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Dna structure

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Dna structure & concept explained easily

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Dna structure

  1. 1. DNA STRUCTURE STRUCTURE, FORCES AND TOPOLOGY
  2. 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. 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. 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
  5. 5. 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
  6. 6. 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
  7. 7. 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
  8. 8. 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
  9. 9. 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
  10. 10. 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
  11. 11. 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
  12. 12. 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?
  13. 13. 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
  14. 14. 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
  15. 15. FORCES THAT STABILIZE NUCLEIC ACID STRUCTURES  SUGAR-PHOSPHATE CHAIN CONFORMATIONS  BASE PAIRING  BASE-STACKING,HYDROPHOBIC  IONIC INTERACTIONS
  16. 16. 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
  17. 17. 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
  18. 18. 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
  19. 19. IN MOST DOUBLE-HELICAL STRUCTURES, ALL BASES IN ANTI FORM
  20. 20. 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
  21. 21. 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-
  22. 22. 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
  23. 23. 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?
  24. 24. 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
  25. 25. 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
  26. 26. 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
  27. 27. HYDROGEN BONDING  REQUIRED FOR SPECIFICITY OF BASE PAIRING  NOT VERY IMPORTANT IN DNA STABILIZATION  HYDROPHOBIC FORCES ARE THE MOST IMPT.’
  28. 28. 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
  29. 29. 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
  30. 30. 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”?

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