22 DNA structure Flashcards

1
Q

what do we need for DNA origami?

A

short staple strands (colored) and long DNA strand (black)
using the staple to fold the long strand

To create these shapes, need to twist the DNA
DNA is double strand tho to be stable
so use short staple DNA that are reverse complementary and can stabilize the single strand by forming a double strand - double helix at certain parts
* computer software to help design the staples (where to put it)
* then generate all the long and short DNA sequences and mix tgt, give time to assemble

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2
Q

What happens if we dont use staples to shape DNA

A

if no staple = flexible and moving, structure wont hold

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3
Q

which are the staples and which are the long strands?

A

staples in the middle
Long strand on the outside is the DNA

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4
Q

How can 3D DNA origami be designed?

A
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5
Q

How to make turns in DNA?

A

via holliday junctions
* shifting the positions of the crossovers at the helixes generate the turns

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6
Q

What are holliday junctions?

A

Holliday Junction:
* A Holliday junction is a structure formed during the process of genetic recombination, where two double-stranded DNA molecules become linked.
* It consists of four strands of DNA arranged in a cross-like structure.

Function in DNA Origami:
* In DNA origami, Holliday junctions serve as flexible joints that can change the direction of the DNA strands.
By strategically placing Holliday junctions, designers can create sharp turns or bends in the DNA structure.

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7
Q

what do holliday junctions allow for?

A

allows the generation of double crossovers to stabilize the pair of double helices and create junctions

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8
Q

How can DNA origami be a future cancer treatment?

A

DNA can be twisted into a box for drug delivery into cell
* attach protein enzyme to cleave the DNA and open it up

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9
Q

Is using DNA nanostructures unstable?

A

when deliver in to the actual cell - will either be degraded or digested - not desired
more research needed
gets denatured if too low Mg2+
or gets digested with nuclease

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10
Q

How can one pack DNA in cell?

A

DNA supercoiling

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11
Q

What level of structure is DNA supercoiling?

A

tertiary structure of DNA

double helix (coil) is not enough = supercoil

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12
Q

How is a eukaryotic chromosome formed?

A
  • DNA wraps around hisones to form nucleosomes
  • nucleosomes are packed into higher order structures (supercoiled)
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13
Q

What are the 3 biological roles of DNA supercoiling?

A
  • genome organization: DNA can be compacted into small volume
  • supercoiling favours strand seperation during replication and transcription (Lot of potential energy when twisted, if cell wants to rep or transcrip, and open up, it tends to favor that reaction in terms of energy)
  • control of gene expression: binding of RNA polymerase and regulatory proteins - cant access if supercoiled, protective mechanisms

GO, PE, GE

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