METHODS OF MACROMOLECULAR ANALYSIS USING NANOCHANNEL ARRAYS

• US 20080242556A1
• Filed: 03/28/2008
• Published: 10/02/2008
• Est. Priority Date: 03/28/2007
• Status: Active Grant

• Current Assignee: BioNano Genomics, Inc.
• Original Assignee: BioNano Genomics, Inc.
• Inventors: Boyce-Jacino, Michael, Cao, Han, Austin, Michael D., Deshpande, Parikshit A.
• Granted Patent: US 8,722,327 B2
• Time in Patent Office: Days
• US Class Current: 506/9
• CPC Class Codes: B01L 2200/0663 Stretching or orienting elongated molecules or particles
• CPC Class Codes: B01L 2200/0668 Trapping microscopic beads
• CPC Class Codes: B01L 2200/12 Specific details about manufacturing devices
• CPC Class Codes: B01L 2300/041 Connecting closures to device or container
• CPC Class Codes: B01L 2300/0627 Sensor or part of a sensor is integrated
• CPC Class Codes: B01L 2300/0654 Lenses; Optical fibres
• CPC Class Codes: B01L 2300/0816 Cards, e.g. flat sample carriers usually with flow in two horizontal directions
• CPC Class Codes: B01L 2300/0861 Configuration of multiple channels and/or chambers in a single devices
• CPC Class Codes: B01L 2300/0864 comprising only one inlet and multiple receiving wells, e.g. for separation, splitting
• CPC Class Codes: B01L 2300/0887 Laminated structure
• CPC Class Codes: B01L 2300/089 Virtual walls for guiding liquids
• CPC Class Codes: B01L 2300/0896 Nanoscaled
• CPC Class Codes: B01L 2300/161 Control and use of surface tension forces, e.g. hydrophobic, hydrophilic
• CPC Class Codes: B01L 2400/0406 capillary forces
• CPC Class Codes: B01L 2400/0415 electrical forces, e.g. electrokinetic
• CPC Class Codes: B01L 2400/0487 fluid pressure, pneumatics
• CPC Class Codes: B01L 2400/086 using baffles or other fixed flow obstructions
• CPC Class Codes: B01L 3/50273 characterised by the means or forces applied to move the fluids micropumps F04B19/006, of the membrane type F04B43/043
• CPC Class Codes: B01L 3/502761 specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads, for physically stretching molecules investigating characteristics of particles G01N15/00
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 1/6876 : Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 2563/107 : fluorescence
• CPC Class Codes: C12Q 2600/172 : Haplotypes
• CPC Class Codes: G01N 21/6428 : Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" in vivo A61B5/00; immunoassay G01N33/53
• CPC Class Codes: G01N 21/645 : Specially adapted constructive features of fluorimeters
• CPC Class Codes: G01N 33/582 : with fluorescent label

Abstract

Methods of analyzing features such as the physical size of macromolecules or biomarkers along large genomic DNA molecules were disclosed as well as the devices for carrying out such high throughput analysis in a massively parallel fashion. Methods of fabricating such devices are also disclosed.

Claims

1. A nanofluidic device capable of manipulating a single elongated macromolecule, comprising:

a substrate comprising a surface and one or more fluidic nanochannel segments disposed substantially parallel to the surface, wherein at least one of the fluidic nanochannel segments is capable of containing and elongating at least a portion of a macromolecule residing within at least a portion of the fluidic nanochannel segment, and wherein each of the fluidic nanochannel segments has a characteristic cross-sectional dimension of less than about 1000 nm and a length of at least about 10 nm; and

at least one viewing window, wherein the viewing window is capable of permitting optical inspection of at least a portion of the contents of the one or more fluidic nanochannel segments.

2. The device of claim 1, comprising a plurality of fluidic nanochannel segments that are not fluidically connected to each other.

3. The device of claim 2, wherein the plurality of fluidic nanochannel segments are essentially parallel.

4. The device of claim 1, comprising a plurality of fluidic nanochannel segments, wherein at least a portion of the fluidic nanochannel segments are fluidically connected to each other.

5. The device of claim 4, wherein the plurality of fluidic nanochannel segments fluidically connected to each other are disposed in a branching pattern.

6. The device of claim 4, wherein the plurality of the fluidic nanochannel segments fluidically connected to each other are disposed in a grid pattern.

