CN116092575A - G DNA structure discrimination method based on GMNS rule - Google Patents
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- 238000012850 discrimination method Methods 0.000 title abstract description 7
- 239000012634 fragment Substances 0.000 claims abstract description 42
- 108020004414 DNA Proteins 0.000 claims abstract description 30
- 238000004458 analytical method Methods 0.000 claims abstract description 15
- 108091028043 Nucleic acid sequence Proteins 0.000 claims abstract description 12
- 238000012216 screening Methods 0.000 claims abstract description 5
- 238000000034 method Methods 0.000 claims description 21
- 230000009286 beneficial effect Effects 0.000 abstract description 2
- 238000011160 research Methods 0.000 description 5
- 150000003384 small molecules Chemical class 0.000 description 5
- 102000053602 DNA Human genes 0.000 description 4
- 239000002773 nucleotide Substances 0.000 description 3
- 125000003729 nucleotide group Chemical group 0.000 description 3
- 108020004682 Single-Stranded DNA Proteins 0.000 description 2
- OPTASPLRGRRNAP-UHFFFAOYSA-N cytosine Chemical compound NC=1C=CNC(=O)N=1 OPTASPLRGRRNAP-UHFFFAOYSA-N 0.000 description 2
- 238000010586 diagram Methods 0.000 description 2
- UYTPUPDQBNUYGX-UHFFFAOYSA-N guanine Chemical compound O=C1NC(N)=NC2=C1N=CN2 UYTPUPDQBNUYGX-UHFFFAOYSA-N 0.000 description 2
- RWQNBRDOKXIBIV-UHFFFAOYSA-N thymine Chemical compound CC1=CNC(=O)NC1=O RWQNBRDOKXIBIV-UHFFFAOYSA-N 0.000 description 2
- GFFGJBXGBJISGV-UHFFFAOYSA-N Adenine Chemical compound NC1=NC=NC2=C1N=CN2 GFFGJBXGBJISGV-UHFFFAOYSA-N 0.000 description 1
- 229930024421 Adenine Natural products 0.000 description 1
- 108091081406 G-quadruplex Proteins 0.000 description 1
- 238000004566 IR spectroscopy Methods 0.000 description 1
- 229960000643 adenine Drugs 0.000 description 1
- 238000012512 characterization method Methods 0.000 description 1
- 238000000978 circular dichroism spectroscopy Methods 0.000 description 1
- 230000000295 complement effect Effects 0.000 description 1
- 229940104302 cytosine Drugs 0.000 description 1
- 238000011161 development Methods 0.000 description 1
- 239000003814 drug Substances 0.000 description 1
- 230000007613 environmental effect Effects 0.000 description 1
- 238000002474 experimental method Methods 0.000 description 1
- 229910052739 hydrogen Inorganic materials 0.000 description 1
- 239000001257 hydrogen Substances 0.000 description 1
- 238000002372 labelling Methods 0.000 description 1
- 238000012986 modification Methods 0.000 description 1
- 230000004048 modification Effects 0.000 description 1
- 108020004707 nucleic acids Proteins 0.000 description 1
- 102000039446 nucleic acids Human genes 0.000 description 1
- 150000007523 nucleic acids Chemical class 0.000 description 1
- 230000003950 pathogenic mechanism Effects 0.000 description 1
- 230000000750 progressive effect Effects 0.000 description 1
- 229940113082 thymine Drugs 0.000 description 1
- 239000013638 trimer Substances 0.000 description 1
- 238000000870 ultraviolet spectroscopy Methods 0.000 description 1
- 238000012795 verification Methods 0.000 description 1
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- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B15/00—ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
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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
Technical Field
The invention belongs to the technical field of biological analysis, and particularly relates to a G-DNA structure discrimination method based on a GMNS rule.
Background
With the intensive research of nucleic acid, the DNA structure is found to have the characteristics of diversity, such as single-stranded DNA, double-stranded DNA, hairpin DNA, I-DNA, G-DNA, DNA trimer and the like, and the diversity of the DNA structure provides a rich mode of action for the action of small molecules and DNA, provides more suitable target sites for specific recognition, namely capture of the small molecules, and provides a basis for developing the action research of the DNA and the small molecules. Therefore, development of DNA structure, particularly three-dimensional structure analysis, has important research significance.
