Hydrogen bonds play a crucial role in stabilizing the structure of DNA and RNA. In DNA, hydrogen bonds occur between the nitrogenous bases on opposite strands, forming the steps of the DNA double helix ladder. Adenine and thymine form two hydrogen bonds, while cytosine and guanine form three. These bonds are strong enough to hold the two strands together but weak enough to allow them to separate during processes like replication and transcription. In RNA, which is typically single-stranded, hydrogen bonds can occur between bases within the same molecule, creating secondary structures like hairpins and loops. These structures are vital for the RNA's function, as they can influence the molecule's interaction with other biomolecules and its overall stability. The specificity and number of hydrogen bonds directly impact the accuracy of DNA replication and RNA synthesis, ensuring genetic fidelity.

The antiparallel nature of DNA strands, where one strand runs in a 5' to 3' direction and the opposite strand runs in a 3' to 5' direction, is essential for nucleotide base pairing and replication. This orientation ensures that the complementary bases align correctly for hydrogen bonding. During DNA replication, DNA polymerase enzymes add nucleotides to the growing strand in a 5' to 3' direction. The antiparallel structure necessitates that the two strands be replicated differently: one continuously (the leading strand) and the other in short segments (the lagging strand). This arrangement allows the enzymes to access the bases on each template strand properly, ensuring accurate and efficient replication. The antiparallel structure thus plays a pivotal role in maintaining the integrity and continuity of genetic information.

Chargaff's rules, discovered by Erwin Chargaff, were pivotal in understanding DNA structure and base pairing. These rules state that in DNA, the amount of adenine (A) equals the amount of thymine (T), and the amount of cytosine (C) equals the amount of guanine (G). This finding was crucial for the formulation of the double helix model of DNA by Watson and Crick. Chargaff's rules implied that A pairs with T and C pairs with G, suggesting a mechanism for the base pairing in DNA. This complementary base pairing is central to the DNA structure, as it allows the formation of a stable double helix with uniform width. Additionally, Chargaff's rules hinted at the semi-conservative mechanism of DNA replication, where each strand serves as a template for a new complementary strand, preserving the base pairing rules and thereby the genetic information.

The chemical structures of purines and pyrimidines are fundamental to nucleotide base pairing and the overall structure of DNA and RNA. Purines, adenine (A) and guanine (G), have a double-ring structure, whereas pyrimidines, cytosine (C), thymine (T), and uracil (U), have a single-ring structure. This size difference allows for efficient stacking within the DNA or RNA molecule. In DNA, the pairing of a purine with a pyrimidine (A with T, G with C) maintains a consistent width of the double helix, crucial for its stability and function. In RNA, this pairing facilitates the formation of secondary structures like loops and hairpins, which are important for the molecule's function. The specific shapes and hydrogen bonding capabilities of these bases ensure accurate base pairing, which is critical for DNA replication and RNA synthesis.

Uracil is used in RNA instead of thymine, which has important implications for RNA's function and stability. Structurally, uracil is similar to thymine but lacks a methyl group present in thymine. This slight difference makes RNA less stable than DNA, which is suitable for RNA's roles in the cell. RNA often acts as a transient carrier of genetic information and is not intended for long-term storage, unlike DNA. The use of uracil instead of thymine contributes to this transient nature. Additionally, the presence of uracil allows for the repair mechanism in DNA. When cytosine deaminates, it turns into uracil. If uracil were normally found in DNA, this change would go unnoticed. However, since DNA does not normally contain uracil, its presence signals a mutation, prompting repair mechanisms to correct it. This difference in base usage is thus a crucial aspect of the distinct roles and stabilities of DNA and RNA.