DNA exists in a double-helical structure, with two anti-parallel strands bound together through hydrogen bonding between complementary nucleotide base pairs. The most common form is B-DNA, which is a right-handed double helix with 10 base pairs per turn. DNA structure and stability are maintained through base pairing, base stacking interactions, sugar-phosphate backbone conformations, and ionic interactions with cations like magnesium. The topology and supercoiling of DNA allow for its compact organization in the cell and play important roles in processes like DNA replication and transcription.

1. DNA STRUCTURE
STRUCTURE, FORCES
AND TOPOLOGY

2. DNA GEOMETRY
 A POLYMER OF DEOXYRIBONUCLEOTIDES
 DOUBLE-STRANDED
 INDIVIDUAL deoxyNUCLEOSIDE TRIPHOSPHATES ARE
COUPLED BY PHOSPHODIESTER BONDS
– ESTERIFICATION
– LINK 3’ CARBON OF ONE RIBOSE WITH 5’ C OF ANOTHER
– TERMINAL ENDS : 5’ AND 3’
 A “DOUBLE HELICAL” STRUCTURE
– COMMON AXIS FOR BOTH HELICES
– “HANDEDNESS” OF HELICES
– ANTIPARALLEL RELATIONSHIP BETWEEN 2 DNA STRANDS

3. DNA GEOMETRY
 PERIPHERY OF DNA
– SUGAR-PHOSPHATE CHAINS
 CORE OF DNA
– BASES ARE STACKED IN PARALLEL FASHION
– CHARGAFF’S RULES
 A = T
 G = C
– “COMPLEMENTARY” BASE-PAIRING

4. TAUTOMERIC FORMS OF BASES
 TWO POSSIBILITIES
– KETO (LACTAM)
– ENOL (LACTIM)
 PROTON SHIFTS BETWEEN TWO FORMS
 IMPORTANT IN ORDER TO SPECIFY HYDROGEN
BONDING RELATIONSHIPS
 THE KETO FORM PREDOMINATES

6. MAJOR AND MINOR GROOVES
 MINOR
– EXPOSES EDGE FROM WHICH C1’ ATOMS EXTEND
 MAJOR
– EXPOSES OPPOSITE EDGE OF BASE PAIR
 THE PATTERN OF H-BOND POSSIBILITIES IS
MORE SPECIFIC AND MORE DISCRIMINATING IN
THE MAJOR GROOVE
– STUDY QUESTION: LOCATE ALL OF THE
POSSIBILITIES FOR H-BONDING IN THE MAJOR AND
MINOR GROOVES FOR THE 4 POSSIBLE BASE-PAIRS

7. STRUCTURE OF THE DOUBLE HELIX
 THREE MAJOR FORMS
– B-DNA
– A-DNA
– Z-DNA
 B-DNA IS BIOLOGICALLY THE MOST COMMON
– RIGHT-HANDED (20 ANGSTROM (A) DIAMETER)
– COMPLEMENTARY BASE-PAIRING (WATSON-CRICK)
 A-T
 G-C
– EACH BASE PAIR HAS ~ THE SAME WIDTH
 10.85 A FROM C1’ TO C1’
 A-T AND G-C PAIRS ARE INTERCHANGEABLE
– “PSEUDO-DYAD” AXIS OF SYMMETRY

8. GEOMETRY OF B-DNA
 IDEAL B-DNA HAS 10 BASE PAIRS PER TURN
 BASE THICKNESS
– AROMATIC RINGS WITH 3.4 A THICKNESS TO RINGS
 PITCH = 10 X 3.4 = 34 A PER COMPLETE TURN
 AXIS PASSES THROUGH MIDDLE OF EACH BP
 MINOR GROOVE IS NARROW
 MAJOR GROOVE IS WIDE
 IN CLASS EXERCISE: EXPLORE THE
STRUCTURE OF B-DNA. PAY SPECIAL
ATTENTION TO THE MAJOR, MINOR GROOVES

