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Dna Structure PowerPoint Presentation

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Dna Structure Presentation Transcript

Slide 1 - DNA STRUCTURE STRUCTURE, FORCES AND TOPOLOGY
Slide 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
Slide 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
Slide 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
Slide 5 - ppt slide no 5 content not found
Slide 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
Slide 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
Slide 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
Slide 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
Slide 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
Slide 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
Slide 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
Slide 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?
Slide 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
Slide 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
Slide 16 - FORCES THAT STABILIZE NUCLEIC ACID STRUCTURES SUGAR-PHOSPHATE CHAIN CONFORMATIONS BASE PAIRING BASE-STACKING,HYDROPHOBIC IONIC INTERACTIONS
Slide 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
Slide 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
Slide 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
Slide 20 - IN MOST DOUBLE-HELICAL STRUCTURES, ALL BASES IN ANTI FORM
Slide 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
Slide 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-
Slide 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
Slide 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?
Slide 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
Slide 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
Slide 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
Slide 28 - HYDROGEN BONDING REQUIRED FOR SPECIFICITY OF BASE PAIRING NOT VERY IMPORTANT IN DNA STABILIZATION HYDROPHOBIC FORCES ARE THE MOST IMPT.’
Slide 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
Slide 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
Slide 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”?
 

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