# US 7,612,184 B2 · Polynucleic acid nanomechanical device controlled by hybridization topology > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 7,612,184 B2 - Document ID: US7612184B2 - Status: Granted - Kind: B2 - Application number: 10/370,101 - Filed: 2003-02-21 - Published: 2003-11-27 - Granted: 2009-11-03 - Earliest claimed: 2002-02-22 - Assignees: New York University - Inventors: Nadrian Seeman; Hao Yan; Xiaoping Zhang; Zhiyong Shen - Web page: https://patentgrep.com/patent/US7612184B2 ## CPC - C12Q 1/68: involving nucleic acids - B82Y 5/00: Nanobiotechnology or nanomedicine, e.g. protein engineering or drug delivery - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES - B82Y: SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES; MEASUREMENT OR ANALYSIS OF NANOSTRUCTURES; MANUFACTURE OR TREATMENT OF NANOSTRUCTURES ## Abstract The present invention is directed to a sequence dependent polynucleotide nanomechanical device based on a nucleic acid paranemic crossover (PX) molecule which is a four-stranded structure related to parallel double crossover molecules, except that every possible crossover takes place. Eliminating two crossovers leads to a topoisomer, termed JX2, in which one pair of ends are switched (rotated 180°) while the other pair of ends remain the same. The device can be cycled between the two states, PX and JX2, by replacing single strands that set the state to be PX or JX2. ## Claims ### Claim 1 A polynucleic acid nanomechanical device capable of cycling between two topoisomeric states upon the sequential addition of fuel and set strands of nucleic acids, comprising a nucleic acid paranemic crossover molecule having a four-stranded coaxial structure of flanking parallel Watson-Crick double helices of nucleic acid strands with two backbones, two pairs of ends, a plurality of major and minor grooves, a central dyad axis, and reciprocal crossovers, where two strands of a strand pair from one helix pass over to the other helix and which reciprocal crossovers flank the central dyad axis at every major and minor groove separation where two strands of a strand pair from one helix approach the central dyad axis, each of said strands being involved in a crossover at the start and end of a Watson-Crick helical turn, wherein: the device is cycled between said nucleic acid paranemic crossover molecule and its JX2 topoisomer, said JX2 topoisomer differing from said nucleic acid paranemic crossover molecule by having one pair of ends rotated relative to the other pair of ends by 180° and by having two adjacent sites where said two backbones juxtapose without the strands being involved in a crossover; and a segment of a strand from each of said strand pairs of said nucleic acid paranemic crossover molecule, which segment is referred to as a PX set strand and which is broken from the rest of the strand, is stripped from said nucleic acid paranemic crossover molecule by the addition of fuel strands complementary to said PX set strands followed by the addition of JX2 set strands to convert said nucleic acid paranemic crossover molecule to its JX2 topoisomer, said JX2 topoisomer being converted/cycled back to said nucleic acid paranemic crossover molecule by the addition of fuel strands complementary to said JX2 set strands to strip said JX2 set strands from said JX2 topoisomer followed by the addition of PX set strands. ### Claim 2 (depends on 1) The polynucleic acid nanomechanical device of claim 1, wherein the ends of said nucleic acid paranemic crossover molecule are closed. ### Claim 3 (depends on 2) The polynucleic acid nanomechanical device of claim 2, wherein each helix has two ends and the strands of the strand pair are joined together at each of said helix ends to form the closed ends of said nucleic acid paranemic crossover molecule. ### Claim 4 (depends on 1) The polynucleic acid nanomechanical device of claim 1, wherein each helix has two ends and a restriction enzyme cleavage site one or both of said two ends. ### Claim 5 (depends on 4) The polynucleic acid nanomechanical device of claim 4, wherein said restriction enzyme cleavage site is different at each of said two ends. ### Claim 6 (depends on 1) The polynucleic acid nanomechanical device of claim 1, which is joined to an array. ### Claim 7 (depends on 6) The polynucleic acid nanomechanical device of claim 6, wherein said array is an array of polynucleic acid molecules. ### Claim 8 (depends on 7) The polynucleic acid nanomechanical device of claim 7, wherein said array of polynucleic acid molecules is an array having a plurality of polynucleic acid nanomechanical devices with different nucleotide sequences. ### Claim 9 (depends on 1) The polynucleic acid nanomechanical device of claim 1, wherein, in said nucleic acid paranemic crossover molecule, said major groove separation is 6, 7, or 8 nucleotide pairs and said minor groove separation is five nucleotide pairs. ### Claim 10 (depends on 1) The polynucleic acid nanomechanical device of claim 1, wherein every strand undergoes a crossover at every helical repeat of 11, 12, or 13 nucleotides with each strand having a period of two helical repeats that corresponds to 22, 24 or 26 nucleotides. ### Claim 11 (depends on 1) The polynucleic acid nanomechanical device of claim 1, wherein each of said PX set strands and each of said JX2 set strands have a single stranded unpaired extension at one end thereof. ### Claim 12 (depends on 11) The polynucleic acid nanomechanical device of claim 11, wherein the fuel strands complementary to said PX set strands are complementary along the entire length of the PX set strands and the fuel strands complementary to said JX2 set strands are complementary along the entire length of the JX2 set strands. ### Claim 13 (depends on 11) The polynucleic acid nanomechanical device of claim 11, wherein said fuel strands are labeled at one end thereof with a non-nucleic acid molecule that is a member of a binding pair. ### Claim 14 (depends on 1) An array comprising a plurality of different polynucleic acid nanomechanical devices of claim 1, wherein said different polynucleic acid nanomechanical devices differ in nucleotide sequence. ### Claim 15 (depends on 14) The array of claim 14, wherein said different polynucleic acid nanomechanical devices differ in the nucleotide sequences of said PX and JX2 set strands.