Scribd
Upload
23 views15 pages

Class 9 - 1 (1) - Reduced

Uploaded by

pradhansnehasis382
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
23 views15 pages

Class 9 - 1 (1) - Reduced

Uploaded by

pradhansnehasis382
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
You are on page 1/ 15

Junction with DNA hairpin

➢ DAE junctions can be constructed using five strands,


where three of the strands are involved in the
crossovers and two are fixed to a given helical domain.
➢ This central strand can also have its 5’ and 3’ ends
complementary, projecting out of the DX framework.
This is known as DX-J (DAE-J)
DNA Crossover motifs

➢ TX tiles or motifs are derived from


DX tiles, where there are three
distinct helices instead of two, and
thus have double the number of
crossovers
➢ Such a structure imparts greater
rigidity in comparison to simple
duplexes as well as DX tiles.
➢ PX motifs result from reciprocal exchange occurring
between both strands of both the helices at the same
crossover points.
➢ The PX motif thus bears a superficial resemblance to
intertwined duplexes
➢ JX2 motifs are similar to the PX motif, except that
reciprocal exchange is omitted at two adjacent points
One-dimensional superstructures

➢ A simple DX or TX tile with self-complementary sticky ends, at appropriate


concentrations, is enough to grow structures that extend along a line.

➢ Each DX tile consists of two parallel double helices and four strands, where two of
the four strands first participate in one helix and then exchange to the other helix,
thus holding the two helices together

➢ Thus, a given DX tile has four single stranded sticky ends that may be programmed
to bind to complementary ends of other DX tiles, allowing fine control of extension
mediated by binding specificity

➢ Superstructures resulting from such association begin to curve upon themselves


when they acquire dimensions beyond the persistence length of the associated
building block
2D superstructures

Nadrian Seeman
New York University

Design principles

➢ A 2D array can be made from a structural motif that can associate in the x and y coordinates, to give a
planar, periodic, 2D crystalline array

➢ 2D arrays made from DNA have been constructed from repeating units that use structural motifs such as
DX, TX, PX motifs

➢ The incorporation of sticky ends at appropriate positions on the motif facilitates its self-association in two
dimensions, where the motif is the repeating unit in a 2D crystal-like array
Two-dimensional arrays of DX and DX+J molecules

Two-dimensional crystal design is derived from the mathematical theory of tiling. The desired lattice is specified by a
set of Wang tiles with coloured edges; the Wang tiles may be placed next to each other only if their edges are
identically colored where they touch
Model structures for DAO and DAE type A units
DAO-E DAE-O
Design of scaffolded DNA origami

➢ Synthesis of DNA nanostructure depends on the self-assembly of many short oligonucleotide

➢ The yield of complete structures is highly sensitive to stoichiometry (the relative ratios of strands)

➢ To prepare a complex structure individual tiles (DX, TX etc) have to prepare separately and purified
before their final assembly.

➢ The ultimate complexity of DNA nanostructures limited by necessarily low yields


DNA Origami

Paul W. K. Rothemund
California Institute of Technology
➢ Short single strands of DNA is used to direct the folding of a long, single strand of DNA into desired
shapes that are roughly 100nm in diameter and have a spatial resolution of about 6 nm.

➢ The long DNA strand is known as scaffold strand. Circular genomic DNA from the virus M13mp18
was chosen as the scaffold strand (7,249-nt sequence)

➢ Short single stranded DNA is known as staple strand. Majority of staple strand has 20-32 nt
https://cadnano.org/
3D superstructure

You might also like