Thus far we have been focusing on the primary structure of nucleic acids
- how the basic components join together to form a single strand.
Now we need to consider the how nucleic acids interact with the solvent (usually water) and each other.
Water is a polar solvent.
The backbone of nucleic acids is composed of phosphate (which is charged)
and sugar (which is hydrophillic due to the numerous OH groups).
The aromatic ring(s) of the N-bases however are hydrophobic.
Attached to the edges of the ring are hydrophillic dipolar groups (-NH2 and =O)
In the absence of other interactions, we might envision nucleic acid polymers to behave as flexible strings,
the backbone being enveloped by a large hydration shell of water, and the N-bases all lined up on one side, shielding one another from the polar solvent and the dipole substituents facing out into the aqueous environment.
Nucleic acids interact with one another via complementary base pairing
- A pairs with T (& U), G pairs with C.
- how the basic components join together to form a single strand.
Now we need to consider the how nucleic acids interact with the solvent (usually water) and each other.
Water is a polar solvent.
The backbone of nucleic acids is composed of phosphate (which is charged)
and sugar (which is hydrophillic due to the numerous OH groups).
The aromatic ring(s) of the N-bases however are hydrophobic.
Attached to the edges of the ring are hydrophillic dipolar groups (-NH2 and =O)
In the absence of other interactions, we might envision nucleic acid polymers to behave as flexible strings,
the backbone being enveloped by a large hydration shell of water, and the N-bases all lined up on one side, shielding one another from the polar solvent and the dipole substituents facing out into the aqueous environment.
Nucleic acids interact with one another via complementary base pairing
- A pairs with T (& U), G pairs with C.
This base pairing results from the ability of the dipolar substituents of the N-bases
to share protons with their complementary base.
The A:T pair share 2 H-bonds, while the G:C pair share three H-bonds.
Figure 9: G:C and A:T base pairs
H-bonding between individual complementary bases is relatively weak,
however when long stretches of N-bases can form H-bonds with a complementary sequence,
the resulting hybrid is very stable. .
however when long stretches of N-bases can form H-bonds with a complementary sequence,
the resulting hybrid is very stable. .
Base pairing can occur within a single strand (intramolecular pairing)
or between molecules (intermolecular pairing).
The first is an important feature of RNA molecules, the second is one of the defining properties of DNA.
(ss-DNA virus genomes excepted).
The two strands are complementary - the sequence of one strand determines the sequence on the opposite strand.
This feature is responsible for the information storage function of this molecule in biological systems and provides the necessary mechanism underlying accurate copying.
How are the two strands of a DNA molecule arranged with respect to one another?
Double-stranded DNA exists primarily in the
right-handed B-form under physiological conditions.
In the B-form, the bases are oriented perpendicular to the long axis of the helix.
