Methods for capturing long polynucleotides for sequencing specific genomic regions

Abstract

The invention relates to methods for capturing a polynucleotide comprising a DNA target segment from a population of polynucleotide molecules. The method may use a mixture comprising the population of the polynucleotide molecules, one or more polynucleotide primers, nucleotides, biotinylated nucleotides, a polymerase enzyme and a buffered liquid medium. The method may denature the polynucleotide molecules in the mixture so as to create single stranded portions of the polynucleotide molecules which can be accessible to the polynucleotide primers; hybridizing the polynucleotide primers to the polynucleotide comprising the DNA target segment. The method may create an extended polynucleotide primer by using the nucleotides, the biotinylated nucleotides and the polymerase enzyme as a means for labeling with biotin and increasing the extent of hybridization of the extended polynucleotide primer to the polynucleotide comprising the DNA target segment. The method may add streptavidin-labeled magnetic beads to the mixture. The method may use a magnetic field to move the streptavidin-labeled magnetic beads relative to the buffered liquid medium as a means for increasing binding of the biotinylated nucleotides of the extended polynucleotide primer to the streptavidin-labeled magnetic beads. The method may use either a rotation of the magnetic field relative to the mixture or a rotation of the mixture relative to the magnetic field for causing a streptavidin-labeled magnetic bead rotation in the buffered liquid medium as a means for performing the steps of increasing the binding of the biotinylated nucleotides of the extended polynucleotide primer to the streptavidin-labeled magnetic beads and increasing the winding of the biotinylated nucleotides of the extended polynucleotide primer onto the streptavidin-labeled magnetic beads, so as to increase the probability of capturing a long polynucleotide comprising a DNA target segment and so as to increase the probability of preventing damage to the long polynucleotide comprising a DNA target segment. Also the method may use a magnetic field to collect the streptavidin-labeled magnetic beads so as to capture the polynucleotide comprising the DNA target segment which is bound to the streptavidin-labeled magnetic beads.

What is claimed is: 
     
         1 . A method for capturing a long polynucleotide comprising a DNA target segment from a population of polynucleotide molecules, the method comprising:
 providing a mixture comprising the population of the polynucleotide molecules, capture molecules comprising one or more polynucleotide primers and/or biotinylated nucleotides, and a buffered liquid medium;   denaturing the polynucleotide molecules in the mixture so as to create single stranded portions of the polynucleotide molecules which can be accessible to the one or more polynucleotide primers;   hybridizing the one or more capture molecules to the polynucleotide comprising the DNA target segment;   adding streptavidin-labeled magnetic beads to the mixture;   using a magnetic field to move the streptavidin-labeled magnetic beads relative to the buffered liquid medium as a means for increasing binding of the biotinylated nucleotides of the capture molecules to the streptavidin-labeled magnetic beads;   using either a rotation of the magnetic field relative to the mixture or a rotation of the mixture relative to the magnetic field for causing a streptavidin-labeled magnetic bead rotation in the buffered liquid medium as a means for performing the steps of increasing the binding of the biotinylated nucleotides of the capture molecules to the streptavidin-labeled magnetic beads and increasing the winding of the biotinylated nucleotides of the capture molecules onto and around the streptavidin-labeled magnetic beads, so as to increase the probability of capturing a long polynucleotide comprising the DNA target segment, wherein the long polynucleotide is at least 10 kb, and so as to increase the probability of preventing damage to the long polynucleotide comprising the DNA target segment; and   using the magnetic field to collect the streptavidin-labeled magnetic beads so as to capture the polynucleotide comprising the DNA target segment which is bound to the streptavidin-labeled magnetic beads.   
     
     
         2 . The method according to  claim 1 , wherein the winding of the biotinylated nucleotides of the capture molecules onto the streptavidin-labeled magnetic beads lessens entanglement of the captured long polynucleotide with the population of polynucleotides so as to avoid an increase in off-target capture during capturing of the polynucleotide comprising the DNA target segment from a population of polynucleotide molecules. 
     
     
         3 . The method according to  claim 1 , wherein the one or more polynucleotide primers are capable of binding to the same polynucleotide strand or to two or more separate polynucleotide strands. 
     
     
         4 . The method according to  claim 1 , wherein two different polynucleotide primers have two complementary origami tails which are capable of binding to each other, so as to result into the condensation of two separate DNA target segments which are located on at least one polynucleotide strand and which are hybridized to two different polynucleotide primers. 
     
     
         5 . The method according to  claim 1 , wherein a polynucleotide may comprise two origami tails and may be capable of binding to at least two different DNA target segments so as to result into the condensation of two different DNA target segments which are located on at least one polynucleotide strand. 
     
     
         6 . The method according to  claim 1 , wherein the polynucleotide primer has a length of between about 15 to about 30 DNA bases and polynucleotide primers designed to hybridize to adjacent DNA target segments are spaced at a distance of between about 1 to about 20 kilobases, to pull down the polynucleotide comprising the DNA target segment from a population of polynucleotide molecules. 
     
     
         7 . The method according to  claim 1 , where the step of using either a rotation of the magnetic field relative to the mixture or a rotation of the mixture relative to the magnetic field for causing a streptavidin-labeled magnetic bead rotation in the buffered liquid medium comprises a streptavidin-labeled structure. 
     
     
         8 . The method according to  claim 1 , wherein condensation of at least one polynucleotide is effected by a condensation reagent or moiety selected from the group consisting of: DNA origami tails, DNA origami oligonucleotides, origami oligonucleotides comprising modified nucleotides, Cot-1 DNA, oligonucleotides comprising Cot-1, SINE, LINE, transposon or other types of repeat sequences, heterochromatin protein 1 (HP1), HP1α (wild-type, nPhos-HP1α, and HP1α (BPM)), HP1β, histones, spermidine, spermine, ethanol, streptavidin-labeled magnetic bead, streptavidin-labeled structure, cobalt(III) examine ion [Co(NH3)6]3+ or any combination thereof. 
     