9. A-DNA
 RIGHT-HANDED HELIX
 WIDER AND FLATTER THAN B-DNA
 11.6 BP PER TURN
 PITCH OF 34 A
  AN AXIAL HOLE
 BASE PLANES ARE TILTED 20 DEGREES WITH RESPECT
TO HELICAL AXIS
– HELIX AXIS PASSES “ABOVE” MAJOR GROOVE
  DEEP MAJOR AND SHALLOW MINOR GROOVE
 OBSERVED UNDER DEHYDRATING CONDITIONS

10. A-DNA
 WHEN RELATIVE HUMIDITY IS ~ 75%
– B-DNA  A-DNA (REVERSIBLE)
 MOST SELF-COMPLEMENTARY OLIGONUCLEO-
TIDES OF < 10 bp CRYSTALLIZE IN A-DNA CONF.
 A-DNA HAS BEEN OBSERVED IN 2 CONTEXTS:
– AT ACTIVE SITE OF DNA POLYMERASE (~ 3 bp )
– GRAM (+) BACTERIA UNDERGOING SPORULATION
 SASPs INDUCE B-DNA TO  A-DNA
 RESISTANT TO UV-INDUCED DAMAGE
– CROSS-LINKING OF PYRIMIDINE BASES

11. Z-DNA
 A LEFT-HANDED HELIX
 SEEN IN CONDITIONS OF HIGH SALT CONCENTRATIONS
– REDUCES REPULSIONS BETWEEN CLOSEST PHOSPHATE
GROUPS ON OPPOSITE STRANDS (8 A VS 12 A IN B-DNA)
 IN COMPLEMENTARY POLYNUCLEOTIDES WITH
ALTERNATING PURINES AND PYRIMIDINES
– POLY d(GC) · POLY d(GC)
– POLY d(AC) ⋅ POLY d(GT)
 MIGHT ALSO BE SEEN IN DNA SEGMENTS WITH ABOVE
CHARACTERISTICS

12. Z-DNA
 12 W-C BASE PAIRS PER TURN
 A PITCH OF 44 DEGREES
 A DEEP MINOR GROOVE
 NO DISCERNIBLE MAJOR GROOVE
 REVERSIBLE CHANGE FROM B-DNA TO Z-DNA
IN LOCALIZED REGIONS MAY ACT AS A
“SWITCH” TO REGULATE GENE EXPRESSION
– ? TRANSIENT FORMATION BEHIND ACTIVELY TRAN-
SCRIBING RNA POLYMERASE

13. STRUCTURAL VARIANTS OF DNA
 DEPEND UPON:
– SOLVENT COMPOSITION
 WATER
 IONS
– BASE COMPOSITION
 IN-CLASS QUESTION: WHAT FORM OF
DNA WOULD YOU EXPECT TO SEE IN
DESSICATED BRINE SHRIMP EGGS?
WHY?

14. RNA
 UNLIKE DNA, RNA IS SYNTHESIZED AS A SINGLE STRAND
 THERE ARE DOUBLE-STRANDED RNA STRUCTURES
– RNA CAN FOLD BACK ON ITSELF
– DEPENDS ON BASE SEQUENCE
– GIVES STEM (DOUBLE-STRAND) AND LOOP (SINGLE-
STRAND STRUCTURES)
 DS RNA HAS AN A-LIKE CONFORMATION
– STERIC CLASHES BETWEEN 2’-OH GROUPS PREVENT THE
B-LIKE CONFORMATION

15. HYBRID DNA-RNA STRUCTURES
 THESE ASSUME THE A-LIKE CONFORMATION
 USUALLY SHORT SEQUENCES
 EXAMPLES:
– DNA SYNTHESIS IS INITIATED BY RNA “PRIMERS”
– DNA IS THE TEMPLATE FOR TRANSCRIPTION TO RNA

16. FORCES THAT STABILIZE NUCLEIC
ACID STRUCTURES
 SUGAR-PHOSPHATE CHAIN CONFORMATIONS
 BASE PAIRING
 BASE-STACKING,HYDROPHOBIC
 IONIC INTERACTIONS

