Nucleic Acid Terms
Refers to the orientations of the two single strands that compose a double-stranded DNA helix. Strands are oriented such that one strand's 5' end is directly across from the other strand's 3' end.
Term used to refer to the natural pairing of the nitrogen bases within DNA and RNA. In DNA, cytosine pairs with guanine and adenine with thymine. In RNA, the thymine is replaced with uracil, which pairs with adenine. Each member of these pairs are said to be a "complements" of the other.
A five-membered sugar ring that lacks a hydroxyl group at one position, and is the sugar group for DNA.
A common structural motif of DNA. Two linear strands of single-stranded DNA fold into a helical shape stabilized internally by hydrogen bonds between complementary base pairs.
In DNA, refers to the oxygen-carbon linkage between the triphosphate group and the 5' carbon of the ribose sugar group in a single DNA or RNA nucleotide.
In DNA, refers to the nitrogen-carbon linkage between the 9' nitrogen of purine bases or 1' nitrogen of pyrimidine bases and the 1' carbon of the sugar group.
Helical Twist - The angular rotation needed to get from one nucleotide to another in helical structures. Hydrogen Bonding - Weak, noncovalent linkages between a donor and an acceptor which, when lined up next to each other, have favorable electrostatic interactions. Provide small amount of stability to DNA and RNA helices. Provide specificity of the interactions between polynucleotide strands. Hydrogen Bond Acceptor - A group with at least one free lone pair of electrons. In DNA and RNA, common acceptor groups include: carbonyls, hydroxyls, and tertiary amines. Hydrogen Bond Donor - A group with a free hydrogen group. In DNA and RNA, common donors include secondary amines and hydroxyl groups. Major groove - In a helix, refers to the larger of the unequal grooves that are formed as a result of the double-helical structure of DNA. As a result of the patterns of hydrogen bonding between complementary bases of DNA, the sugar groups stick out at 120 degree angles from each other instead of 180.
The major groove is generated by the larger angular distance between sugars. Minor groove - In a helix, refers to the smaller of the unequal grooves that are formed as a result of the double-helical structure of DNA. As a result of the patterns of hydrogen bonding between complementary bases of DNA, the sugar groups stick out at 120 degree angles from each other instead of 180. The minor groove is generated by the smaller angular distance between sugars. Nitrogen Base - One of three components of a nucleotide, nitrogen bases come in two general types: purines and pyrimidines. Of the four nitrogen bases, adenine and guanine are purines, while cytosine and thymine are pyrimidines. Through hydrogen bonding, base pairs link in a complementary nature: adenine with thymine and guanine with cytosine, forming the double-stranded helix of DNA. In RNA, thymine is replaced by uracil. Nucleic Acid - A chain of nucleotides joined together by phosphodiester bonds. Both DNA and RNA are nucleic acids. Nucleotide - A five-membered sugar group with a purine or pyrimidine nitrogen base group attached to its 1' carbon via a glycosidic bond and one or more phosphate groups attached to its 5' carbon via an ester bond. Phosphate Backbone - Refers to the structural organization of the DNA double-helix in which the pyrimidine and purine basic groups face the interior while the phosphate groups line the exterior of the helix. The phosphate backbone carries a negative charge. Phosphate Group - One of three components of a nucleotide, comprised of a central phosphorous surrounded by four oxygens. The phosphate links to the sugar group, carries a negative charge because of the chemical interaction between phosphorous and oxygen, and forms the exterior of the phosphate backbone. Phosphodiester linkage - In a polynucleotide, refers to the bond between the 3' hydroxyl of a sugar group in a nucleotide and a phosphate group attached to the 5' carbon of another sugar group. Pitch - In a helix, refers to the vertical distance traveled in one full turn (360 degrees of twist). Primary Structure - In DNA and RNA, refers to the linear sequence of base pairs or amino acids in a polynucleotide chain. Purine - One of two categories of nitrogen base ring compounds found in DNA and RNA. A purine is a nine-membered double ring composed of one five-membered joined to a six membered ring containing four nitrogens. See pyrimidine. Pyrimidine - One of two categories of nitrogen base ring compounds found in DNA and RNA. A six-membered ring containing two nitrogens. See purine. Ribose - The sugar group of RNA, a five-membered sugar ring containing one oxygen and four carbons with one additional carbon attached to the 4' carbon in the ring and hydroxyl groups attached to the 1', 2', 3', and 5' carbons. See deoxyribose. Right Hand Rule - A trick used to quickly determine the "handedness" or orientation of a helix. In a right-handed helix, if one extends his or her right hand and traces with fingers along the backbone of the helix, the hand and thumb move upwards. Rise - In a helix, the vertical distance traveled when moving from one base pair to the adjacent base pair. Secondary Structure - In DNA and RNA, the local folding patterns of a polynucleotide based on complementary base- pairing. Common motifs include alpha helices and bet-pleated sheets. Sugar Group - One of three components of a nucleotide, a five-ringed carbon sugar, either ribose or deoxyribose in form. The sugar group bonds to the nitrogen base and to the phosphate group. Tertiary Structure - In DNA and RNA, the complex three-dimensional form of a polynucleotide.