7. The device of claim 1, wherein one or more of the fluidic nanochannel segments are characterized as being curved in form.

8. The device of claim 1, wherein one or more of the fluidic nanochannel segments are characterized as being tortuous in form.

9. The device of claim 1, wherein one or more of the fluidic nanochannel segments is described as having a varying cross-sectional dimension.

10. The device of claim 1, wherein at least one of the fluidic nanochannel segments comprises a cross-sectional dimension that is different than the cross-sectional dimension of another of the fluidic nanochannel segments.

11. The device of claim 1, wherein at least one of the fluidic nanochannel segments comprises a bulge, an expansion, a bump, a post, an occlusion, or any combination thereof.

12. The device of claim 1, wherein the substrate comprises a metal, a ceramic, a polymer, a glass, silicon, a semiconductor, a plastic, a dielectric, SiGe, GaAs, ITO, fused silica, or any combination thereof.

13. The device of claim 1, wherein at least one of the fluidic nanochannel segments has a characteristic cross-sectional dimension of less than about 500 nm.

14. The device of claim 1, wherein at least one of the fluidic nanochannel segments has a characteristic cross-sectional dimension of less than about 200 nm.

15. The device of claim 1, wherein at least one of the fluidic nanochannel segments has a characteristic cross-sectional dimension of less than about 100 nm.

16. The device of claim 1, wherein at least one of the fluidic nanochannel segments has a characteristic cross-sectional dimension of less than about 50 nm.

17. The device of claim 1, wherein at least one of the fluidic nanochannel segments has a characteristic cross-sectional dimension of less than about 10 nm.

18. The device of claim 1, wherein at least one of the fluidic nanochannel segments has a characteristic cross-sectional dimension of less than about 5 nm.

19. The device of claim 1, wherein at least one of the fluidic nanochannel segments has a characteristic cross-sectional dimension of less than about 2 nm.

20. The device of claim 1, wherein at least one of the fluidic nanochannel segments has a characteristic cross-sectional dimension of less than about 0.5 nm.

21. The device of claim 1, wherein at least one of the fluidic nanochannel segments has a characteristic cross-sectional dimension of less than about twice the radius of gyration of the macromolecule.

22. The device of claim 1, wherein at least one of the fluidic nanochannel segments has a characteristic cross-sectional dimension of at least about the persistence length of the macromolecule.

23. The device of claim 1, wherein at least one of the fluidic nanochannel segments has a length of at least about 100 nm.

24. The device of claim 1, wherein at least one of the fluidic nanochannel segments has a length of at least about 500 nm.

25. The device of claim 1, wherein at least one of the fluidic nanochannel segments has a length of at least about 1000 nm.

26. The device of claim 1, wherein at least one of the fluidic nanochannel segments has a length of at least about 2 microns.

27. The device of claim 1, wherein at least one of the fluidic nanochannel segments has a length of at least about 5 microns.

28. The device of claim 1, wherein at least one of the fluidic nanochannel segments has a length of at least about 10 microns.

29. The device of claim 1, wherein at least one of the fluidic nanochannel segments has a length of at least about 1 mm.

30. The device of claim 1, wherein at least one of the fluidic nanochannel segments has a length of at least about 10 mm.

31. The device of claim 1, wherein the fluidic nanochannel segments are present at a density of at least 1 fluidic nanochannel segment per cubic centimeter.

32. The device of claim 1, wherein the viewing window comprises a slit.

33. The device of claim 1, wherein the viewing window is removable.

34. The device of claim 1, wherein the viewing window is capable of placing the contents of one or more fluidic nanochannel segments into fluid communication with the environment external to the fluidic nanochannel segment.

35. The device of claim 1, wherein one or more of the fluidic nanochannel segments is characterized as a trench.

36. The device of claim 35, further comprising a cap capable of covering at least a portion of at least one trench.

37. The device of claim 36, wherein at least a portion of the cap is permeable to soluble analytes capable of interaction with a macromolecule residing in the fluidic nanochannel segment.

38. The device of claim 36, wherein the cap is removable.

39. The device of claim 36, wherein the cap is optically transparent.

40. The device of claim 36, wherein one or more macromolecules are at least partially elongated in the fluidic nanochannel segment, and remain in a substantially elongated form after the cap is removed.