17. SUGAR-PHOSPHATE CHAIN IS
FLEXIBLE TO AN EXTENT
 CONFORMATIONAL FLEXIBILITY IS
CONSTRAINED BY:
– SIX TORSION ANGLES OF SUGAR-PHOSPHATE
BACKBONE
– TORSION ANGLES AROUND N-GLYCOSIDIC BOND
– RIBOSE RING PUCKER

18. TORSION ANGLES
 SIX OF THEM
 GREATLY RESTRICTED RANGE OF ALLOWABLE
VALUES
– STERIC INTERFERENCE BETWEEN RESIDUES IN
POLYNUCLEOTIDES
– ELECTROSTATIC INTERACTIONS OF PHOS. GROUPS
 A SINGLE STRAND OF DNA ASSUMES A
RANDOM COIL CONFIGURATION

19. THE N-GLYCOSIDIC TORSION ANGLE
 TWO POSSIBILITIES, STERICALLY
– SYN
– ANTI
 PYRIMIDINES
– ONLY ANTI IS ALLOWED
 STERIC INTERFERENCE BETWEEN RIBOSE AND THE C2’
SUBSTITUENT OF PYRIMIDINE
 PURINES
– CAN BE SYN OR ANTI

20. IN MOST DOUBLE-HELICAL STRUCTURES,
ALL BASES IN ANTI FORM

21. GLYCOSIDIC TORSION ANGLES IN
Z-DNA
 ALTERNATING
– PYRIMIDINE: ANTI
– PURINE: SYN
 WHAT HAPPENS WHEN B-DNA SWITCHES TO Z-DNA?
– THE PURINE BASES ROTATE AROUND GLYCOSIDIC BOND
FROM ANTI TO SYN
– THE SUGARS ROTATE IN THE PYRIMIDINES
 THIS MAINTAINS THE ANTI CONFORMATIONS

22. RIBOSE RING PUCKER
 THE RING IS NOT FLAT
– SUBSTITUENTS ARE ECLIPSED IF FLAT
 CROWDING IS RELIEVED BY PUCKERING
 TWO POSSIBILITIES FOR EACH OF C2’ OR C3’:
– ENDO: OUT-OF-PLANE ATOM ON SAME SIDE OF RING AS C5’
– EXO; DISPLACED TO OPPOSITE SIDE
– C2’ ENDO IS MOST COMMON
– CAN ALSO SEE C3’-ENDO AND C3’-EXO
 LOOK AT RELATIONSHIPS BETWEEN THE PHOSPHATES:
– IN C3’ ENDO- THE PHOSPHATES ARE CLOSER THAN IN C2’
ENDO-

23. RIBOSE RING PUCKER
 B-DNA HAS THE C2’-ENDO-FORM
 A-DNA IS C3’-ENDO
 Z-DNA
– PURINES ARE ALL C3’-ENDO
– PYRIMIDINES ARE ALL C2’-ENDO
 CONCLUSION: THE RIBOSE PUCKER GOVERNS
RELATIVE ORIENTATIONS OF PHOSPHATE
GROUPS TO EACH SUGAR RESIDUE

24. IONIC INTERACTIONS
 THE DOUBLE HELIX IS ANIONIC
– MULTIPLE PHOSPHATE GROUPS
 DOUBLE-STRANDED DNA HAS HIGHER ANIONIC
CHARGE DENSITY THAT SS-DNA
 THERE IS AN EQUILIBRIUM BETWEEN SS-DNA
AND DS-DNA IN AQUEOUS SOLUTION:
– DS-DNA == SS-DNA
 QUESTION: WHAT HAPPENS TO THE Tm OF DS-
DNA AS [CATION] INCREASES? WHY?