     
         9 . The method according to  claim 1 , wherein the polynucleotide primer has a number of nucleotide bases selected from the group consisting of 5 bases, 6 bases, 7 bases, 8 bases, 9 bases, 10 bases, 15 bases, 16 bases, 17 bases, 18 bases, 19 bases, 20 bases, 21 bases, 22 bases, 23 bases, 24 bases, 25 bases, 26 bases, 27 bases; 28 bases, 29 bases, 30 bases, 31q bases, 32 bases, 33 bases, 34 bases, 35 bases, 36 base, 37 bases, 38 bases, 39 base, 40 bases, 41 base, 42 bases, 43 bases, 44 bases, 45 bases, 46 bases, 47 bases, 48 bases, 49, bases, 50 bases and any combination thereof. 
     
     
         10 . The method according to  claim 1 , wherein the polymerase enzyme is selected from the group consisting of 129 DNA polymerase, BST 2.0 polymerase, and a combination thereof. 
     
     
         11 . The method according to  claim 10 , wherein the 129 polymerase is used at temperature of between 40° C.-50° C. 
     
     
         12 . The method according to  claim 1 , wherein a temperature range during the hybridization to specific genomic regions of interest is selected from the group consisting of 20° C. to 90° C., 25° C. to 80° C., 30° C. to 70° C., 35° C. to 65° C., 40° C. to 60° C., 45° C. to 65° C., 45° C. to 60° C., 50° C. to 60° C., 55° C. to 65° C., 55° C. to 60° C., and any combination thereof. 
     
     
         13 . The method according to  claim 1 , further comprising using non-extendable blocking oligonucleotides which is longer or has a higher Guanosine and Cytosine content than the polynucleotide primer which is used. 
     
     
         14 . The method according to  claim 1 , further comprising performing a pre-extension with terminating nucleotides which are dideoxynucleotides triphosphates selected from the group consisting of ddATP, ddTTP, ddCTP, ddGTP, and any combination thereof so as to repair a strand break and terminate free 3′-polynucleotide ends so as to reduce off-target capture. 
     
     
         15 . The method according to  claim 1 , further comprising using a nucleotide base selected from the group consisting of a 5′ Bromo dU, a 5′ 2-Aminopurine, a 3′ 2-Aminopurine, a 5′ 2,6-Diaminopurine (2-Amino-dA), a 3′ 2,6-Diaminopurine (2-Amino-dA), a 5′ deoxyUridine, a 3′ deoxyUridine, an Inverted DT, an Inverted Dideoxy-T, a Dideoxy-C, a 5-Methyl dC, a deoxylnosine, a Super T, a Super G, Locked Nucleic Acids (LNA's), a 5-Nitroindole, a 2′-O-Methyl RNA Bases, a Hydroxmethyl dC, an Iso-dG, an Iso-dC, a 5′ Fluoro C, a 5′ Fluoro U, a 5′ Fluoro A, a 5′ Fluoro G, a 5′ 2-MethoxyEthoxy A, a 5′ 2-MethoxyEthoxy MeC, a 5′ 2-MethoxyEthoxy G, a 5′ 2-MethoxyEthoxy T, a 3′ Fluoro C, a 3′ Fluoro U, a 3′ Fluoro A, a 3′ Fluoro G, a 3′ 2-MethoxyEthoxy A, a 3′ 2-MethoxyEthoxy MeC, a 3′ 2-MethoxyEthoxy G, a 3′ 2-MethoxyEthoxy T, and a combination thereof. 
     
     
         16 . The method according to  claim 1 , wherein a nucleotide linker is selected from the group consisting of Acrydite™, Adenylation, Azide NHS ester, Digoxigenin NHS Ester, Cholesterol-TEG, I-Linker™, biotin, streptavidin, and any combination thereof. 
     
     
         17 . The method according to  claim 1 ,
 wherein the buffered liquid medium is a buffer MBSA which comprises an aqueous solution comprising 10 mM Tris pH 7.5, 2 mM EDTA, 0.2% Tween-20, 1 M NaCl, 5 μg/ml BSA, 1.25 mg/ml Nestle Carnation dried milk, and 1 mg/ml glycine,   wherein the polynucleotide molecules can be selected from the group consisting of a DNA sample, a genomic DNA sample, a plasmid DNA sample, an amplified DNA sample, a cDNA, a mitochondrial nucleotide sample, an oligonucleotide sample, an oligo-peptide nucleic acid (PNA) sample, an oligo-LNA, and any combination thereof, and wherein the polynucleotide molecules may be obtained from a human, a mammal, a plant, a bacteria, an archaea, a fungi, a viruses, a single biological cell, a biological tissue, a biological organ, and any combination thereof,   wherein each of the magnetic beads have a diameter of about one micron and the rotation of each magnetic bead is at least one winding turn to increase the binding and winding of the biotinylated nucleotides of the capture molecules around the magnetic bead,   wherein the long polynucleotide is from about 10 kb to about 5 Mb in length, or   a combination thereof.   
     
     
         18 . A kit, comprising:
 streptavidin-labeled magnetic beads;   polynucleotide primers comprising nucleotides and/or biotinylated nucleotides; and   a polymerase enzyme.   
     
     
         19 . The kit according to  claim 18 , further comprising a buffered liquid medium. 
     
     
         20 . The kit according to  claim 18 , further comprising a rotating magnetic field.