1. Nucleic Acid-Small Molecule Interactions Blackburn & Gait Ch. 9 Know three main ways nucleic acids interact with small molecules Understand Manning/Rich hypothesis and counterion condensation theory Understand electrostatic interactions between proteins and NA Know hydrogen bond donor and acceptor groups needed for groove binding Understand how netropsin and distamycin bind DNA/RNA Review intercalation Understand how ethidium binds to DNA/RNA Know why streptomycin and kanamycin inhibit translation

2. Nucleic Acid-Small Molecule Interactions Nucleic acids interact reversibly with many chemicals H 2 O, metal ions, small organics, proteins Three main ways to interact with DNA/RNA: 1. Electrostatics 2. Groove-binding 3. Intercalation - needs conformational change ds/ss DNA and ds/ss RNA all can engage in reversible interactions

3. Nucleic Acid-Small Molecule Interactions Three main ways to interact with DNA/RNA: 1. Electrostatics 2. Groove-binding 3. Intercalation - needs conformational change

4. Nucleic Acid-Small Molecule Interactions Three main ways to interact with DNA/RNA: 1. Electrostatics Condensation-type reactions - DNA/RNA very negatively charged Manning/Rich hypothesis - shown that simple ions (alkali metals) associate with NA because of polymer charge density

5. Nucleic Acid-Small Molecule Interactions Three main ways to interact with DNA/RNA: 1. Electrostatics Condensation-type reactions - DNA/RNA very negatively charged Manning/Rich hypothesis - shown that simple ions (alkali metals) associate with NA because of polymer charge density

6. 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

7. Nucleic Acid-Small Molecule Interactions Nucleic acids interact reversibly with many chemicals H 2 O, metal ions, small organics, proteins Three main ways to interact with DNA/RNA: 1. Electrostatics Water binding - interactions with polar groups on bases, sugars, and phosphates are essential for stability of NA conformations H 2 O-ligand + DNA  DNA-ligand + H 2 O Entropy increases (favorable) as water released Enthapy increases (unfavorable) as water-ligand interactions are broken

8. Nucleic Acid-Small Molecule Interactions 2. Groove-binding Major and minor grooves of NA differ significantly in electrostatic potential, H-bonding characteristics, steric effects and hydration Many proteins bind DNA primarily in major groove while many groove binders bind to minor groove of DNA Negative electrostatic potential is great in AT minor groove Enhance GC binding specificity by designing molecules that can accept H-bonds

9. Major and minor grooves

10. Major and minor groove features

11. Nucleic Acid-Small Molecule Interactions 2. 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)

12. Nucleic Acid-Small Molecule Interactions Three main ways to interact with DNA/RNA: 2. Groove-binding Distamycin 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

13. Nucleic Acid-Small Molecule Interactions Three main ways to interact with DNA/RNA: 3. Intercalation - needs conformational change Ethidium bromide, daunomycin, adriamycin Bisintercalators 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