The fact shows that although the types of DNA bases are only four types of adenine, guanine, cytosine and thymine, the difference of DNA sequences composed of the four types of bases is thousands, and how to judge the three-dimensional structure of DNA is the first problem to be solved. The current discrimination method for single-stranded DNA, double-stranded DNA and hairpin DNA is easier, and is mainly based on whether the DNA molecules and DNA molecules can be connected through hydrogen bonds to form base complementary pairing. However, no discrimination method is currently available for G-DNA (G quadruplex DNA), and analysis can only be performed by means of experimental results and instrument characterization, such as ultraviolet-visible spectroscopy, infrared spectroscopy, circular dichroism spectroscopy, etc. Therefore, for any given DNA sequence, whether it can be formed in G-DNA or what kind of base, base sequence, and specific structural unit of structural characteristics can form I-DNA or G-DNA, no determination result can be given.
G-DNA has been widely used in the fields of physiological action, biological medicine, food safety analysis, environmental protection, etc., so that the research of rules, the revealing of essence, the provision of a G-DNA structure distinguishing method, and the like are of great significance in the aspects of researching the combination mode, action mode, pathogenic mechanism, etc. between small molecules and DNA molecules.
Disclosure of Invention
The invention discloses a G-DNA structure judging method based on GMNS rule, which can judge whether the G-DNA structure is the G-DNA structure according to DNA sequence without experiment, and is simple and convenient.
In order to achieve the above purpose, the present invention adopts the following technical scheme:
the G-DNA structure distinguishing method based on the GMNS rule comprises the following steps:
(1) Numbering DNA sequences
Numbering of base B of a given DNA fragment starting from either end: b (B) 1 、B 2 、B 3 、B 4 …；
(2) Screening for characteristic fragments
Taking a G-rich base fragment in a given DNA fragment, and calibrating the first base G as an effective base G x X is the number of the first base G in a given DNA fragment; from G x Starting counting of bases to G x+n Cut-off of number of bases, selection of B x-y To B x+n+z Is a fragment of the G-DNA effective characteristic; 35. more than or equal to n more than or equal to 9, more than or equal to y more than or equal to 10 more than or equal to 0, and more than or equal to z more than or equal to 10 more than or equal to 0;
(3) Analysis of G base characteristics
Analyzing G structural units consisting of 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 G base number in the G structural units, such as M1, M2, M3 and M4 … …;
(4) Counting GM building blocks
Respectively calculating the number N of each GM structural unit;
(5) G-DNA Structure discrimination
Marking and respectively calculating the number S of bases between adjacent G structural units;
m is more than or equal to 2, N is more than or equal to 1, S is more than or equal to 8 and more than or equal to 1, and the G-DNA structure is judged if a structural repeating unit exists in the effective characteristic fragment;
the presence of structural repeat units in the effective characteristic fragment means that in the effective characteristic fragment:
for a G building block, repeating discontinuously at least 4;
or for a combined structure formed by at least two G building blocks, repeating discontinuously at least 2; the term "discontinuous" as used herein means that bases other than G are present between adjacent G building blocks.
Further, a G-rich base fragment is a portion of a given DNA fragment where G bases are more concentrated, and particularly refers to a portion of the base sequence of a structural repeat unit.
Further, the number of effective characteristic fragment bases is not more than 36.
Further, either end is the 3 'end and/or the 5' end.
Further, the G base ratio in the effective characteristic fragment is 10% -80%.
Further, the G base ratio in the effective characteristic fragment is 35% -80%.
Further, 35.gtoreq.n.gtoreq.16, 4.gtoreq.y.gtoreq.0, 4.gtoreq.z.gtoreq.0.
Further, 5.gtoreq.M.gtoreq.2, 12.gtoreq.N.gtoreq.3, 4.gtoreq.S.gtoreq.1.
Within the further defined range of M, N, S, the judged G-DNA structure was more stable.
Further, a program for discriminating a G-DNA structure may be written according to the above-described method using a conventional programming language to form a discriminated G-DNA structure for a module or system.
The invention has the beneficial effects that:
1) The GMNS method adopted by the invention is simple and quick, and improves the analysis efficiency;
2) The GMNS method adopted by the invention is suitable for rapid discrimination of the G-DNA structure;
4) The GMNS method adopted by the invention can reduce the experimental cost;
5) The GMNS method adopted by the invention can provide theoretical support for the research of the action modes of the G-DNA and the small molecules.