41. The device of claim 1, wherein one or more of the fluidic nanochannel segments is characterized as a tunnel.

42. The device of claim 1, wherein one or more of the fluidic nanochannels is characterized as a zone bordered by one or more regions having a surface chemistry.

43. The device of claim 42, wherein a surface chemistry comprises a hydrophobic species, a hydrophilic species, a surfactant, a thiol, an amine, a hydroxyl, an alcohol, a carbonyl, or any combination thereof.

44. The device of claim 1, wherein one or more fluidic nanochannel segments is in fluid communication with one or more fluidic devices.

45. The device of claim 44, wherein a fluidic device comprises a conduit, a pump, a filter, a screen, an occlusion, a gel, a heater, a splitter, a reservoir, or any combination thereof.

46. The device of claim 1, wherein the macromolecule is a polymer, double-stranded DNA, single-stranded DNA, RNA, a polypeptide, a biological molecule, or any combination thereof.

47. The device of claim 46, wherein the polymer comprises a homopolymer, copolymer, block copolymer, random copolymer, branched copolymer, a dendrimer, or any combination thereof.

48. The device of claim 1, further comprising one or more connectors capable of placing the device in fluid communication with one or more apparatuses external to the device.

49. The device of claim 48, wherein the one or more apparatuses external to the device comprise a pump, a conduit, a filter, a screen, a gel, a heater, an occlusion, a splitter, a reservoir, or any combination thereof.

50. The device of claim 1 wherein at least a portion of a macromolecule is held within the channel by use of an activated surface, a bead, or any combination thereof so as to enable elongation of at least a portion of the macromolecule within the nanochannel.

123. The device of claim 1, wherein at least one of the fluidic nanochannel segments has a characteristic cross-sectional dimension of less than about twice the radius of gyration of the macromolecule.

124. The device of claim 1, wherein at least one of the fluidic nanochannel segments has a characteristic cross-sectional dimension of at least about the persistence length of the macromolecule.

51. A method of characterizing one or more macromolecules using a nanofluidic device, comprising:

translocating at least a portion of at least one region of the macromolecule through a fluidic nanochannel segment disposed substantially parallel to a surface of a substrate, wherein the fluidic nanochannel segment is capable of containing and elongating at least a portion of a region of the macromolecule, and wherein the fluidic nanochannel segment has a characteristic cross-sectional dimension of less than about 1000 nm and a length of at least about 10 nm; and

monitoring, through a viewing window capable of permitting optical inspection of at least a portion of the contents of the fluidic nanochannel segment, one or more signals related to the translocation of one or more regions of the macromolecule through the nanochannel; and

correlating the monitored signals to one or more characteristics of the macromolecule.

52. The method of claim 51, further comprising exposing at least one biological entity to at least one agent of interest, to a metabolite of the agent of interest, to a salt of the agent of interest, or any combination thereof.

53. The method of claim 52, further comprising isolating at least one macromolecule from the exposed biological entity.

54. The method of claim 52, wherein the exposing the at least one biological entity to at least one agent of interest, to a metabolite of the agent of interest, to a salt of the agent of interest, or any combination thereof, comprises injecting, treating, spraying, transfecting, digesting, immersing, flowing, applying, or any combination thereof.

55. The method of claim 52, wherein a biological entity comprises a living being, a cell, a biological molecule, a protein, or any combination thereof.

56. The method of claim 52, wherein the isolating at least one macromolecule from the exposed biological entity comprises extracting, lysing, purifying, pulling, manipulating, reacting, distilling, electrophoresing, or any combination thereof.

57. The method of claim 52, wherein the one or more macromolecules comprise proteins, single-stranded DNA, double-stranded DNA, RNA, siRNA, or any combination thereof.

58. The method of claim 52, further comprising dividing the one or more macromolecules into two or more segments.

59. The method of claim 52, wherein the dividing comprises lasing, sonicating, chemically treating, physically manipulating, biologically treating, or any combination thereof.

60. The method of claim 51, further comprising binding a fluorescent label, a radioactive label, a magnetic label, or any combination thereof to one or more regions of the macromolecule.

61. The method of claim 51, wherein translocating comprises applying a fluid flow, a magnetic field, an electric field, a radioactive field, a mechanical force, an electroosmotic force, an electrophoretic force, an electrokinetic force, a temperature gradient, a pressure gradient, a surface property gradient, a capillary flow, or any combination thereof.

