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
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
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
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
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
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
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
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
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
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
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?
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
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
FORCES THAT STABILIZE NUCLEIC
ACID STRUCTURES

 SUGAR-PHOSPHATE CHAIN CONFORMATIONS

 BASE PAIRING
 BASE-STACKING,HYDROPHOBIC
 IONIC INTERACTIONS
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

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
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
IN MOST DOUBLE-HELICAL STRUCTURES,
ALL BASES IN ANTI FORM
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
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-
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
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?
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
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
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
HYDROGEN BONDING

 REQUIRED FOR SPECIFICITY OF BASE PAIRING

 NOT VERY IMPORTANT IN DNA STABILIZATION
 HYDROPHOBIC FORCES ARE THE MOST IMPT.’
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
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
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”?