Chemical structure of DNA
Primary structure consists of a linear sequence of nucleotides that are linked together by phosphodiester bonds. It is this linear sequence of nucleotides that make up the Primary structure of DNA or RNA. Nucleotides consist of 3 components:
- Nitrogenous base
- Thymine (present in DNA only)
- Uracil (present in RNA only)
- 5-carbon sugar which is called deoxyribose (found in DNA) and ribose (found in RNA).
- One or more phosphate groups.
The nitrogen bases adenine and guanine are purine in structure and form a glycosidic bond between their 9 nitrogen and the 1' -OH group of the deoxyribose. Cytosine, thymine and uracil are pyrimidines, hence the glycosidic bonds forms between their 1 nitrogen and the 1' -OH of the deoxyribose. For both the purine and pyrimidine bases, the phosphate group forms a bond with the deoxyribose sugar through an ester bond between one of its negatively charged oxygen groups and the 5' -OH of the sugar. The polarity in DNA and RNA is derived from the oxygen and nitrogen atoms in the backbone. Nucleic acids are formed when nucleotides come together through phosphodiester linkages between the 5' and 3' carbon atoms.
A Nucleic acid sequence is the order of nucleotides within a DNA (GACT) or RNA (GACU) molecule that is determined by a series of letters. Sequences are presented from the 5' to 3' end and determine the covalent structure of the entire molecule. Sequences can be complementary to another sequence in that the base on each position is complementary as well as in the reverse order. An example of a complementary sequence to AGCT is TCGA. DNA is double-stranded containing both a sense strand and an antisense strand. Therefore, the complementary sequence will be to the sense strand.
Nucleic acid design can be used to create nucleic acid complexes with complicated secondary structures
such as this four-arm junction. These four strands associate into this structure because it maximizes the number of correct base pairs
, with A
's matched to T
's and C
's matched to G
's. Image from Mao, 2004.
Complexes with alkali metal ions
There are three potential metal binding groups on nucleic acids: phosphate, sugar and base moieties. Solid-state structure of complexes with alkali metal ions have been reviewed.