DNA STRUCTURE STRUCTURE, FORCES AND TOPOLOGY. DNA GEOMETRY A POLYMER OF DEOXYRIBONUCLEOTIDES...
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Transcript of DNA STRUCTURE STRUCTURE, FORCES AND TOPOLOGY. DNA GEOMETRY A POLYMER OF DEOXYRIBONUCLEOTIDES...
![Page 1: DNA STRUCTURE STRUCTURE, FORCES AND TOPOLOGY. DNA GEOMETRY A POLYMER OF DEOXYRIBONUCLEOTIDES DOUBLE-STRANDED INDIVIDUAL deoxyNUCLEOSIDE TRIPHOSPHATES.](https://reader036.fdocuments.us/reader036/viewer/2022062407/56649c7c5503460f9492febf/html5/thumbnails/1.jpg)
DNA STRUCTURE
STRUCTURE, FORCES AND TOPOLOGY
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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?
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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
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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
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FORCES THAT STABILIZE NUCLEIC ACID STRUCTURES
SUGAR-PHOSPHATE CHAIN CONFORMATIONS BASE PAIRING BASE-STACKING,HYDROPHOBIC IONIC INTERACTIONS
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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
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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
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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
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IN MOST DOUBLE-HELICAL STRUCTURES, ALL BASES IN ANTI FORM
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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
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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-
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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
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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?
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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
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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
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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
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HYDROGEN BONDING
REQUIRED FOR SPECIFICITY OF BASE PAIRING NOT VERY IMPORTANT IN DNA STABILIZATION HYDROPHOBIC FORCES ARE THE MOST IMPT.’
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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
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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
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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”?