System, method, computer-accessible medium and apparatus for dna mapping

Abstract

Exemplary embodiments of the present disclosure can include, for example, an atomic force microscopy (AFM) system, including a cantilever(s), an optical pickup unit(s) (OPU(s)) including a laser positioned over the cantilever(s), and a power source providing noise with a noise level that is below 300 Picometers. The noise level of the power source can be below 200 Picometers. A digitizing arrangement can be included which can be associated with the OPU. The digitizing arrangement(s) can have a bandwidth of about 2 MHZ. The OPU(s) can have a detection bandwidth of at least 80 MHZ. The exemplary apparatus can be combined with a chemical protocol and statistical signal processing and image analysis procedures to map DNA at high speed and accuracy.

1 . An atomic force microscopy (AFM) system, comprising:
 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,   wherein the AFM system is configured to generate a displacement noise that is less than 300 Picometers.   
     
     
         2 . The AFM system of  claim 1 , wherein the noise level of the power source is below 200 Picometers. 
     
     
         3 . The AFM system of  claim 1 , further comprising at least one digitizing arrangement associated with the at least one scanning probe arrangement. 
     
     
         4 . The AFM system of  claim 3 , wherein the at least one digitizing arrangement has a bandwidth of about 2 MHZ. 
     
     
         5 . The AFM system of  claim 1 , wherein the at least one scanning probe arrangement has a detection bandwidth of at least 80 MHZ. 
     
     
         6 . The AFM system of  claim 1 , further comprising a transparent sample plate positioned below the at least one cantilever. 
     
     
         7 . The AFM system of  claim 6 , further comprising at least one light emitting arrangement positioned under the sample plate configured to emit a light through the sample plate. 
     
     
         8 . The AFM system of  claim 7 , wherein the at least one light emitting arrangement includes at least one light and at least one mirror. 
     
     
         9 . The AFM system of  claim 1 , wherein the at least one cantilever has a spring constant of less than about 0.03 newton meters. 
     
     
         10 . The AFM system of  claim 1 , further comprising at least one camera positioned above the at least one scanning probe arrangement. 
     
     
         11 . The AFM system of  claim 1 , wherein the laser is positioned directly above the at least one cantilever. 
     
     
         12 . The AFM system of  claim 1 , wherein (i) the at least one scanning probe arrangement includes a plurality of scanning probe arrangements, (ii) the at least one cantilever includes a plurality of cantilevers, and (iii) each of the scanning probe arrangements is positioned above a corresponding one of the cantilevers. 
     
     
         13 . The AFM system of  claim 1 , further comprising a computer hardware arrangement configured to adjust a position of the laser relative to the at least one cantilever. 
     
     
         14 . A method of mapping nucleotide molecules, comprising:
 incubating a target nucleotide in a magnesium-free mixture, wherein the 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 atomic force microscopy, wherein prior to imaging, substantially all unbound CRISPR-Cas protein or guide RNA is removed and wherein the atomic force microscopy comprises an atomic force microscopy (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, wherein the AFM system is configured to generate a displacement noise that is less than 300 Picometers.   
     
     
         15 . The method of  claim 14 , wherein the target nucleotide is deoxyribonucleic acid (DNA). 
     
     
         16 . The method of  claim 14 , wherein the target nucleotide is a DNA/RNA hybrid. 
     
     
         17 . The method of  claim 15 , wherein the DNA is a polymerase chain reaction (PCR) amplicon. 
     
     
         18 . The method of  claim 15 , wherein the DNA is genomic DNA obtained from a biological sample. 
     
     
         19 . (canceled) 
     
     
         20 . The method of  claim 14 , wherein the magnesium-free mixture includes EDTA, wherein the EDTA chelates any magnesium in the mixture to render the mixture magnesium-free. 
     
     
         21 . The method of  claim 14 , wherein the magnesium-free mixture is a magnesium-free deposition buffer that comprises magnesium-alternates selected from the group consisting of zinc, polyamine, and nickel. 
     
     
         22 . The method of  claim 14 , wherein the CRISPR-Cas protein is Cas9. 
     
     
         23 . The method of  claim 14 , wherein the CRISPR-Cas protein is a modified Cas9. 
     
     
         24 . The method of  claim 14 , wherein the guide RNA is an sgRNA, wherein the sgRNA is designed to target a specific target nucleotide sequence marker. 
     
     
         25 . The method of  claim 14 , wherein at least two or more guide RNA targeting different nucleotide sequences are present in the mixture. 
     
     
         26 . The method of  claim 14 , wherein before depositing the CRISPR-Cas/target nucleotide complex on a flat surface, any unbound CRISPR-Cas protein or guide RNA is removed. 
     
     
         27 . The method of  claim 14 , wherein after depositing the CRISPR-Cas/target nucleotide complex on a flat surface, any unbound CRISPR-Cas protein or guide RNA is removed. 
     
     
         28 . The method of  claim 14 , wherein the flat surface is a mica surface. 
     
     
         29 . The method of  claim 14 , wherein the flat surface is a transparent surface. 
     
     
         30 - 31 . (canceled) 
     
     
         32 . The method of  claim 14 , wherein after imaging the CRISPR-Cas/target nucleotide complex on the flat surface, the image is used for de novo mapping of the target nucleotide. 
     
     
         33 . The method of  claim 14 , wherein after imaging the CRISPR-Cas/target nucleotide complex on the flat surface, the image is used for quantitating the amount of the target nucleotide. 
     
     
         34 . The method of  claim 14 , further comprising a step of fixing the CRISPR-Cas protein to the target nucleotide after said incubating step. 
     
     
         35 . A method of mapping nucleotide molecules, comprising:
 incubating a double-stranded deoxyribonucleic acid (dsDNA) molecule in a magnesium-free mixture, wherein the mixture comprises a CRISPR-Cas9 protein and an sgRNA, and wherein incubating the dsDNA molecule with the CRISPR-Cas9 protein binds the CRISPR-Cas9 protein to the dsDNmolecule to form a CRISPR-Cas9/dsDNcomplex without the CRISPR-Cas9 protein cleaving the dsDNmolecule;   fixing the CRISPR-Cas9/dsDNA complex by adding formaldehyde to the mixture;   depositing the CRISPR-Cas9/dsDNA complex on a mica surface, wherein after the deposition the CRISPR-Cas9/dsDNA complex is bound to the mica surface; and   imaging the CRISPR-Cas9/dsDNA complex on the mica surface by using AFM, wherein before imaging any unbound CRISPR-Cas9 protein or sgRNA is removed;   
       wherein the AFM comprises:
 an AFM system, comprising:
 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, 
 
 wherein the AFM system is configured to generate a displacement noise that is less than 300 Picometers. 
 
     
     
         36 - 45 . (canceled)