NYU ECG STUDY GUIDE COMPLETE 2026
QUESTIONS WITH SOLUTIONS GRADED
A+
>> Robust vs conventional nanostructures
Answer: robust: maintains structure and function in biological settings
>> Assembly of robust nanostructures vs conventional nanostructures
Answer: robust: monovalent solns, which mimic physiological conditions, can be used in vivo
>> Describe the goal of 3D self-assembly of robust DNA motifs and some characteristics
Answer: -organize other species, ranging from nanoelectronics to potential drug targets.
>> Two different principles of multi-state nanomechanical devices
Answer: [1] DNA structural transitions (can be based on contents of solution or by forming knots)
>> Characteristics of robust devices
Answer: behaves like a macroscopic device made of simple machines:
>> Definition of a robust device
Answer: all of the molecules undergo the same transition, looking the same after the transition as they
did before
>> Definition of a non-robust device
Answer: if strands of its framework can recombine and perhaps form another species OR if exchange
of strands occurs while in an intermediate state
>> Shape-shifter devices
Answer: molecules that have different structures under different conditions, something must upset
equilibrium of the molecule for it to change shape
>> Closed sequence-dependent tweezer
Answer: when F binds to the rest of the device, it brings the two double helical domains together; red
section of F aka toehold bind to complementary toehold of F’ which forms a F-F’ duplex (waste) and
restores the open state
>> Open sequence-dependent tweezer
Answer: dyes are too far apart to interact; they are brought together by a strand F, where part of F is
complementary to the blue unpaired section and part of F is complementary to the green unpaired
section
, >> PX-JX2 device
Answer: based on the PX state of DNA and one of its topoisomers, the JX2 state; makes tweezer
system robust by preventing dimerization during transitions
>> 1a. What are the 2 components of 2D and 3D DNA origami constructs?
Answer: The two key components of 2D and 3D DNA origami constructs are:
>> 1a. What type of crossover is used to fold a DNA origami structure?
Answer: DAO
>> 1a.Describe the difference between the components of an RNA origami construct and a DNA
origami construct
Answer: DNA origami uses many short staple strands to fold a long DNA scaffold into shape.
>> 1a. How was RNA origami generated in vivo?
Answer: The entire RNA origami design is encoded as a DNA gene construct and inserted into a
plasmid vector.This plasmid is then transformed into E. coli. Inside the cell, the cell’s own RNA
polymerase transcribes the designed RNA sequence.
>> 1b. What is the difference between a DNA origami tile and a DNA brick?
Answer: DNA origami tiles are scaffold-based structures folded by short staple strands, whereas DNA
bricks are scaffold-free, modular units that self-assemble through complementary domain pairing into
arbitrary 2D or 3D shape
>> 1b. What is the difference in the constitutional strands between a 2D DNA brick and a 3D DNA
brick?
Answer: 2D DNA brick = strand is 42-mer long strand segmented in 4 regions of either 10 or 11 bases
>> 2a. What type of DNA tiles were used for the XOR computation experiment in 1D? in 2D?
Answer: The 1D cumulative XOR used TX tiles.
>> 2a. Where was the input and output signals encoded in the tiles?
Answer: The bottom domains of the calculational tiles carried the input signals, represented by
sticky-end sequences corresponding to logical 0 and 1.
>> 2b. What is the difference in topology between the reporter strand generated for the XOR
computation experiment in 1D and the one generated for the 3-colorability graph?
Answer: XOR reporter = linear (open chain); 3-colorability reporter = cyclic (closed loop
>> 2b. How do Wang tiles assemble?
Answer: Wang tiles assemble by following a local matching rule: each tile can attach to another only
when the “colors” (or sequences) of their adjacent edges match.
QUESTIONS WITH SOLUTIONS GRADED
A+
>> Robust vs conventional nanostructures
Answer: robust: maintains structure and function in biological settings
>> Assembly of robust nanostructures vs conventional nanostructures
Answer: robust: monovalent solns, which mimic physiological conditions, can be used in vivo
>> Describe the goal of 3D self-assembly of robust DNA motifs and some characteristics
Answer: -organize other species, ranging from nanoelectronics to potential drug targets.
>> Two different principles of multi-state nanomechanical devices
Answer: [1] DNA structural transitions (can be based on contents of solution or by forming knots)
>> Characteristics of robust devices
Answer: behaves like a macroscopic device made of simple machines:
>> Definition of a robust device
Answer: all of the molecules undergo the same transition, looking the same after the transition as they
did before
>> Definition of a non-robust device
Answer: if strands of its framework can recombine and perhaps form another species OR if exchange
of strands occurs while in an intermediate state
>> Shape-shifter devices
Answer: molecules that have different structures under different conditions, something must upset
equilibrium of the molecule for it to change shape
>> Closed sequence-dependent tweezer
Answer: when F binds to the rest of the device, it brings the two double helical domains together; red
section of F aka toehold bind to complementary toehold of F’ which forms a F-F’ duplex (waste) and
restores the open state
>> Open sequence-dependent tweezer
Answer: dyes are too far apart to interact; they are brought together by a strand F, where part of F is
complementary to the blue unpaired section and part of F is complementary to the green unpaired
section
, >> PX-JX2 device
Answer: based on the PX state of DNA and one of its topoisomers, the JX2 state; makes tweezer
system robust by preventing dimerization during transitions
>> 1a. What are the 2 components of 2D and 3D DNA origami constructs?
Answer: The two key components of 2D and 3D DNA origami constructs are:
>> 1a. What type of crossover is used to fold a DNA origami structure?
Answer: DAO
>> 1a.Describe the difference between the components of an RNA origami construct and a DNA
origami construct
Answer: DNA origami uses many short staple strands to fold a long DNA scaffold into shape.
>> 1a. How was RNA origami generated in vivo?
Answer: The entire RNA origami design is encoded as a DNA gene construct and inserted into a
plasmid vector.This plasmid is then transformed into E. coli. Inside the cell, the cell’s own RNA
polymerase transcribes the designed RNA sequence.
>> 1b. What is the difference between a DNA origami tile and a DNA brick?
Answer: DNA origami tiles are scaffold-based structures folded by short staple strands, whereas DNA
bricks are scaffold-free, modular units that self-assemble through complementary domain pairing into
arbitrary 2D or 3D shape
>> 1b. What is the difference in the constitutional strands between a 2D DNA brick and a 3D DNA
brick?
Answer: 2D DNA brick = strand is 42-mer long strand segmented in 4 regions of either 10 or 11 bases
>> 2a. What type of DNA tiles were used for the XOR computation experiment in 1D? in 2D?
Answer: The 1D cumulative XOR used TX tiles.
>> 2a. Where was the input and output signals encoded in the tiles?
Answer: The bottom domains of the calculational tiles carried the input signals, represented by
sticky-end sequences corresponding to logical 0 and 1.
>> 2b. What is the difference in topology between the reporter strand generated for the XOR
computation experiment in 1D and the one generated for the 3-colorability graph?
Answer: XOR reporter = linear (open chain); 3-colorability reporter = cyclic (closed loop
>> 2b. How do Wang tiles assemble?
Answer: Wang tiles assemble by following a local matching rule: each tile can attach to another only
when the “colors” (or sequences) of their adjacent edges match.
