People
Processes
Parts or Components
Benefits/Drawbacks
Miscellaneous
100
Who pioneered the use of branched DNA to make multidimensional objects?
Nadrian Seeman Page 248
100
For the Turing machine presented by Ehud Shapiro, how is the computation performed?
By snipping off data one digit at a time, using the location of the cut to encode the state of the machine. Page 266
100
What are the two states of the Turing Machine?
S0 and S1 Page 265
100
What are 2 advantages of DNA in nanotechnology?
1- Programmable and Predictable 2- DNA oligonucleotides of any sequence are readily synthesized by automated solid support techniques 3- DNA double helices are stiff polymers Page 248
100
What is a Turing machine?
A machine that reads a list of data and performs operations based on the values at each point along the list. Page 265
200
Who designed a modular concept for the self-assembly of nanotubes?
Reza Ghadiri Page 250
200
How did researchers create a pair of tweezers composed of DNA?
A hinged molecule is created, double stranded in the center with a gap to make it bendable, and with single-stranded extensions at each end. Then another DNA strand (set strand), is made to match the two extensions. When added to solution, the set strand pairs with the two ends, bringing them closer together. A competing fuel strand is then added, which is designed to pair with the entire length of the set strand. Page 259
200
What are the two types of unique DNA sequences chosen for the three segments mentioned in the satisfiability problems section?
1- True 2- False Page 265
200
Because each component is molecule-sized in DNA computing, what the two benefits for it in the computations?
1- Energy efficient 2- Cheap Page 262
200
What are crossover structures and how are they designed?
Designed by arranging two or more helices side by side and then exchanging strands at the points where they touch. By appropriate choice of sequence, the strands will assemble in these side-by-side structures with all bases paired with their appropriate neighbors, forming a structure that mimics two helices rigidly locked together. Page 250
300
Who pioneered the design of micrometer to centimeter scale objects that self-assemble into larger structures?
George Whitesides Page 254
300
What is the method Todd Yeates developed to make nanoassemblies composed of protein subunits?
They start with proteins that naturally form low-order assemblies, such as dimers or timers. Then they fuse two of these proteins together back-to-back, leaving the natural combining sites exposed. When mixed together, these fusion proteins link up one to the next using natural combining sites. By appropriate choice of the linker connecting the two proteins, many different types may be created. Page 252
300
In molecular machines, besides allowing defined construction, the ____ and ___ or strands may also be used to do work.
Binding and unbinding Page 259
300
What are advantages of self-assembly at micrometer to centimeter scale objects?
1- Intrinsically parallel 2- Allows submicrometer accuracy in positioning 3- Relatively insensitive to errors in registration of components Page 255
300
What was the "clever aspect" of the nanotube side chains that Ghadiri designed? What makes them clever?
The clever aspect is in the side chains. Ghadiri builds these circles from amino acids with alternating handedness so that the side chains all face radially out from the center of the circle, leaving a smooth channel through the center. Page 250
400
Who made a machine that could read a list of data and perform operations based on values in the list?
Ehud Shapiro Page 266
400
In the satisfiability problems section, describe the renewable method did Adleman used to remove all the wrong answers.
A gel electrophoresis column is created that contains complementary DNA strands attached to the gel. For the first clause, it has strands complementary for "a is true" and "b is true" and the column retains any DNA strands with these values, letting "a is false" and "b is false" pass through. Then strands are released and subjected to a second column that tests for the second clause. The strands that remain bound are the answer for the problem. Page 265
400
What are the two types of single-stranded DNA Adleman created?
First type corresponds to each allowed path through a node, with 10 base pairs representing the incoming path and 10 base pairs representing the outgoing path. A different nucleotide sequence was chosen for each, to ensure that each path was represented uniquely Second type was created to correspond to each of the paths between nodes. Designed to match with the ends of the node DNA segments. page 263
400
What are 2 disadvantages to DNA computing?
1- Error rate in copying reactions 2- Not reusable Page 262
400
Who first proposed the controversial rotation of ATP synthase?
Paul Boyer Page 257
500
Who first showed that DNA can be used as a molecular computer?
Leonard M. Adleman Page 262
500
In the section relating to DNA computing, after Adleman combined all the DNA strands, what method did he use to isolate the 1 DNA helix?
Adleman subjected the mixture of ligated double helices to three screens. The first was a PCR amplification using primers that correspond to sequences at the desired beginning and end of the path. This amplifies only those DNA helices that being and end at the proper node. Then he used gel electrophoresis to screen for size. Finally he did any affinity screen to check for presence of corresponding sequences. Page 264
500
What two methods did Whitesides use for assembly? Describe them.
1- Preorganization by tethering 2+ rings in desired orientation 2- Added large substituents in strategic positions on the rings, why crowd out potential neighbors Page 253-4
500
Name 2 attractive properties/advantages of DNA in computing.
1- DNA strands can be selected and copied with PCR to give quantities of material for testing 2- Under right conditions, single strands of DNA pairs specifically to exact complement 3- Large number of computations can be done with DNA computers 4- Massively parallel Page 261-2
500
Describe the modular approach taken by Seeman in branched DNA structures?
The building blocks are designed from several strands that assemble to form a cross-shaped complex. The sequences of each leg of the cross must be unique to ensure that only 1 final structure is formed. Sticky ends are left of each branch and are used to link blocks together into larger structures. By matching the sequences of these sticky ends, assemblies of any shape may be designed. Page 248
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