In summary, the invention provides a GMNS method for rapidly distinguishing the G-DNA structure, establishes a G-DNA structure distinguishing method which is applicable to short-chain DNA and is based on G base distribution characteristics, provides a theoretical basis for G-DNA structure verification, and provides theoretical support for revealing the action mechanism of G-DNA and targets. The GMNS method has the characteristics of simplicity, rapidness and high reliability for three-dimensional structure analysis of short-chain DNA, and has great significance and value for enriching and perfecting DNA structure analysis, researching action with a target and the like.
Drawings
FIG. 1 is a schematic diagram showing the base numbers of the DNA sequences of example 1.
FIG. 2 is a schematic diagram showing the base numbers of the DNA sequences of example 2.
Detailed Description
The following description of the embodiments of the present invention will be made clearly and completely, and it is apparent that the described embodiments are only some embodiments of the present invention, but not all embodiments. All other embodiments, which can be made by those skilled in the art based on the embodiments of the invention without making any inventive effort, are intended to be within the scope of the invention.
EXAMPLE 1 numbering DNA sequence
Given DNA-1, the nucleotide sequence is as follows: 3'-GGGTTGGGCTGGGTGGGGCT-5', SEQ ID NO.1;
the bases were numbered starting from the 3' end as shown in FIG. 1.
Example 2
(1) Numbering DNA sequences
Given DNA-2, the nucleotide sequence is as follows: 3'-CATCTTGGGGTTGGGGTTGGGGTT GGGGTCATCT-5', SEQ ID NO.2;
numbering the bases from the 3' end as shown in FIG. 2;
wherein the total number of bases is 34; the number of G bases was 16, and the G bases accounted for 47%. DNA-2 can be directly used as a G-base-rich fragment for subsequent analysis.
(2) Screening for characteristic fragments
Starting from the beginning of numbering, calibrating the first base G as an effective base Gx, wherein x=7;
from G x (G 7 ) Starting counting of bases to G x+n (G 28 ) Cut-off of number of bases, G 7 To G 28 22 bases are added, the base difference n is 21, the number of the bases is more than or equal to 35 and more than or equal to 9, and B is selected x-y To B x+n+z (G 7 -G 30 ) Is an effective characteristic fragment of G-DNA, y=0, and z=2, and satisfies that y is more than or equal to 10 and more than or equal to 0, and z is more than or equal to 10 and more than or equal to 0; the effective characteristic fragment is 24 bases or less than 36, the number of G bases is 16, the G bases account for 67 percent, and the effective characteristic fragment accords with 10 to 80 percent.
Example 3
(1) Numbering DNA sequences
Given DNA-3, the nucleotide sequence is as follows: 5'-ATTCAGGGTGGGTGGGTGGGTATT CA-3', SEQ ID No.3;
numbering the bases from the 5' end;
wherein the total number of bases is 26; the number of G bases was 12, and the G bases accounted for 46%. DNA-3 can be directly used as a G-base-rich fragment for subsequent analysis.
(2) Screening for characteristic fragments
Starting from the beginning of numbering, the first base G is marked as the effective base G x ，x＝6；
From G x (G 6 ) Starting counting of bases to G x+n (G 20 ) Cut-off of number of bases, G 6 To G 20 15 bases are added between the two, the base difference n is 14, the number of the bases is more than or equal to 35 and more than or equal to 9, and B is selected x-y To B x+n+z (G 6 -G 21 ) Is an effective characteristic fragment of G-DNA, y=0, and z=1, and satisfies that y is more than or equal to 10 and more than or equal to 0, and z is more than or equal to 10 and more than or equal to 0; effective characteristic fragment is 16 bases, not more than 36, G base numberThe amount is 12, the G base accounts for 75 percent, and the amount is in line with 10 to 80 percent.
(3) Analysis of G base characteristics
Analyzing G structural units formed by continuous G bases in the 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 units:
including G3 (GGG);
(4) Counting GM building blocks
The number of GM structural units N: g3 is 4;
the structural repeat unit (GGG) B exists in the effective characteristic fragment, and the requirement that the structural repeat unit exists in the effective characteristic fragment is satisfied: for a G building block, repeating discontinuously at least 4;
(5) G-DNA Structure discrimination
Labeling and calculating the number of bases S between adjacent G structural units respectively: sequentially 1, 1 and 1;
m is 3, which is consistent with M being more than or equal to 2; n is 4, N is more than or equal to 1, S is more than or equal to 8 and more than or equal to 1, and the structural repeat unit exists in the effective characteristic fragment, so that the G-DNA structure is judged.
