A primer to scaffolded DNA origami

Question 1

What are the forms of DNA and which is the most common one used in DNA origami?

Answer 1

A, B, Z

B form is most common and commonly used

Question 2

What is the typical size of a double-stranded DNA(diameter), single-stranded DNA, base pairs?

Answer 2

Double-stranded DNA (dsDNA) diameter: The diameter of a double helix of DNA is approximately 2 nanometers (nm), or about 20 angstroms (Å). This is a consistent measurement regardless of the length of the DNA molecule.

Single-stranded DNA (ssDNA): Single-stranded DNA does not have a defined diameter like double-stranded DNA since it does not form a double helix structure. However, the diameter of a single DNA strand is often considered to be similar to the diameter of the double-stranded form, around 2 nanometers.

Base pairs (bp): Each base pair contributes approximately 0.34 nanometers (nm) to the length of the DNA molecule when it is in the double-stranded form. Therefore, for every base pair added, the length increases by about 0.34 nm.

Question 3

Software for DNA origami design?

Answer 3

caDNAno (http://cadnano.org/)

Question 4

What is the nature of interhelix connections in DNA origami?

Answer 4

Hollyday junctions

Question 5

What is the influence of crossovers on doublehelical domains and why?

Answer 5

Double-helical domains tend to bow out between cross-overs owing to effects such as electrostatic repulsion and/or detailed geometry of cross-overs. The extent of the bowing out depends on the distance between consecutive cross-overs.

Question 6

bowing gap for ssDNA crossover density of 26bp^-1

Answer 6

1.5nm

Question 7

bowing gap for ssDNA crossover density of 16bp^-1

Answer 7

1nm

Question 8

In multilayer DNA origami structures with high cross-over densities of one every 7 bp or 8 bp, the interhelical gap appears smaller than …

Answer 8

0.5nm

Question 9

What is scaffold route?

Answer 9

The desired path the scaffold will take when folded by the staples

Question 10

Types of scaffolds

Answer 10

circular and linear

Question 11

Types of staples oligos?

Answer 11

only linear

Question 12

Unpaired scaffolds usefulness?

Answer 12

can be used as entropic springs to support tensegrityentropic springs for tensegrity structuresand they are useful in preventing unwanted basestacking interactions at object interfaces

Question 13

Describe the the steps in molecular self-assembly with scaffolded DNA origami

Answer 13

Question 14

Methods for synthesising scaffold and staples

Answer 14

Generally from phage genome or plasmids but can also be done through PCR amplicons to get smaller ones

*from meeting 1: PCR plus strand displacement to get smaller scaffolds

Question 15

pool subsets of concentration-normalized oligonucleotides

Answer 15

Equal amounts of concentration-normalized staple oligonucleotides belonging to a structural module are mixed to form a common pool

Question 16

How do people usually characterize DNA origami structures?

Answer 16

Analysis of the quality of folding of DNA origami objects and purification of a desired species can be accomplished with agarose gel electrophoresis. For multilayer objects it has been found that for a given object, the objects with lowest defect rate as judged by direct imaging by TEM were those that migrate with the highest speed through a 2% agarose gel

TEM and AFM can be used to find structural flaws or make single particle models (TEM)