US 2002O103350A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2002/0103350 A1 Lyles (43) Pub. Date: Aug. 1, 2002

(54) MATERIALS AND METHODS FOR BINDING Publication Classification NUCLECACDS TO SURFACES (51) Int. CI.7. ... C12O 1/68; CO7H 21/04 (76) Inventor: Mark B. Lyles, San Antonio, TX (US) (52) U.S. Cl...... 536/23.1; 435/6 Correspondence Address: (57) ABSTRACT Baker Botts L.L.P. Surfaces containing high purity Silica (Silicon dioxide) One Shell Plaza exhibit high loading potential for nucleic acids. 901 Louisiana Houston, TX 77002-4995 (US) Formulations containing nucleic acids and materials which mask the electroStatic interactions between the nucleic acids (21) Appl. No.: 09/910,697 and Surfaces are disclosed. By masking the phosphate charges of the nucleic acids, undesired interactions may be (22) Filed: Jul. 20, 2001 minimized or eliminated, thereby allowing the covalent bonding of the nucleic acids to the Surface to proceed. The use of Such formulations additionally minimizes nonspecific Related U.S. Application Data binding of the nucleic acids to the Surface. Examples of materials to be included in Such formulations include cat (60) Provisional application No. 60/220,096, filed on Jul. ions, Xanthines, heXOSes, purines, arginine, lysine, polyargi 21, 2000. nine, polylysine, and quaternary ammonium Salts. US 2002/0103350 A1 Aug. 1, 2002

MATERIALS AND METHODS FOR BINDING DETAILED DESCRIPTION OF THE NUCLEIC ACIDS TO SURFACES INVENTION 0009. The prior art materials and formulations have been FIELD OF THE INVENTION plagued with two general problems; a) low loading potential 0001. The invention relates to silica Surfaces useful for of the Surfaces, and b) nonspecific binding of nucleic acids binding nucleic acids, and formulations to improve the to the Surface. binding of nucleic acids to Surfaces. In particular, high purity Silica (Silicon dioxide) Surfaces are disclosed. Additionally, 0010) A first embodiment of the invention relates to the nucleic acid formulations containing materials which mask use of Substantially pure Silica (Silicon dioxide) in Surfaces. the electroStatic interactions between nucleic acids and AS there are essentially no impurities in the material, essen tially the entire surface of the material is available for Surfaces are disclosed. binding nucleic acids. Preferably the material is at least about 70% pure, about 80% pure, about 90% pure, about BACKGROUND OF THE INVENTION 95% pure, about 96% pure, about 97% pure, about 98% 0002 The binding of nucleic acids, especially DNA, to pure, about 99% pure, about 99.5% pure, about 99.9% pure, Surfaces has been reported many times in the Scientific and ideally about 100% pure by weight. The resulting literature. Binding may be accomplished either through Surface will exhibit higher loading potential for nucleic acids nonspecific electroStatic or hydrophobic means, or through than does conventional glass Surfaces. At a microscopic formation of covalent bonds to the terminus of the nucleic level, the Silica Surface preferably has a three dimensional acid. Structure, and is not planar. An example of a three dimen Sional Structure is an array of Silica fibers. 0.003 Covalent bonding of nucleic acids to surfaces is generally preferred, as it specifically orients the nucleic 0011. The surface may be generally be any shape, and acids in a given manner. The bonded nucleic acids may be preferably is macroscopically planar (e.g. a chip or disk) or used for hybridization experiments when contacted with three dimensional (e.g. a sphere or bead). other nucleic acids in Solution. 0012. The surface properties of the materials may be 0004 Traditionally, glass has been used as the substrate modified by chemical reactions. Examples include modify for binding nucleic acids. The glass is heated in order to ing the hydrophobicity or hydrophilicity of the materials. produce Slides or beads. During heating, impurities tend to 0013 The surface may be constructed entirely of the migrate towards the Surface of the material, reducing the substantially pure silica, or may comprise a layer of sub Surface area available for binding nucleic acids. Stantially pure Silica mounted on top of a flat Surface Such as 0005 Electrostatic interactions between the nucleic acids glass or metal. The Substantially pure