Related Experiment Video
Updated: Jun 14, 2025
10:34
Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
Published on: December 9, 2022
4.1K
3dRNA/DNA: 3D Structure Prediction from RNA to DNA.
Yi Zhang1, Yiduo Xiong1, Chenxi Yang1
1Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
Journal of Molecular Biology
|September 5, 2024
Summary
A new scoring function, 3dDNAscore, enhances DNA structure prediction by ranking models. This computational tool helps identify accurate three-dimensional DNA structures, improving DNA aptamer selection efficiency.
Area of Science:
- Computational biology
- Structural biology
- Bioinformatics
Background:
- Determining three-dimensional (3D) DNA structures is crucial for applications like DNA aptamer selection.
- Existing computational methods, such as 3dDNA, predict DNA 3D structures but lack a scoring function for ranking predictions.
Purpose of the Study:
- To introduce 3dDNAscore, a novel energy function for assessing the quality of predicted DNA 3D structures.
- To enhance the capabilities of the 3dDNA prediction tool by enabling structure ranking.
Main Methods:
- Development of 3dDNAscore, an all-atom, knowledge-based potential.
- Integration of 86 atomic types from nucleic acids into the scoring function.
- Benchmarking 3dDNAscore against decoys generated by the 3dDNA prediction method.
Main Results:
- 3dDNAscore effectively distinguishes near-native DNA structures from inaccurate models (decoys).
- The scoring function significantly improves the completeness and reliability of the 3dDNA prediction pipeline.
Conclusions:
- 3dDNAscore provides a robust method for evaluating predicted DNA 3D structures.
- This advancement enhances the utility of computational tools for DNA structure determination and related applications.
Related Concept Videos
01:19RNA Structure
4.7K
The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
4.7K
01:25Nucleic Acid Structure
6.1K
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
DNA Structure
DNA...
6.1K
02:43Nucleic acids
160.8K
Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes,...
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes,...
160.8K
01:53RNA Stability
33.4K
Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
33.4K
01:07The DNA Helix
20.0K
Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA is composed of two strands of nucleotides that wind around each other to form a spring-like structure called a double helix. However, the double helix is not perfectly symmetrical. Instead, there are regularly occurring grooves in the structure. The major groove occurs where the sugar-phosphate backbones are relatively far apart. This space...
20.0K
02:43Nucleic Acids
44.0K
Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes,...
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes,...
44.0K