Hydrogen bonding between purines and pyrimidines established the appropriate pairs and reinforced Chargaff’s Rules – 2 hydrogen bonds between A and T – 3 hydrogen bonds between G and C

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

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 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?

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

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 T m OF DS-DNA AS [CATION] INCREASES? WHY?

IONIC INTERACTIONS DIVALENT CATIONS ARE GOOD SHIELDING AGENTS MONOVALENT CATIONS INTERACT NON-SPECIFICALLY – FOR EXAMPLE, IN AFFECTING T m 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

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