Silica may be adhered and the Surface result in a fraction of the nucleic acids to the flat Surface by an adhesive, applied using a Solvent, or becoming nonspecifically bound to the Surface. This may cast directly onto the flat Surface. result in nucleic acids “laying down” or orienting them 0014 Substantially pure silica may be purchased from a Selves parallel to the Surface, rather than being perpendicular commercial Supplier, may be prepared de novo, or may be to the Surface. This orientation reduces or eliminates the prepared by purifying Silica containing impurities. Methods ability of the bound nucleic acid to interact with other for treating and purifying Silica fibers are taught in U.S. Pat. nucleic acids in Solution, and additionally may result in the No. 5,951,295. These methods may be used to purify com blockage of other covalent bonding sites on the Surface. mercial or prepared Silica materials So as to render them 0006 There exists a need for improved materials for the Substantially pure. The purified Silica materials may then be preparation of nucleic acids bound to Surfaces, and methods used to prepare the Surfaces described herein. to improve the Specific covalent bonding of nucleic acids to 0015 The surface may be used to bind generally any Surfaces. nucleic acids, preferably DNA or RNA, and more preferably DNA. The nucleic acids may be bound to the surface using SUMMARY OF THE INVENTION any acceptable chemical method. Chemical reactions for the 0007 Surfaces containing high purity silica (silicon diox covalent bonding of nucleic acids to Surfaces containing ide) exhibit high loading potential for nucleic acids. Silica are known in the art. 0008 Formulations containing nucleic acids and materi 0016. An additional embodiment of the invention relates als which mask the electroStatic interactions between the to formulations Suitable for the binding of nucleic acids to nucleic acids and Surfaces are disclosed. By masking the Surfaces. Formulations are prepared comprising nucleic phosphate charges of the nucleic acids, undesired interac acids and a charged material. The charged material prefer tions may be minimized or eliminated, thereby allowing the ably is partially or fully cationic. The charged material may covalent bonding of the nucleic acids to the Surface to generally be any partially or fully positively charged mate proceed. The use of Such formulations additionally mini rial Suitable for interaction with the phosphate groups of mizes nonspecific binding of the nucleic acids to the Surface. nucleic acids. Examples of Suitable charged materials Examples of materials to be included in Such formulations include Xanthines, hexoses, purines, arginine, lysine, pol include cations, Xanthines, heXOSes, purines, arginine, yarginine, polylysine, and quaternary ammonium Salts. The lysine, polyarginine, polylysine, and quaternary ammonium Xanthine may generally be any Xanthine, and preferably is Salts. Other materials Such as amines may be used if the pH Xanthine, 1,3,7-trimethylxanthine (caffeine), 1,3,9-trimeth of the formulation is such that the material is positively ylxanthine, 1,3-diethyl-7-methylxanthine, 1,3-diethyl-8- charged. phenylxanthine, 1,3-dimethyl-7-(2-hydroxyethyl)xanthine, US 2002/0103350 A1 Aug. 1, 2002

1,3-dimethylxanthine-7-acetic acid, 1,3-dipropyl7-methylx used to covalently bond the nucleic acids to the Surface in anthine, 1,3-dipropyl-8-p-Sulfophenylxanthine, 1,7-dimeth the presence of the formulation. ylxanthine, 1,7-dimethylxanthine (paraxanthine), 1,9-dim 0020. The charged material in the formulation reduces ethylxanthine, 1-allyl-3,7-dimethyl-8-phenylxanthine, nonspecific binding of the nucleic acids to the Surface 1-allyl-3,7-dimethyl-8-p-sulfophenylxanthine, 1-butyl-4,5- relative to nonspecific binding of nucleic acids to the Surface dihydro-3-ethyl-8-hydroxyXanthine, 1-ethyl-3-isobutylxan in the absence of the charged material. Preferably, the thine, 1-methylxanthine, 2,6-dithiopurine, 2'-deoxyinosine, method Substantially eliminates nonspecific binding of the 3,7-dimethyl-1-propargylxanthine, 3,7-dimethylxanthine, nucleic acids to the Surface, and more preferably eliminates 3,8-dimethyl-2-thioxanthine, 3,9-dimethylxanthine, 3-allyl nonspecific binding of the nucleic acids to the Surface. After 1-ethyl-8-hydroxyxanthine, 