGTTTTGGGGTTTTGGGGA-3', SEQ ID NO.8;

The DNA structure analysis information and judgment results are shown in Table 1.

Table 1

Each embodiment in this specification is described in a progressive manner, each embodiment focuses on the difference from other embodiments, and the same and similar parts of each embodiment can be referred to each other.

The above description of the disclosed embodiments is provided to enable any person skilled in the art to make or use the invention. Various modifications to the above-described embodiments will be readily apparent to those skilled in the art, and the general principles defined herein may be implemented in other embodiments without departing from the spirit or scope of the invention. Therefore, the present invention will not be limited to the embodiments shown herein, but is to be accorded the widest scope consistent with the principles and novel features disclosed herein.

Claims (9)

1. the G-DNA structure discriminant method based on GMNS rule, is characterized in that, comprises the steps: (1) Numbered DNA sequence Starting from any end, the base B of a given DNA fragment is numbered sequentially: B ₁ , B ₂ , B ₃ , B ₄ ...; (2) Screening of characteristic fragments Take the G-rich base fragment in the given DNA fragment, and calibrate the first base G as an effective base G _x , where x is the number of the first base G in the given DNA fragment ; Start counting from G _x bases to G _{x + n} bases, select B _xy to B _{x + n + z} as effective characteristic fragments of G-DNA; 35≥n≥9, 10≥y≥0 , 10≥z≥0; (3) Analysis of G base characteristics Analyze the G structural unit consisting of several consecutive G bases in the effective characteristic fragment, wherein the G structural units with different base numbers are respectively marked as GM, and M is the number of G bases in the G structural unit; (4) Counting GM structural units Calculate the number N of each GM structural unit separately; (5) G-DNA structure discrimination Mark and calculate the number of bases S between adjacent G structural units; M≥2, N≥1, 8≥S≥1, and there are structural repeating units in the effective characteristic fragments, it is judged as G-DNA structure; There is a structural repeat unit in the effective characteristic fragment, which refers to the effective characteristic fragment: For a G structural unit, at least 4 non-consecutive repeats; Or for a combined structure formed by at least two G structural units, at least 2 are non-continuously repeated. 2. the G-DNA structure discrimination method based on GMNS rule according to claim 1, is characterized in that, described effective characteristic fragment base number is no more than 36. 3. the G-DNA structure discrimination method based on GMNS rule according to claim 1, is characterized in that, described arbitrary end is 3 ' end and/or 5 ' end. 4. The method for discriminating G-DNA structure based on the GMNS rule according to claim 1, characterized in that the proportion of G bases in the effective characteristic fragments is 10% to 80%. 5 . The method for discriminating G-DNA structure based on GMNS rule according to claim 4 , characterized in that the proportion of G bases in the effective characteristic fragments is 35-80%. 6 . 6. The method for discriminating G-DNA structure based on GMNS rule according to claim 1, characterized in that 35≥n≥16, 4≥y≥0, 4≥z≥0. 7. The method for discriminating G-DNA structure based on GMNS rule according to claim 1, characterized in that, 5≥M≥2. 8. The method for discriminating G-DNA structure based on GMNS rule according to claim 1, characterized in that, 12≥N≥3. 9. The method for discriminating G-DNA structure based on GMNS rule according to claim 1, characterized in that, 4≥S≥1.

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