62. The method of claim 61, wherein the translocating comprises controllably moving at least a portion of the macromolecule into at least a portion of a fluidic nanochannel segment.

63. The method of claim 61, wherein the translocating comprises moving at least a portion of the macromolecule through at least a portion of a fluidic nanochannel segment at a controlled speed and a controlled direction.

64. The method of claim 51, wherein monitoring comprises recording, displaying, analyzing, plotting, or any combination thereof.

65. The method of claim 51, wherein the one or more signals comprise an optical signal, a radiative signal, a fluorescent signal, an electrical signal, a magnetic signal, a chemical signal, or any combination thereof.

66. The method of claim 51, wherein the signal is generated by an electron spin resonance molecule, a fluorescent molecule, a chemiluminescent molecule, a radioisotope, an enzyme substrate, a biotin molecule, an avidin molecule, an electrical charged transferring molecule, a semiconductor nanocrystal, a semiconductor nanoparticle, a colloid gold nanocrystal, a ligand, a microbead, a magnetic bead, a paramagnetic particle, a quantum dot, a chromogenic substrate, an affinity molecule, a protein, a peptide, a nucleic acid, a carbohydrate, an antigen, a hapten, an antibody, an antibody fragment, a lipid, or any combination thereof.

67. The method of claim 51, wherein the molecule is unlabeled and monitored by infrared spectroscopy, ultraviolet spectroscopy, or any combination thereof.

68. The method of claim 51, wherein the signal is generated by using one or more excitation sources to induce fluorescence, chemoluminescence, phosphorescence, bioluminescence, or any combination thereof.

69. The method of claim 68, wherein the excitation source is a laser, a visible light source, a source of infrared light, a source of ultraviolet light, or any combination thereof.

70. The method of claim 51, wherein correlating comprises determining the features of a distinct macromolecule or a portion thereof from a population of macromolecules by partial or full elongation of the macromolecule in a fluidic nanochannel segment.

71. The method of claim 51, wherein at least a portion of the macromolecule is stationary during the monitoring.

72. The method of claim 51, wherein at least a portion of the macromolecule is translocated within at least a portion of the fluidic nanochannel segment more than one time.

73. The method of claim 51, wherein the correlating comprises determining the length of at least a portion of the macromolecule.

74. The method of claim 51, wherein the correlating comprises determining the apparent partially elongated length of at least a portion of the macromolecule as confined within one or more fluidic nanochannel segments.

75. The method of claim 74, wherein the apparent partially elongated length is determined as the linear distance along the fluidic nanochannel segment within which a partially elongated macromolecule is confined.

76. The method of claim 51, wherein the correlating comprises determining the identity of one or more components of the macromolecule.

77. The method of claim 51, wherein the correlating comprises determining the sequence of one or more components of the macromolecule.

78. The method of claim 51, wherein the correlating comprises determining the presence of one or more modifications to at least a portion of the macromolecule.

79. The method of claim 51, wherein the correlating is performed by automated means, computerized means, mechanical means, manual means, or any combination thereof.

80. The method of claim 51, wherein the correlating comprises an algorithm for characterizing a duplex nucleic acid molecule based on observed signal modulations through the detection region of a nanochannel, wherein said algorithm is present on a computer readable medium.

81. The method of claim 51, wherein the one or more characteristics of the macromolecule comprise one or more target features present on at least a portion of the macromolecule.

82. The method of claim 81, wherein a target feature comprises an epigenetic factor.

83. The method of claim 82, wherein an epigenetic factor comprises one or more methylation patterns.

84. The method of claim 81, wherein a target feature comprises one or more genomic structures.

85. The method of claim 84, wherein a genomic structure comprises the position of one or more particular molecular sequences, SNPs, haplotypes, repetitive elements, copy numbers polymorphisms, a change in one or more loci on a DNA molecule, open reading frames, introns, exons, regulatory elements, or any combination thereof.

86. The method of claim 81, wherein a target feature comprises compound/drug binding sites/complex, DNA repairing or cleaving binding sites/complex, SiRNA or anti-sense nucleotides binding sites/complex, transcription/regulatory factor binding sites/complex, restriction enzyme binding/cleaving sites/complex, or any other genetically engineered or chemically modified binding sites/complexes, or any combination thereof.