3-cyclopropyl-1-ethyl-8-hy the contacting Step, the charged material may be removed, droxy Xanthine, 3-ethyl-1-propylxanthine, 3-ethyl-8-hy e.g. by a Washing Step. droxy-1-methylxanthine, 3-isobutyl-1-methylxanthine, 3-isobutyl-1-methylxanthine, 3-isobutyl-1-methylxanthine, 0021 All of the compositions and/or methods disclosed 3-isobutyl-1-methylxanthine, 3-methyl-1-(5-oxohexyl)-7- and claimed herein can be made and executed without undue propylxanthine, 3-methyl-8-phenyl-2-thiohypoxanthine, experimentation in light of the present disclosure. While the 3-methylxanthine, 3-propylxanthine, 6-thiohypoxanthine, compositions and methods of this invention have been 6-thioxanthine, 7-methylxanthine, 8-(3-carboxypropyl)-1,3- described in terms of preferred embodiments, it will be dimethylxanthine, 8-azaxanthine monohydrate, 8-bromo-1, apparent to those of Skill in the art that variations may be 3-diethylxanthine, 8-cyclopentyl-1,3-dimethylxanthine, applied to the compositions and/or methods and in the Steps 8-cyclopentyl-1,3-dipropylxanthine, 8-methoxymethyl-3- or in the Sequence of Steps of the methods described herein isobutyl-1-methylxanthine, 8-methylxanthine, 9-methylxan without departing from the concept, Spirit and Scope of the thine, azaserine-hypoxanthine, hypoxanthine, hypoxanthine invention. More specifically, it will be apparent that certain 9-beta-d-arabinofuranoside, hypoxanthine 9-d-ribofurano agents which are both chemically and physiologically Side (inosine), nicotinamide hypoxanthine dinucleotide related may be Substituted for the agents described herein phosphate, nicotinamide hypoxanthine dinucleotide phoS while the same or similar results would be achieved. All phate disodium Salt, nicotinamide hypoxanthine dinucle Such similar Substitutes and modifications apparent to those otide Sodium Salt, Selenohypoxanthine, or Xanthosine. The skilled in the art are deemed to be within the Spirit, Scope and hexose may generally be any hexose, and preferably is alose, concept of the invention. altrose, fructose, galactose, glucose, mannose, Sorbose, taga What is claimed is: tose, or talose, and more preferably is glucose. The hexose 1. A material consisting essentially of: may be the D- or L-isomer. The purine may generally be any purine, and preferably is purine, 6-purinecarbonitrile, 6-pu Silica; and rinethiol, or 6-purinethiol riboside. The quaternary ammo nucleic acids covalently bonded to the Silica. nium Salt may generally be any quaternary ammonium Salt, 2. The material of claim 1, wherein the nucleic acids are and preferably is benzyltriethyl ammonium chloride DNA (BTEAC), benzyltrimethyl ammonium chloride (BTMAC), 3. The material of claim 1, wherein the material is a flat benzyltributyl ammonium chloride (BTBAC), tetrabutyl Surface. ammonium bromide (TBAB), tetramethyl ammonium chlo 4. The material of claim 1, wherein the material is a bead. ride (TMAC), tetrabutyl ammonium hydrogensulfate 5. The material of claim 1, wherein the material is an array (TBAHS), trioctylmethyl ammonium chloride (TOMAC), of fibers. N-lauryl pyridinium chloride (PYLC), or N-alkyl- (pyri 6. The material of claim 1, wherein the silica is at least dinium/picolinium) chloride. about 80% pure silicon dioxide. 7. The material of claim 1, wherein the Silica is at least 0.017. The charged material may serve multiple roles in about 90% pure silicon dioxide. the formulation, e.g. a Surfactant may also interact with the 8. The material of claim 1, wherein the Silica is at least phosphate groups of nucleic acids. The charged material about 95% pure silicon dioxide. may be affected by the pH of the formulation, e.g. amines 9. The material of claim 1, wherein the silica is pure may be protonated at low pH and deprotonated at high pH. Silicon dioxide. The formulation is preferably a homogeneous mixture, and 10. A material consisting of: more preferably is a homogeneous aqueous mixture. Silica; and 0.018. The charged material “masks” the charged phos phate groups of the nucleic acids, reducing or eliminating nucleic acids covalently bonded to the Silica. the potential for nonspecific binding of the nucleic acids to 11. The material of claim 10, wherein the nucleic acids are the Silica Surface by electrostatic attraction. As a result, the DNA amount of nucleic acids nonspecifically binding to the 12. The material of claim 10, wherein the material is a flat Surface is reduced or eliminated. Surface. 