Nucleic Acid-Small Molecule Interactions

Blackburn & Gait Ch. 8, p. 331-341, 362-3

Know three main ways nucleic acids interact with small molecules Understand Manning/Rich hypothesis and counterion condensation theoryUnderstand electrostatic interactions between proteins and NAKnow hydrogen bond donor and acceptor groups needed for groove binding Understand how netropsin and distamycin bind DNA/RNAReview intercalationUnderstand how ethidium binds to DNA/RNAKnow why streptomycin and kanamycin inhibit translation

Nucleic Acid-Small Molecule Interactions

Nucleic acids interact reversibly with many chemicalsH2O, metal ions, small organics, proteins

Three main ways to interact with DNA/RNA:1. Electrostatics2. Groove-binding3. Intercalation - needs conformational change

ds/ss DNA and ds/ss RNA all can engage in reversible interactions

Nucleic Acid-Small Molecule InteractionsThree main ways to interact with DNA/RNA:1. Electrostatics2. Groove-binding3. Intercalation - needs conformational change

Nucleic Acid-Small Molecule Interactions

Three main ways to interact with DNA/RNA:1. Electrostatics

Condensation-type reactions - DNA/RNA very negatively chargedManning/Rich hypothesis - shown that simple ions (alkali metals) associate with NA because of polymer charge density

Nucleic Acid-Small Molecule Interactions

Three main ways to interact with DNA/RNA:1. Electrostatics

Condensation-type reactions - DNA/RNA very negatively chargedManning/Rich hypothesis - shown that simple ions (alkali metals) associate with NA because of polymer charge density

Nucleic Acid-Small Molecule Interactions

Three main ways to interact with DNA/RNA:1. Electrostatics

Counterion-condensation association of ions with polyelectrolyte (NA) counterions condensed per phosphate charge remains constant for a particular conformation as [salt] varies 0.76 monovalent counterions (Na+) condensed/phos Reduces effective charge on NA Divalents will displace monovalents

Nucleic Acid-Small Molecule Interactions

Nucleic acids interact reversibly with many chemicalsH2O, metal ions, small organics, proteins

Three main ways to interact with DNA/RNA:1. ElectrostaticsWater binding - interactions with polar groups on bases, sugars, and phosphates are essential for stability of NA conformations

H2O-ligand + DNA DNA-ligand + H2O

Entropy increases (favorable) as water releasedEnthapy increases (unfavorable) as water-ligand interactions are broken

Nucleic Acid-Small Molecule Interactions2. Groove-bindingMajor and minor grooves of NA differ significantly in electrostatic potential, H-bonding characteristics, steric effects and hydrationMany proteins bind DNA primarily in major groove while many groove binders bind to minor groove of DNANegative electrostatic potential is great in AT minor grooveEnhance GC binding specificity by designing molecules that can accept H-bonds

Major and minor grooves

Major and minor groove features

Nucleic Acid-Small Molecule Interactions2. Groove-binding Some aminoglycoside antibiotics bind to major groove of rRNA Usually minor groove binders have simple aromatic rings (pyrrole, furan, benzene) Groove binders can extend to fit over many bp and have high sequence-specificity for NA Netropsin bound to NA at AATT center and displaces spine of hydration (cationic ends in groove)

Nucleic Acid-Small Molecule Interactions

Three main ways to interact with DNA/RNA:2. Groove-bindingDistamycin has crescent shape which matches curvature of minor groove ; 5 NH groups H-bond to N3 of A and O2 of T

Design of other molecules to bind GC and AT sequences - lexitropsins

Nucleic Acid-Small Molecule Interactions

Three main ways to interact with DNA/RNA:3. Intercalation - needs conformational change

Ethidium bromide, daunomycin, adriamycinBisintercalators

RNA Intercalation - different intercalators have different affinities for DNA vs. RNA

small organic cations interact with RNA antibiotics that bind to ribosomes and inhibit translation streptomycin/kanamycin bind to 16S rRNA