1. 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

2. 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

3. 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

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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?

10. 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

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

12. 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?

13. 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

14. 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

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

16. 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

17. 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