US 12,455,296 B2
System, method, computer-accessible medium and apparatus for DNA mapping
Jason Reed, Midlothian, VA (US); Andrey Mikheykin, Richmond, VA (US); Loren Picco, Bristol (GB); Oliver Payton, Bristol (GB); and Freddie Russell-Pavier, Bristol (GB)
Assigned to Virginia Commonwealth UniversityNCE:, Richmond, VA (US); and University of Bristol, Bristol (GB)
Filed by VIRGINIA COMMONWEALTH UNIVERSITY, Richmond, VA (US); NEW YORK UNIVERSITY, New York, NY (US); and UNIVERSITY OF BRISTOL, Bristol (GB)
Filed on Aug. 8, 2023, as Appl. No. 18/446,093.
Application 18/446,093 is a continuation of application No. 16/475,704, abandoned, previously published as PCT/US2018/012449, filed on Jan. 5, 2018.
Claims priority of provisional application 62/442,672, filed on Jan. 5, 2017.
Claims priority of provisional application 62/443,325, filed on Jan. 6, 2017.
Prior Publication US 2024/0077516 A1, Mar. 7, 2024
Int. Cl. G01Q 20/02 (2010.01); C12N 9/22 (2006.01); C12N 15/11 (2006.01); C12Q 1/683 (2018.01); G01Q 60/42 (2010.01)
CPC G01Q 20/02 (2013.01) [C12N 9/22 (2013.01); C12N 15/11 (2013.01); C12Q 1/683 (2013.01); G01Q 60/42 (2013.01); C12N 2310/20 (2017.05); C12N 2800/80 (2013.01); C12Q 2565/601 (2013.01)] 26 Claims
 
1. A method of mapping nucleotide molecules, comprising:
incubating a target nucleotide in a magnesium-free mixture, wherein the magnesium-free mixture comprises a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-cellular apoptosis susceptibility (Cas) protein and a guide ribonucleic acid (RNA), and wherein incubating the target nucleotide with the CRISPR-Cas protein binds the CRISPR-Cas protein to the target nucleotide to form a CRISPR-Cas/target nucleotide complex without the CRISPR-Cas protein cleaving the target nucleotide;
depositing the CRISPR-Cas/target nucleotide complex on a flat surface, wherein after deposition the CRISPR-Cas/target nucleotide complex is bound to the flat surface; and
imaging the CRISPR-Cas/target nucleotide complex on the flat surface by using high-speed atomic force microscopy (AFM) operating in contact mode, wherein the high speed AFM has a probe linear speed of 4 to 10 millimeters per second, wherein the high-speed atomic force microscopy comprises an AFM system which comprises: at least one cantilever; at least one scanning probe arrangement including a laser positioned over a portion of the at least one cantilever which contacts a surface of at least one sample, wherein a tilt angle of the at least one cantilever with respect to the at least one scanning probe arrangement is less than 10 degrees; and a power source configured to generate a displacement noise that is less than 300 Picometers.