Related Experiment Video
Updated: Jun 28, 2026
16:24
Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
Sequence-dependence and prediction of nucleotide solvent accessibility in double stranded DNA
1National Institute of Biomedical Innovation, 7-6-8 Saito-asagi, Ibaraki-shi, Osaka, Japan. shandar@nibio.go.jp
Gene
|October 29, 2008
Summary
This study introduces methods to predict nucleotide solvent accessibility in DNA, finding Thymine has a higher exposed surface area. Nucleotide exposure is predictable using sequence neighbor information.
Area of Science:
- Biophysics
- Computational Biology
- Genomics
Background:
- Solvent accessibility is crucial for protein function and extensively studied.
- Current DNA structural analyses focus on elasticity, neglecting nucleotide solvent accessibility.
- No methods exist to predict nucleotide solvent accessibility from DNA sequences.
Purpose of the Study:
- To analyze nucleotide distribution across solvent accessibility ranges.
- To develop predictive models for nucleotide solvent accessibility.
- To investigate the influence of neighboring nucleotides on exposure.
Main Methods:
- Analysis of nucleotide distribution in different solvent accessibility ranges.
- Development of a linear perceptron model using sequence information.
- Prediction of five types of nucleotide solvent accessibility.
Main Results:
- Thymine exhibits a significantly higher exposed surface area, especially its side chain and non-polar atoms.
- Nucleotide solvent accessibility is strongly influenced by adjacent nucleotides.
- The developed model predicts nucleotide solvent accessibility with fair success.
Conclusions:
- Nucleotide solvent accessibility is a quantifiable property with implications for DNA structure and function.
- Sequence context is a key determinant of nucleotide exposure.
- This work provides a foundation for predicting nucleotide solvent accessibility in DNA.
More Related Videos
09:04Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
Published on: September 21, 2017
09:17Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
Published on: March 1, 2022
Related Concept Videos
01:03Single-Strand DNA Binding Proteins
For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
02:05DNA as a Genetic Template
Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
01:31Proofreading
Synthesis of new DNA molecules is carried out by the enzyme DNA polymerase, which adds nucleotides on the daughter strand complementary to the template DNA strand. DNA polymerase has a higher affinity to add the correct base and ensures fidelity during DNA replication. Furthermore, it exhibits proofreading activity during replication, using an exonuclease domain that cuts off incorrect nucleotides from the nascent DNA strand.
Errors During Replication are Corrected by the DNA Polymerase Enzyme
Errors During Replication are Corrected by the DNA Polymerase Enzyme
01:43Proofreading
Synthesis of new DNA molecules starts when DNA polymerase links nucleotides together in a sequence that is complementary to the template DNA strand. DNA polymerase has a higher affinity for the correct base to ensure fidelity in DNA replication. The DNA polymerase furthermore proofreads during replication, using an exonuclease domain that cuts off incorrect nucleotides from the nascent DNA strand.Errors during Replication Are Corrected by the DNA Polymerase EnzymeGenomic DNA is synthesized in...
02:10Translesion DNA Polymerases
Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...
02:04Fixing Double-strand Breaks
The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...