DNA and nucleic acid structures and properties:

Structural properties of nucleotides: Backbones are hydrophilic (pentose hydroxyls form hydrogen bonds with water), phosphates are completely ionized at pH 7.0 = negative charged, and bases "stack" to minimize contact with water.

Nucleic acid: same thing as polynucleotide, more than 50 bases.

Polymeric form: 5' phosphate + 3' hydroxyl, creates backbone of pentose-phosphate-pentose-phosphate. DNA and RNA have the same backbone structure, staggered.

Chemical properties of nucleotides that explain DNA structures: (1) bases are hydrophobic (2) H-bonds form between nucleotide bases of two different strands (3) Both 1 and 2 stabilize binding between two or more strands.  A + T make two hydrogen bonds and C + G make 3 hydrogen bonds.

- A Form: favored in anhydrous solutions and is a right handed helix ( favored by DNA-RNA hybrids and RNA alone).

B Form: Most stable in biological systems for random sequence DNA , in aqueous solution, and it is a right handed helix.

Z Form: Certain base sequences and high salt favor this form, it is a left handed helix, it is more elongated than A or B, it has almost no minor groove, and has a flat major groove. Short stretches found in eukaryotes and prokaryotes, plays a role in gene regulation, and it is stable. The bases are exposed and protein can bind in major groove to regulate DNA.

• Hairpins: thermodynamically favorable, it they can pair they will.
• Cruciform:
• Bulge: important kink for RNA, causes point mutation in DNA.
• Internal loop: need for RNA function, mutation in DNA.

DNA sequences lead to specific DNA structures: (1) Four or more adenosine residues lead to a tight bend in the helix, causes change in direction of DNA (2) Repeated DNA sequences: (a) palindrome is the same sequence forwards and backwards (b) inverted repeats occur over 2 strands of DNA, self complimentary: hairpins and cruciforms (c) mirror repeats occur often on the same strand

Triplex DNA: b-form of DNA makes additional H-bonds in major groove. Special hydrogen bonds: Hoogsteen positions (the atoms that make the bonds). Non-Watson-Crick pairing: Hoogsteen paring (the bases that make the bonds). The Hoogsteen pairings add stability to DNA and the 3rd strand lays in major groove.

Tetraplex DNA: 4-stranded DNA where there is a high proportion of Guanosine residues, it is very stable. It occurs at end of chromosomes to stabilize DNA. Just think 4G.

Adenine, Thymine, and Uracil can make two H-bonds.Cytosine and Guanine can make three H-bonds.