Example 4
According to the GMNS method in example 3, the following DNA sequences were determined:
DNA-4：5’-AATGGGTAGGGCGGGTTGGGATGAA-3’，SEQ ID NO.4；
DNA-5：5’-AAGGGTTAGGGTTAGGGTTAGGGTTAC-3’，SEQ ID NO.5；
DNA-6：5’-ATTGGGGTTGGGGTTGGGGTTGGGGTTATTA-3’，SEQ IDNO.6；
DNA-7：5’-ATTGGTTGGTTGTTGTTGTTGGGTTACT-3’，SEQ ID NO.7；
DNA-8：5’-AGGGGTTTTGGGGTTTTGGGGTTTTGGGGA-3’，SEQ IDNO.8；
the analysis information and the judgment result of the DNA structure are shown in Table 1.
TABLE 1
In the present specification, each embodiment is described in a progressive manner, and each embodiment is mainly described in a different point from other embodiments, and identical and similar parts between the embodiments are all enough to refer to each other.
The previous description of the disclosed embodiments is provided to enable any person skilled in the art to make or use the present invention. Various modifications to the embodiments described above will be readily apparent to those skilled in the art, and the generic principles defined herein may be applied to other embodiments without departing from the spirit or scope of the invention. Thus, the present invention is not intended to 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 distinguishing method based on the GMNS rule is characterized by comprising the following steps:
(1) Numbering DNA sequences
Base B of a given DNA fragment is numbered sequentially starting from either end: b (B) 1 、B 2 、B 3 、B 4 …；
(2) Screening for characteristic fragments
Taking the G-rich base fragment in the given DNA fragment, and calibrating the first base G as the effective base G x X is the number of the first base G in the given DNA fragment; from G x Starting counting of bases to G x+n Cut-off of number of bases, selection of B x-y To B x+n+z Is a fragment of the G-DNA effective characteristic; 35. more than or equal to n more than or equal to 9, more than or equal to y more than or equal to 10 more than or equal to 0, and more than or equal to z more than or equal to 10 more than or equal to 0;
(3) Analysis of G base characteristics
Analyzing G structural units consisting of a plurality of 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 units;
(4) Counting GM building blocks
Respectively calculating the number N of each GM structural unit;
(5) G-DNA Structure discrimination
Marking and respectively calculating the number S of bases between adjacent G structural units;
m is more than or equal to 2, N is more than or equal to 1, S is more than or equal to 8 and more than or equal to 1, and the G-DNA structure is judged if a structural repeating unit exists in the effective characteristic fragment;
the presence of structural repeat units in the effective characteristic fragment means that in the effective characteristic fragment:
for a G building block, repeating discontinuously at least 4;
or for a combined structure formed by at least two G building blocks, repeating discontinuously at least 2.
2. The method of claim 1, wherein the number of effective characteristic fragments is not more than 36.
3. The method according to claim 1, wherein the arbitrary end is 3 'end and/or 5' end.
4. The method for discriminating a G-DNA structure based on the GMNS rule according to claim 1 wherein the effective characteristic fragment has a G base ratio of 10% to 80%.
5. The method for discriminating a G-DNA structure based on the GMNS rule according to claim 4 wherein the effective characteristic fragment has a G base ratio of 35.about.80%.
6. The method for discriminating G-DNA structure based on GMNS rule according to claim 1, wherein 35.gtoreq.n.gtoreq.16, 4.gtoreq.y.gtoreq.0, 4.gtoreq.z.gtoreq.0.
7. The method for discriminating a G-DNA structure based on the GMNS rule according to claim 1, wherein 5.gtoreq.M.gtoreq.2.
8. The method for discriminating a G-DNA structure based on the GMNS rule according to claim 1, wherein 12.gtoreq.N.gtoreq.3.
9. The method for discriminating a G-DNA structure based on the GMNS rule according to claim 1, wherein 4.gtoreq.S.gtoreq.1.
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