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DNA STRUCTURE

STRUCTURE, FORCES AND TOPOLOGY


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


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


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


MAJOR AND MINOR GROOVES 

MINOR –

MAJOR –

EXPOSES EDGE FROM WHICH C1’ ATOMS EXTEND 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


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


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 

BASE PLANES ARE TILTED 20 DEGREES WITH RESPECT TO HELICAL AXIS – 

 AN AXIAL HOLE

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 OLIGONUCLEOTIDES 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 –

IN COMPLEMENTARY POLYNUCLEOTIDES WITH ALTERNATING PURINES AND PYRIMIDINES – –

REDUCES REPULSIONS BETWEEN CLOSEST PHOSPHATE GROUPS ON OPPOSITE STRANDS (8 A VS 12 A IN B-DNA)

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 TRANSCRIBING 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?


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 (SINGLESTRAND STRUCTURES)

DS RNA HAS AN A-LIKE CONFORMATION –

STERIC CLASHES BETWEEN 2’-OH GROUPS PREVENT THE B-LIKE CONFORMATION


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


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


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


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


IN MOST DOUBLE-HELICAL STRUCTURES, ALL BASES IN ANTI FORM


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


RIBOSE RING PUCKER 

THE RING IS NOT FLAT –

 

CROWDING IS RELIEVED BY PUCKERING TWO POSSIBILITIES FOR EACH OF C2’ OR C3’: – – – –

SUBSTITUENTS ARE ECLIPSED IF FLAT

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-


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


IONIC INTERACTIONS 

THE DOUBLE HELIX IS ANIONIC –

 

DOUBLE-STRANDED DNA HAS HIGHER ANIONIC CHARGE DENSITY THAT SS-DNA THERE IS AN EQUILIBRIUM BETWEEN SS-DNA AND DS-DNA IN AQUEOUS SOLUTION: –

MULTIPLE PHOSPHATE GROUPS

DS-DNA == SS-DNA

QUESTION: WHAT HAPPENS TO THE Tm OF DSDNA AS [CATION] INCREASES? WHY?


IONIC INTERACTIONS  

DIVALENT CATIONS ARE GOOD SHIELDING AGENTS MONOVALENT CATIONS INTERACT NON-SPECIFICALLY –

DIVALENT INTERACT SPECIFICALLY –

FOR EXAMPLE, IN AFFECTING T m 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


BASE-PAIRING 

WATSON-CRICK GEOMETRY –

THE A-T PAIRS USE ADENINE’S N1 AS THE H-BOND ACCEPTOR

HOOGSTEEN GEOMETRY –

N7 IS THE ACCEPTOR 

IN DOUBLE HELICES, W-C IS MORE STABLE –

SEEN IN CRYSTALS OF MONOMERIC A-T BASE PAIRS

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


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


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”?

DNA STRUCTURE  
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