FCH 532 Lecture 10. Extra credit posted on website, due on Friday (email or typed copy) Chapter 29. Sugar Pucker. Ribose rings will undergo sugar pucker (become slightly nonplanar).
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Extra credit posted on website, due on Friday (email or typed copy)
Figure 29-9bSugar ring pucker. (b) The steric strain resulting in Part a is partially relieved by ring puckering in a half-chair conformation in which C3¢ is the out-of-plane atom (same as C5’ so C3’-endo).
Figure 29-10aNucleotide sugar conformations. (a) The C3-endo conformation (on the same side of the sugar ring as C5), which occurs in A-RNA and RNA-11.
Adenine pairs with thymine. Guanine pairs with cytosine.
These base pairs are interchangeable in the double helix without altering the positions of the sugar phosphate backbone.
The top edge of each base pair is structurally distinct from the bottom edge.
The deoxyribose residues are asymmetric.
Minor groove exposes the edge from the C1’ atom (open toward bottom)
Major groove exposes the opposite edge of each bp.
Figure 29-12bSome non-Watson–Crick base pairs. (b) Hoogsteen pairing between adenine and thymine residues in the crystal structure of 9-methyladenine·1-methylthymine.
[B1 • B2]
B1 • B2
B1 + B2
For solutions that aggregate, van’t Hoff law is rewritten as
the osmotic coefficient: indicates the solute’s degree of association and varies from 1 (no association) to 0 (infinite association)
A + A A2 + A A3 + A … An
Where n is at least 5 (if the reaction goes to completion, 1/n)
This result is not based on hydrogen bonding since N6, N6-dimethyladenosine cannot form hydrogen bonds to itself.
Aggregation instead results from stacks of planar molecules.
Corroborated with NMR studies.
Single-stranded polynucleotides show a similar trend.
molality of solution (mol solute/kg solvent)
Broad increase in UV abs with increase in temp for poly(A) and dinucleotides
0.3< 1XG+C <0.7 and 10-3 M< [Na+]< 1.0 M
Can be used for other monovalent cations (K+, Li+)
Divalent cations such as Mg2+, Mn2+, Co2+ bind specifically to phophate groups and are more effective shielding agents.
1 Mg2+ ion is the equivalent of 100 to 1000 Na+ ions.
The two circular molecules have
the same mass but very different
RG (open circle) >
ccounts for the
Relative radius of gyration
Frictional coefficient influences
electrophoretic mobility and
A. Electrophoretic mobility
B. Sedimentation rate
Which form goes fastest in each technique?
with increasing twists
Gel electrophoresis of a mixture
of linear, open, and supercoiled
DNA treated with EB
Top (- electrotrode)
(Ethidium bromide concentration)
Bottom (+ electrotrode)
Tertiary structure in DNA
Varieties of supercoiled DNA
Toroidal spirals within supercoil