25. IONIC INTERACTIONS
 DIVALENT CATIONS ARE GOOD SHIELDING AGENTS
 MONOVALENT CATIONS INTERACT NON-SPECIFICALLY
– FOR EXAMPLE, IN AFFECTING Tm
 DIVALENT INTERACT SPECIFICALLY
– BIND TO PHOSPHATE GROUPS
 MAGNESIUM (2+) ION
– STABILIZES DNA AND RNA STRUCTURES
– ENZYMES THAT ARE INVOLVED IN RXNS’ WITH NUCLEIC
ACID USUALLY REQUIRE Mg(2+) IONS FOR ACTIVITY

26. BASE STACKING
 PARTIAL OVERLAP OF PURINE AND PYRIMIDINE
BASES
 IN SOLID-STATE (CRYSTAL)
– VANDERWAALS FORCES
 IN AQUEOUS SOLUTION
– MOSTLY HYDROPHOBIC FORCES
– ENTHALPICALLY-DRIVEN
– ENTROPICALLY-OPPOSED
– OPPOSITE TO THAT OF PROTEINS

27. BASE-PAIRING
 WATSON-CRICK GEOMETRY
– THE A-T PAIRS USE ADENINE’S N1 AS THE H-BOND
ACCEPTOR
 HOOGSTEEN GEOMETRY
– N7 IS THE ACCEPTOR
 SEEN IN CRYSTALS OF MONOMERIC A-T BASE PAIRS
 IN DOUBLE HELICES, W-C IS MORE STABLE
– ALTHOUGH HOOGSTEIN IS MORE STABLE FOR A-T PAIRS,
W-C IS MORE STABLE IN DOUBLE HELICES
 CO-CRYSTALLIZED MONOMERIC G-C PAIRS
ALWAYS FOLLOW W-C GEOMETRY
– THREE H-BONDS

28. HYDROGEN BONDING
 REQUIRED FOR SPECIFICITY OF BASE PAIRING
 NOT VERY IMPORTANT IN DNA STABILIZATION
 HYDROPHOBIC FORCES ARE THE MOST IMPT.’

29. THE TOPOLOGY OF DNA
 “SUPERCOILING” : DNA’S “TERTIARY STRUCTURE
 L = “LINKING NUMBER”
– A TOPOLOGIC INVARIANT
– THE # OF TIMES ONE DNA STRAND WINDS AROUND THE
OTHER
 L = T + W
– T IS THE “TWIST
 THE # OF COMPLETE REVOLUTIONS THAT ONE DNA STRAND
MAKES AROUND THE DUPLEX AXIS
– W IS THE “WRITHE”
 THE # OF TIMES THE DUPLEX AXIS TURNS AROUND THE
SUPERHELICAL AXIS

30. DNA TOPOLOGY
 THE TOPOLOGICAL PROPERTIES OF DNA HELP
US TO EXPLAIN
– DNA COMPACTING IN THE NUCLEUS
– UNWINDING OF DNA AT THE REPLICATION FORK
– FORMATION AND MAINTENANCE OF THE
TRANSCRIPTION BUBBLE
 MANAGING THE SUPERCOILING IN THE ADVANCING
TRANSCRIPTION BUBBLE

31. DNA TOPOLOGY
 AFTER COMPLETING THE 13 IN-CLASS EXERCISES, TRY
TO ANSWER THE FOLLOWING QUESTIONS:
 (1) THE HELIX AXIS OF A CLOSED CIRCULAR DUPLEX DNA IS
CONSTRAINED TO LIE IN A PLANE. THERE ARE 2340 BASE PAIRS IN THIS
PIECE OF DNA AND, WHEN CONSTRAINED TO THE PLANE, THE TWIST IS
212.
– DETERMINE “L”, “W” AND “T” FOR THE CONSTRAINED AND UNCONSTRAINED
FORM OF THIS DNA.
 (2) A CLOSED CIRCULAR DUPLEX DNA HAS A 100 BP SEGMENT OF
ALTERNATING C AND G RESIDUES. ON TRANSFER TO A SOLUTION
WITH A HIGH SALT CONCENTRATION, THE SEGMENT MAKES A
TRANSITION FROM THE B-FORM TO THE Z-FORM. WHAT IS THE
ACCOMPANYING CHANGE IN “L”, “W”. AND “T”?