87. The method of claim 51, further comprising:

contacting a macromolecule with a first labeled probe of known length L1, wherein the first labeled probe is complementary to a control genomic sequence whose copy number is known, and with a second labeled probe of known length L2, wherein the second labeled probe is specific to a nucleotide sequence of interest;

introducing the macromolecule into at least a portion of the fluidic nanochannel segment;

elongating the labeled macromolecule within the fluidic nanochannel segment;

detecting binding between the first labeled probe and the genomic control sequence and between the second labeled probe and the nucleotide sequence of interest; and

ascertaining the total length of the hybridization signals that correspond to the first labeled probe (S1) and the second labeled probe (S2).

88. The method of claim 87, further comprising calculating the copy number of the nucleotide sequence of interest, wherein the copy number is calculated by calculating the ratios N1=S1/L1 and N2=S2/L2, wherein N1 corresponds to the copy number of the genomic control sequence and N2 corresponds to the copy number of the nucleotide sequence of interest.

89. The method of claim 87, wherein the copy number of the control sequence is an integer.

90. The method of claim 87, wherein a difference between N2 and N1 indicates an abnormality in the genome.

91. The method of claim 87, wherein the control genomic sequence comprises separate portions whose total length per genome is known, wherein the sequence of interest comprises separate portions whose length per normal gene is known, and wherein a significant difference between N2 and N1 indicates a genetic abnormality in the genome.

92. The method of claim 87, wherein the sequence of interest relates to a trisomy-linked chromosome, wherein the control genomic sequence is from a chromosome other than the trisomy-linked chromosome, and wherein a N2/N1 ratio of approximately 1.5 indicates a trisomic genotype.

93. The method of claim 87, wherein the nucleotide sequence of interest comprises a deletion of a portion of a genome.

94. The method of claim 87, wherein the nucleotide sequence of interest comprises a repeating sequence.

95. The method of claim 87, wherein the control genomic sequence and the nucleotide sequence of interest are identical for a given genome, and wherein one or more different genomes are analyzed within one or more fluidic nanochannel segments so as to determine the respective quantities of each genome present.

96. The method of claim 87, wherein the N2/N1 ratio has a statistical error of less than 20%.

97. The method of claim 87, wherein the control genomic sequence and nucleotide sequence of interest are from the same genome.

98. The method of claim 87, wherein the control genomic sequence is from the same chromosome as the nucleotide sequence of interest.

99. The method of claim 51, further comprising labeling regions of a sample nucleotide at either end of a nucleotide zone of interest and regions of a control nucleotide at either end of a nucleotide zone of interest.

100. The method of claim 99, further comprising (a) introducing the labeled nucleotides into separate fluidic nanochannel segments having a cross-sectional diameters sufficient to at least substantially elongate the labeled nucleotides, (b) determining the distance between the labels on the sample nucleotide and the control nucleotide, respectively, and repeating steps (a) and (b) one or more times so as to further linearize the sample and control nucleotides and so as to obtain additional information regarding the distance between the labels on the control and sample nucleotides as the nucleotides elongate.

101. The method of claim 100, further comprising determining the length of the zone of interest on the sample nucleotide by comparing the distance between the labels on the control and sample nucleotides.

102. The method of claim 101, wherein a difference between the distance between the labels on the control and sample nucleotides indicates an abnormality in the zone of interest on the sample nucleotide.

103. A device, comprising:

a substrate comprising a surface and one or more fluidic nanochannel segments disposed substantially parallel to the surface, wherein at least one of the fluidic nanochannel segments is capable of containing and elongating at least a portion of a macromolecule residing within at least a portion of the fluidic nanochannel segment, and wherein each of the fluidic nanochannel segments has a characteristic cross-sectional dimension of less than about 1000 nm and a length of at least about 10 nm; and

wherein at least a portion of at least one fluidic nanochannel segment is illuminated by one or more excitation sources.

104. The device of claim 103, comprising a plurality of fluidic nanochannel segments that are not fluidically connected to each other.

105. The device of claim 104, wherein the plurality of fluidic nanochannel segments are essentially parallel.

106. The device of claim 103, comprising a plurality of fluidic nanochannel segments, wherein at least a portion of the fluidic nanochannel segments are fluidically connected to each other.

107. The device of claim 106, wherein the plurality of fluidic nanochannel segments fluidically connected to each other are disposed in a branching pattern.

