When discussing nucleosides, it's important to understand that a nucleoside consists of a sugar (like ribose or deoxyribose) linked to a nitrogenous base, such as adenine. In this case, ribose attached to adenine forms adenosine, which is classified as a nucleoside because it lacks a phosphate group. If a phosphate group were present, it would be termed a nucleotide, specifically adenosine monophosphate (AMP). However, since adenosine does not contain a phosphate, it cannot be classified as a nucleotide.
The structure of DNA is stabilized by various interactions, primarily through nonspecific base stacking interactions between adjacent bases within the same strand. These stacking forces, which are hydrophobic in nature, help maintain the integrity of the double helix. Additionally, the negatively charged phosphate groups on the DNA's exterior interact with water, creating hydrophilic forces that further stabilize the structure. It's crucial to note that while covalent bonds, such as phosphodiester bonds, exist between the strands, they do not contribute to the stabilization of the double helix itself.
In terms of DNA structure, double-stranded RNA adopts an A-form helix, while most DNA exists in a B-form. The Z-form of DNA is less common and typically found in specific regulatory sequences. Understanding the orientation of DNA strands is also essential; DNA is always written from the 5' to 3' end. When determining complementary strands, one must reverse the order of the bases while ensuring the correct pairing (A with T, and C with G).
When DNA is subjected to high temperatures, such as 95 degrees Celsius, certain changes occur. The DNA strands will denature, leading to the unwinding of the helix and the breaking of hydrogen bonds between base pairs. However, covalent bonds remain intact, and the viscosity of the solution decreases as the strands separate. This phenomenon is known as the hyperchromic shift, where UV light absorbance increases due to the exposure of bases.
In DNA sequencing, particularly the classical Sanger method, dideoxynucleotides play a critical role by terminating the synthesis of the complementary strand. These dideoxynucleotides lack a 3' hydroxyl group, preventing further elongation of the DNA strand once incorporated. This results in fragments of varying lengths, which can be analyzed to determine the sequence of the DNA. The concentration of dideoxynucleotides is significantly lower than that of regular deoxynucleotides, ensuring that termination occurs at random points during synthesis. Radioactively labeled dideoxynucleotides are used to identify the fragments during analysis, but they do not play a role in cutting the DNA.