13. The material of claim 10, wherein the material is a 0019. An additional embodiment of the invention is a bead. method for the binding of nucleic acids to a Surface. The 14. The material of claim 10, wherein the material is an method generally involves contacting the above described array of fibers. formulation with a Surface containing Silica. A particularly 15. The material of claim 10, wherein the silica is at least preferred embodiment involves contacting the above about 80% pure silicon dioxide. described formulation with a Surface consisting essentially 16. The material of claim 10, wherein the silica is at least of Silica. Any acceptable chemical methodology may be about 90% pure silicon dioxide. US 2002/0103350 A1 Aug. 1, 2002

17. The material of claim 10, wherein the silica is at least 3-methylxanthine, 3-propylxanthine, 6-thiohypoxanthine, about 95% pure silicon dioxide. 6-thioxanthine, 7-methylxanthine, 8-(3-carboxypropyl)-1,3- 18. The material of claim 10, wherein the silica is pure dimethylxanthine, 8-azaxanthine monohydrate, 8-bromo-1, Silicon dioxide. 3-diethylxanthine, 8-cyclopentyl-1,3-dimethylxanthine, 19. A method for binding nucleic acids to a surface, the 8-cyclopentyl-1,3-dipropylxanthine, 8-methoxymethyl-3- method comprising: isobutyl-1-methylxanthine, 8-methylxanthine, 9-methylxan thine, azaserine-hypoxanthine, hypoxanthine, hypoxanthine providing a mixture comprising nucleic acids and a 9-beta-d-arabinofuranoside, hypoxanthine 9-d-ribofurano charged material; and Side (inosine), nicotinamide hypoxanthine dinucleotide contacting the mixture and a Surface to produce a bound phosphate, nicotinamide hypoxanthine dinucleotide phos material, wherein the bound material comprises nucleic phate disodium Salt, nicotinamide hypoxanthine dinucle acids covalently bonded to the Surface. otide Sodium Salt, Selenohypoxanthine, or Xanthosine. 20. The method of claim 19, wherein the charged material 23. The method of claim 21, wherein the hexose is alose, is a cationic material or a partially cationic material. altrose, fructose, galactose, glucose, mannose, Sorbose, taga 21. The method of claim 19, wherein the charged material tose, or talose. is a Xanthine, a hexose, a purine, arginine, lysine, polyargi 24. The method of claim 21, wherein the purine is purine, nine, polylysine, or a quaternary ammonium Salt. 6-purinecarbonitrile, 6-purinethiol, or 6-purinethiol ribo 22. The method of claim 21, wherein the Xanthine is Side. Xanthine, 1,3,7-trimethylxanthine (caffeine), 1,3,9-trimeth ylxanthine, 1,3-diethyl-7-methylxanthine, 1,3-diethyl-8- 25. The method of claim 21, wherein the quaternary phenylxanthine, 1,3-dimethyl-7-(2-hydroxyethyl)xanthine, ammonium Salt is benzyltriethyl ammonium chloride 1,3-dimethylxanthine-7-acetic acid, 1,3-dipropyl-7-meth (BTEAC), benzyltrimethyl ammonium chloride (BTMAC), ylxanthine, 1,3-dipropyl-8-p-Sulfophenylxanthine, 1,7-dim benzyltributyl ammonium chloride (BTBAC), tetrabutyl ethylxanthine, 1,7-dimethylxanthine (paraxanthine), 1.9- ammonium bromide (TBAB), tetramethyl ammonium chlo dimethylxanthine, 1-allyl-3,7-dimethyl-8-phenylxanthine, ride (TMAC), tetrabutyl ammonium hydrogensulfate 1-allyl-3,7-dimethyl-8-p-sulfophenylxanthine, 1-butyl-4,5- (TBAHS), trioctylmethyl ammonium chloride (TOMAC), dihydro-3-ethyl-8-hydroxyXanthine, 1-ethyl-3-isobutylxan N-lauryl pyridinium chloride (PYLC), or N-alkyl- (pyri thine, 1-methylxanthine, 2,6-dithiopurine, 2'-deoxyinosine, dinium/picolinium) chloride. 3,7-dimethyl-1-propargylxanthine, 3,7-dimethylxanthine, 26. The method of claim 19, wherein the Surface consists 3,8-dimethyl-2-thioxanthine, 3,9-dimethylxanthine, 3-allyl essentially of Silica. 1-ethyl-8-hydroxyxanthine, 3-cyclopropyl-1-ethyl-8-hy 27. The method of claim 19, wherein the Surface consists droxy Xanthine, 3-ethyl-1-propylxanthine, 3-ethyl-8-hy of Silica. droxy-1-methylxanthine, 3-isobutyl-1-methylxanthine, 28. The method of claim 19, further comprising removing 3-isobutyl-1-methylxanthine, 3-isobutyl-1-methylxanthine, the charged material after the contacting Step. 3-isobutyl-1-methylxanthine, 3-methyl-1-(5-oxohexyl)-7- propylxanthine, 3-methyl-8-phenyl-2-thiohypoxanthine, k k k k k