108. The device of claim 106, wherein the plurality of the fluidic nanochannel segments are characterized as fluidically connected to each other in a gridded pattern.

109. The device of claim 103, wherein one or more of the fluidic nanochannel segments are characterized as being curved in form.

110. The device of claim 103, wherein one or more of the fluidic nanochannel segments are characterized as being tortuous in form.

111. The device of claim 103, wherein one or more of the fluidic nanochannel segments is described as having a cross-sectional dimension that varies along the length of the fluidic nanochannel segment.

112. The device of claim 106, wherein at least one of the fluidic nanochannel segments comprises a cross-sectional dimension that is different than the cross-sectional dimension of another of the fluidic nanochannel segments.

113. The device of claim 103, wherein at least one of the fluidic nanochannel segments comprises a bulge, an expansion, a bump, a post, an occlusion, or any combination thereof.

114. The device of claim 103, wherein the substrate comprises a metal, a ceramic, a polymer, a glass, silicon, a semiconductor, a plastic, a dielectric, SiGe, GaAs, ITO, fused silica, or any combination thereof.

115. The device of claim 103, wherein at least one of the fluidic nanochannel segments has a characteristic cross-sectional dimension of less than about 500 nm.

116. The device of claim 103, wherein at least one of the fluidic nanochannel segments has a characteristic cross-sectional dimension of less than about 200 nm.

117. The device of claim 103, wherein at least one of the fluidic nanochannel segments has a characteristic cross-sectional dimension of less than about 100 nm.

118. The device of claim 103, wherein at least one of the fluidic nanochannel segments has a characteristic cross-sectional dimension of less than about 50 nm.

119. The device of claim 103, wherein at least one of the fluidic nanochannel segments has a characteristic cross-sectional dimension of less than about 10 nm.

120. The device of claim 103, wherein at least one of the fluidic nanochannel segments has a characteristic cross-sectional dimension of less than about 5 nm.

121. The device of claim 103, wherein at least one of the fluidic nanochannel segments has a characteristic cross-sectional dimension of less than about 2 nm.

122. The device of claim 103, wherein at least one of the fluidic nanochannel segments has a characteristic cross-sectional dimension of less than about 0.5 nm.

125. The device of claim 103, wherein at least one of the fluidic nanochannel segments has a length of at least about 100 nm.

126. The device of claim 103, wherein at least one of the fluidic nanochannel segments has a length of at least about 500 nm.

127. The device of claim 103, wherein at least one of the fluidic nanochannel segments has a length of at least about 1000 nm.

128. The device of claim 103, wherein at least one of the fluidic nanochannel segments has a length of at least about 2 microns.

129. The device of claim 103, wherein at least one of the fluidic nanochannel segments has a length of at least about 5 microns.

130. The device of claim 103, wherein at least one of the fluidic nanochannel segments has a length of at least about 10 microns.

131. The device of claim 103, wherein at least one of the fluidic nanochannel segments has a length of at least about 1 mm.

132. The device of claim 103, wherein at least one of the fluidic nanochannel segments has a length of at least about 10 mm.

133. The device of claim 103, wherein the fluidic nanochannel segments are present at a density of at least 1 fluidic nanochannel segment per cubic centimeter.

134. The device of claim 103, further comprising a viewing window disposed between the the illuminated fluidic nanochannel segment and the illumination source.

135. The device of claim 134, wherein the viewing window comprises a slit.

136. The device of claim 134, wherein the viewing window is removable.

137. The device of claim 134, wherein the viewing window is capable of placing the contents of one or more fluidic nanochannel segments into fluid communication with the environment external to the fluidic nanochannel segment.

138. The device of claim 103, wherein one or more of the fluidic nanochannel segments is characterized as a trench.

139. The device of claim 138, further comprising a cap capable of covering at least a portion of at least one trench.

140. The device of claim 139, wherein at least a portion of the cap is permeable to soluble analytes capable of interaction with a macromolecule residing in the fluidic nanochannel segment.

141. The device of claim 139, wherein the cap is removable.

142. The device of claim 139, wherein one or more macromolecules are at least partially elongated in the fluidic nanochannel segment, and remain in a substantially elongated form after the cap is removed.

143. The device of claim 103, wherein one or more of the fluidic nanochannel segments is characterized as a tunnel.

144. The device of claim 103, wherein one or more of the fluidic nanochannels is characterized as a zone bordered by one or more regions having a surface chemistry.

