Nucleic acids transcript DS

Nucleic Acid

A polymer formed by linking nucleotides together. They have directionality based on the ribose sugar's 5' and 3' positions. DNA and RNA are the two main types of nucleic acids.

Directionality (of Nucleic Acids)

A property of nucleic acids where one end has a free 5' phosphate and the other has a free 3' hydroxyl. This creates a "five-prime to three-prime" direction for the polymer chain.

5' to 3' Direction

The standard convention for writing and reading nucleic acid sequences. It refers to the direction from the fifth carbon of the ribose sugar to the third carbon of the next ribose in the chain. Arrows in diagrams indicate this direction.

Double Helix

The structure formed when two strands of DNA (or DNA and RNA) twist around each other. It is stabilized by base pairing, hydrophobic effect, and van der Waals interactions.

Reverse Complimentary Strands

The two strands that form a double helix run in opposite directions (antiparallel). One strand runs 5' to 3' downwards, while the other runs 5' to 3' upwards. Their sequences are complementary, meaning A pairs with T (or U in RNA) and G pairs with C.

Base Pairing

The specific hydrogen-bonding interactions between nitrogenous bases on opposite strands of a nucleic acid. The standard pairs are Adenine (A) with Thymine (T) [or Uracil (U) in RNA] and Guanine (G) with Cytosine (C).

Intermolecular Duplex

A double helix formed by two separate, distinct nucleic acid molecules coming together, as is the case for DNA. This is in contrast to an intramolecular duplex formed within a single strand.

Forces Stabilizing the Double Helix

The double helix is stabilized by three main forces: the hydrophobic effect (burying the non-polar bases), van der Waals interactions (stacking of the flat bases), and hydrogen bonding (specific base pairing).

Base Stacking

The arrangement in the double helix where the flat, planar bases stack on top of one another in the interior. This maximizes van der Waals interactions and is a major driver of duplex stability, independent of base pairing.

Hydrophobic Effect

A key stabilizing force for the double helix where the non-polar, hydrophobic nitrogenous bases are hidden from water in the core of the helix, while the polar, hydrophilic sugar-phosphate backbone is exposed to the outside.

B Form DNA

The most common and biologically relevant helical structure of DNA. It is a hydrated form with a regular structure featuring 10 base pairs per helical turn and a consistent diameter.

Base Pairs Per Turn (B Form)

A characteristic of B form DNA where the helix makes one full turn every 10 base pairs.

Constant Helix Diameter

A feature of the DNA double helix maintained by the base pairing rules. Because a purine (two rings) always pairs with a pyrimidine (one ring), the distance across the helix remains relatively constant, regardless of the specific base pair (AT/TA or GC/CG).

A Form DNA

An alternative helical structure of nucleic acids that forms under dehydrated conditions or in DNA-RNA hybrids. It is more compact and has a different number of base pairs per turn compared to B form DNA.

Z Form DNA

A left-handed helical form of DNA that has been observed in vitro. It is less common in cells but can be specifically bound by certain proteins. It has a zig-zag appearance in the backbone.

Major Groove

The wider of the two grooves in the DNA double helix. It exposes the edges of the base pairs and contains more specific information (hydrogen bond donors and acceptors) that allows proteins to distinguish between different base pairs (e.g., AT vs. GC).

Minor Groove

The narrower of the two grooves in the DNA double helix. It is a shorter distance around the helix and contains less distinct information for differentiating base pairs compared to the major groove.

Glycosidic Bond

The bond connecting the nitrogenous base to the 1' carbon of the sugar. In the double helix, the rotation of these bonds allows the bases to become flat and stack on top of one another. The sides of these bonds define the major and minor grooves.

DNA-RNA Hybrid

A double helix formed by one strand of DNA base-paired with one strand of RNA. This hybrid structure typically adopts the A form conformatio