Dna structure with nucleotides
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DNA Structure with Nucleotides
Introduction to DNA Structure
DNA, or deoxyribonucleic acid, is a polymer composed of nucleotides, which are the building blocks of nucleic acids. Each nucleotide in DNA consists of three components: a five-carbon sugar called deoxyribose, a phosphate group, and a nitrogenous base 710. The nitrogenous bases in DNA are adenine (A), guanine (G), cytosine (C), and thymine (T), with adenine pairing with thymine and guanine pairing with cytosine through hydrogen bonds .
Double Helix and Antiparallel Strands
The structure of DNA is famously known as a double helix, where two polynucleotide chains run in opposite directions (antiparallel) and are twisted around each other. The two strands are held together by hydrogen bonds between the complementary bases . This double helical structure is not only found in extracted DNA from various sources but also in intact biological materials such as sperm heads and bacteriophages .
Major and Minor Grooves
The double helix of DNA features major and minor grooves, which are critical for protein binding and the regulation of gene expression. These grooves are formed due to the helical twist of the DNA strands and the specific angles at which the bases pair . The major groove is wider and allows proteins to interact with the bases more easily, while the minor groove is narrower.
Coarse-Grained Models of DNA
Recent advancements in coarse-grained models of DNA, such as the 3-Site-Per-Nucleotide model, have improved our understanding of DNA's structural properties. These models include anisotropic potentials between bases involved in base stacking and base pair interactions, accurately describing the major and minor grooves and the persistence length of both single-stranded (ssDNA) and double-stranded DNA (dsDNA) . These models are useful for simulating non-canonical structures like hairpins and for applications in biological and engineering fields .
Crystal Structures and Nucleotide Conformations
Crystallographic studies have provided detailed insights into the DNA structure. For instance, the crystal structure of a B-form DNA duplex containing (L)-alpha-threofuranosyl nucleosides (TNA) shows that a four-carbon sugar can be easily accommodated into the DNA backbone without significantly altering base stacking interactions . Additionally, the solution structure of an LNA (locked nucleic acid) hybridized to DNA reveals that the high stability of LNA:DNA duplexes is due to local changes in the phosphate backbone geometry, which favor a higher degree of stacking .
Dinucleotide Conformers and Structural Alphabet
A comprehensive analysis of dinucleotides in nucleic acid crystal structures has led to the definition of 96+1 diNucleotide Conformers (NtCs), which describe the geometry of RNA and DNA dinucleotides. These NtCs are grouped into 15 codes of the Conformational Alphabet of Nucleic Acids (CANA), simplifying the symbolic annotation of nucleic acid structures and their graphical display . This structural alphabet aids in the unbiased analysis of nucleic acid structures by structural and molecular biologists .
Single-Stranded DNA and Helical Conformations
Interestingly, single-stranded DNA oligonucleotides, from dimeric to hexameric sequences, retain rise coordinates characteristic of double helices. Computational studies show that single-stranded helices adopt conformations very close to crystallographic B-DNA, with rise coordinates up to 3.3 Å. Sequences rich in stacked adenines are particularly ordered, favoring the B-DNA pattern and inducing regular arrangements in flanking nucleobases .
Conclusion
The structure of DNA is a complex and highly organized system that plays a crucial role in genetic information storage and transmission. Advances in experimental and computational models have significantly enhanced our understanding of DNA's structural properties, from the double helix and major/minor grooves to the detailed conformations of nucleotides and dinucleotides. These insights are essential for various applications in biology and engineering, including nucleosome positioning and DNA-templated engineering.
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