145. The device of claim 144, wherein a surface chemistry comprises a hydrophobic species, a hydrophilic species, a surfactant, a thiol, an amine, a hydroxyl, an alcohol, a carbonyl, or any combination thereof.

146. The device of claim 103, wherein one or more fluidic nanochannel segments is in fluid communication with one or more fluidic devices.

147. The device of claim 146, wherein a fluidic device comprises a conduit, a pump, a filter, a screen, an occlusion, a gel, a heater, a splitter, a reservoir, or any combination thereof.

148. The device of claim 103, wherein the macromolecule is a polymer, double-stranded DNA, single-stranded DNA, RNA, a polypeptide, a biological molecule, or any combination thereof.

149. The device of claim 148, wherein the polymer comprises a homopolymer, copolymer, block copolymer, random copolymer, branched copolymer, a dendrimer, or any combination thereof.

150. The device of claim 103, further comprising one or more connectors capable of placing the device in fluid communication with one or more apparatuses external to the device.

151. The device of claim 150, wherein the one or more apparatuses external to the device comprise a pump, a conduit, a filter, a screen, a gel, a heater, an occlusion, a splitter, a reservoir, or any combination thereof.

152. The device of claim 103, wherein the excitation source is a laser, a halogen light, a mercury lamp, a source of infrared light, a source of ultraviolet light, a diode, a waveguide, a radioactive source, or any combination thereof.

153. The device of claim 103, further comprising a filter capable of transmitting a spectrum of excitation source light.

154. The method of claim 103, wherein the portion of the at least one illuminated fluidic nanochannel segment illuminated by one or more excitation sources is characterized as being one or more slits.

155. The device of claim 103, wherein the area of excitation is characterized as being one or more circular spots, ovals, polygons, or any combination thereof.

156. The device of claim 103, wherein the excitation source is capable of being scanned across at least a portion of at least one fluidic nanochannel segment.

157. The device of claim 103, further comprising one or more excitation sources.

158. The device of claim 103, further comprising a detector disposed so as to be capable of receiving an optical signal originating from within one or more illuminated fluidic nanochannel segments.

159. The device of claim 158, wherein the detector comprises a charge coupled device (CCD) detection system, a complementary metal-oxide semiconductor (CMOS) detection system, a photodiode detection system, a photo-multiplying tube detection system, a scintillation detection system, a photon counting detection system, an electron spin resonance detection system, a fluorescent detection system, a photon detection system, an electrical detection system, a photographic film detection system, a chemiluminescent detection system, an enzyme detection system, an atomic force microscopy (AFM) detection system, a scanning tunneling microscopy (STM) detection system, a scanning electron microscopy (SEM) detection system, an optical detection system, a nuclear magnetic resonance (NMR) detection system, a near field detection system, a total internal reflection (TIR) detection system, a patch clamp detection system, a capacitive detection system, or any combination thereof.

160. A macromolecular analysis device, comprising:

one or more nanochannels disposed on a surface,

one or more of the nanochannels having a width of less than about 1000 nm, and

one or more of the nanochannels being defined by one or more borders and being capable of constraining at least a portion of the macromolecule so as to maintain in linear form that portion of the macromolecule.

161. The macromolecular analysis device of claim 160, wherein one or more of the nanochannels comprises a length in the range of from about 10 nm to about 10 cm.

162. The macromolecular analysis device of claim 161, wherein one or more of the nanochannels comprises a length in the range of from about 100 nm to about 1 cm.

163. The macromolecular analysis device of claim 161, wherein one or more of the nanochannels comprises an essentially straight portion in the length of from about 10 nm to about 100 cm.

164. The macromolecular analysis device of claim 161, wherein one or more of the nanochannels comprises at least one essentially straight portion in the length of from about 100 nm to about 10 cm.

165. The macromolecular analysis device of claim 161, wherein one or more of the nanochannels comprises at least one essentially straight portion in the length of from about 1 mm to about 1 cm.

166. The macromolecular analysis device of claim 160, wherein one or more of the nanochannels comprises a width of less than about 500 nm.

167. macromolecular analysis device of claim 160, wherein one or more of the nanochannels comprises a width of less than about 100 nm.

168. macromolecular analysis device of claim 160, wherein one or more of the nanochannels comprises a width of less than about 50 nm.

