# User:Allison K. Alix/Notebook/Thesis Research/2013/04/02

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## Objectives

• Bind DNA to MB and AuNP
• React AuNP with ethanethiol

## Procedures

Part 1: Reacting DNA with MB first, followed by a reaction of the DNA-MB hybrid with AuNP

1) Prepare 727.5nm 8-repeat DNA-thiol and 800nm MB

a) 727.5nm 8-repeat DNA-thiol

(Original concentration of DNA is 53.1μM)

53.1μM(x)=(500μL)(1455nm)

x= 13.7μL in 486.3μL H2O

1455nM(x) = 727.5nm(200μL)

x= 100μL 1455nM in 100μL H2O

b) Prepare 800nm MB

(Original concentration of MB is 7.31μM)

7130nm(x) = (800nM)(50μL)

x = 5.47μL 7.31μM in 44.53 μL H2O

3) Mix 50μL 727.5nM DNA with 50μL 800nM MB

4) Hybridize by placing mixture on heat block @ 76°C for ~25minutes

5) Turn off heat block and allow cooling to room temperature

Part 2: Reacting DNA with ThT first, followed by a reaction of the DNA-ThT hybrid with AuNP

1) Prepare 727.5nM DNA (see Part 1, step 1a)

2) Prepare 800nM ThT

• Note that the ThT prepared on 01/29/2013 assumed a 100% mass, when it was actually 75%. Use a 5mM ThT solution prepared by Dr. Miller.

5mM(x) = (5μM)(10mL)

10μL of 5mM ThT in 9990μL buffer

5μM (x) = (800nm)(1mL)

x= 160μL 5μM ThT in 840μL buffer

3) Mix 50μL 727.5nM DNA with 50μL 800nM ThT

Part 3: React AuNP's with ethanethiol

1) Calculate how many sulfur atoms to cover 1 nanoparticle

• Diameter of AuNP (synthesized 3/1/13 by Dr. Miller) is 14nm, so radius, r=7nm
• A = 4π(r2)= 4π(7x10-9)2= 6.1575x10-16m2
• atomic radius of 1 sulfur atom = 100pm so, diameter of 1 S = 200pm

(200x10-12m)2 = 4x10-20m2

6.1575x10-16m2/4x10-20m2 = 15393 Sulfur atoms for every 1 AuNP

2) Prepare 1mL ethanethiol solution

• original concentrationof AuNP = 19.4nM

desired concentration of ethanethiol = 19.4nM x(15393) = 298624.2nM = 298μM

density of ethanethiol = 0.839g/mL

298x10-6mol/L