Nucleic acid secondary structure in the context of "Hydroxyl"

In molecular biology, the double helix is the structure formed by double-stranded molecules of nucleic acids such as DNA. The double-helical structure of a nucleic acid complex arises as a consequence of its secondary structure, and is a fundamental component in determining its tertiary structure.

The DNA double-helix biopolymer of nucleic acids is held together by nucleotides which base pair together. In B-DNA, the most common double-helical structure found in nature, the double helix is right-handed with about 10–10.5 base pairs per turn. The double-helix structure of DNA contains a major groove and minor groove. In B-DNA the major groove is wider than the minor groove. Given the difference in widths of the major groove and minor groove, many proteins which bind to B-DNA do so through the wider major groove.

In molecular biology, complementarity describes a relationship between two structures each following the lock-and-key principle. In nature complementarity is the base principle of DNA replication and transcription as it is a property shared between two DNA or RNA sequences, such that when they are aligned antiparallel to each other, the nucleotide bases at each position in the sequences will be complementary, much like looking in the mirror and seeing the reverse of things. This complementary base pairing allows cells to copy information from one generation to another and even find and repair damage to the information stored in the sequences.

The degree of complementarity between two nucleic acid strands may vary, from complete complementarity (each nucleotide is across from its opposite) to no complementarity (each nucleotide is not across from its opposite) and determines the stability of the sequences to be together. Furthermore, various DNA repair functions as well as regulatory functions are based on base pair complementarity. In biotechnology, the principle of base pair complementarity allows the generation of DNA hybrids between RNA and DNA, and opens the door to modern tools such as cDNA libraries.While most complementarity is seen between two separate strings of DNA or RNA, it is also possible for a sequence to have internal complementarity resulting in the sequence binding to itself in a folded configuration.

Nucleic acid design is the process of generating a set of nucleic acid base sequences that will associate into a desired conformation. Nucleic acid design is central to the fields of DNA nanotechnology and DNA computing. It is necessary because there are many possible sequences of nucleic acid strands that will fold into a given secondary structure, but many of these sequences will have undesired additional interactions which must be avoided. In addition, there are many tertiary structure considerations which affect the choice of a secondary structure for a given design.

Nucleic acid design has similar goals to protein design: in both, the sequence of monomers is rationally designed to favor the desired folded or associated structure and to disfavor alternate structures. However, nucleic acid design has the advantage of being a much computationally simpler problem, since the simplicity of Watson-Crick base pairing rules leads to simple heuristic methods which yield experimentally robust designs. Computational models for protein folding require tertiary structure information whereas nucleic acid design can operate largely on the level of secondary structure. However, nucleic acid structures are less versatile than proteins in their functionality.

In genetics, a transcription terminator is a section of nucleic acid sequence that marks the end of a gene or operon in genomic DNA during transcription. This sequence mediates transcriptional termination by providing signals in the newly synthesized transcript RNA that trigger processes which release the transcript RNA from the transcriptional complex. These processes include the direct interaction of the mRNA secondary structure with the complex and/or the indirect activities of recruited termination factors. Release of the transcriptional complex frees RNA polymerase and related transcriptional machinery to begin transcription of new mRNAs.