169. macromolecular analysis device of claim 160, wherein one or more of the nanochannels comprises a width of less than about 10 nm.

170. macromolecular analysis device of claim 160, wherein one or more of the nanochannels comprises a width of less than about 5 nm.

171. The macromolecular analysis device of claim 160, wherein two or more nanochannels are connected.

172. The macromolecular analysis device of claim 160, wherein one or more of the nanochannels has a non-constant cross section.

173. The macromolecular analysis device of claim 160, wherein at least a portion of two or more nanochannels are oriented parallel to one another.

174. The macromolecular analysis device of claim 160, wherein a border comprises a physical wall, an electrically charged region, a chemically-treated region, a region of magnetic field, different materials, a self-assembled monolayer, a polymer, or any combination thereof.

175. The macromolecular analysis device of claim 174, wherein a border comprises a hydrophobic region, a hydrophilic region, or any combination thereof.

176. The macromolecular analysis device of claim 174, wherein a border comprises a region of static electrical charge.

177. The macromolecular analysis device of claim 160, wherein the surface comprises glass, a ceramic, silicon, a metal, a polymer, or any combination thereof.

178. The macromolecular analysis device of claim 160, further comprising a viewing window disposed above at least a portion of at least one nanochannel.

179. The macromolecular analysis device of claim 178, wherein the viewing window is permeable to one or more macromolecules.

180. The macromolecular analysis device of claim 160, further comprising a detector.

181. A method of analyzing a macromolecule, comprising:

disposing one or more macromolecules onto a surface having one or more nanochannels capable of constraining at least a portion of the macromolecule so as to maintain in linear form that portion of the macromolecule;

subjecting the one or more macromolecules to a motivating force so as to elongate at least a portion of one or more macromolecules within one or more nanochannels; and

monitoring one or more signals evolved from one or more of the macromolecules.

182. The method of claim 181, wherein the disposing one or more macromolecules comprises dispensing, dropping, flowing, or any combination thereof.

183. The method of claim 181, wherein one or more macromolecules are disposed at least partially within one or more nanochannels.

184. The method of claim 181, wherein a motivating force comprises a pressure gradient, a magnetic field, an electric field, a receding meniscus, a surface tension, a thermal gradient, a pulling force, a pushing force, or any combination thereof.

185. The method of claim 181, wherein the motivating is applied by an optical trap, an optical tweezers, a physical probe, an atomic force microscope, or any combination thereof.

186. The method of claim 184, wherein the force is constant, the force varies, or both.

187. The method of claim 184, wherein the force varies periodically, intermittently, randomly, or any combination thereof.

188. The method of claim 181, wherein monitoring one or more signals comprises recording, plotting, displaying, or any combination thereof.

189. The method of claim 181, further comprising analyzing one or more signals evolved from one or more of the macromolecules.

190. The method of claim 181, further comprising correlating one or more monitored signals to one or more characteristics of one or more macromolecules.

191. The method of claim 181, wherein monitoring one or more signals evolved from one or more of the macromolecules comprises monitoring one or more signals evolved from a portion of a macromolecule in linear form within a nanochannel.

192. The method of claim 181, wherein the monitoring one or more signals evolved from one or more of the macromolecules is performed through a viewing window.

193. The method of claim 181, wherein one or more molecules is tethered to the surface, immobilized within a nanochannel, or both.

194. A method of fabricating a macromolecular analysis device, comprising:

defining one or more nanochannels on a surface by disposition of two or more borders,

one or more of the borders being capable of constraining a macromolecule, and

one or more of the nanochannels having a width of less than about 1000 nm.

195. The method of claim 194, wherein disposition of two or more borders comprises rendering electrically charged at least a portion of the surface, rendering at least a portion of the surface hydrophobic, rendering at least a portion of the surface hydrophilic, rendering at least a portion of the surface magnetic, or any combination thereof.

196. The method of claim 195, wherein disposition of two or more borders comprises contacting at least a portion of the surface with a mold having a surface profile that comprises a surface profile complementary to one or more borders.

197. The method of claim 195, wherein disposition of two or more borders comprises contacting at least a portion of the surface with a mold having a surface profile that comprises one or more nanoscale features.

198. The method of claim 196, wherein the mold is contacted with a charge-carrying species, a hydrophobic species, a hydrophilic species, a magnetic species, a ferromagnetic species, or any combination thereof.