Methods and devices based upon a novel form of nucleic acid duplex on a surface

A method for identifying a nucleotide sequence to which a nucleotide-binding protein binds comprising:

• contacting the biomolecular hybridization device with a nucleotide-binding protein under conditions that permit binding;
• wherein the biomolecular hybridization device comprises:
• a substrate having a surface of functional groups permanently and covalently attached thereto;
• and
• an adsorbed monolayer of unmodified, single-stranded oligonucleotides all of which are about 30 bases in length as a saturated film of constrained oligonucleotides on the surface via direct non-covalent phosphate-surface adsorptive contact of substantially all phosphate groups of each oligonucleotide;
• wherein the constrained oligonucleotides each have a targeted, hybridizing domain of 10 to about 24 bases and a non-targeted, non-hybridizing domain of bases flanking one or both of the 5′ or 3′ ends thereof such that each constrained oligonucleotide base plane within the targeted domain is presented from the surface in a manner effective to dissociably hybridize to a complementary single-stranded nucleic acid target with asymmetric, non-helical base pairing without alteration of the oligonucleotide base plane presentation and without oligonucleotide phosphate group dissociation from the surface;
• a single-stranded nucleic acid reversibly hybridized to at least one of said single-stranded oligonucleotides as a non-helical duplex of 10 to about 24 base pairs long adsorbed to the surface;
• eluting formed duplex-protein complex(es) from the surface with a salt solution with an ionic strength of an aqueous solution of from about 1 M to about 5 M NaCl;
• and
• sequencing at least one strand of the eluted nucleic acid duplex.

A method for identifying a nucleotide sequence to which a nucleotide-binding protein binds comprising:

• contacting the biomolecular hybridization device with a nucleotide-binding protein under conditions that permit binding;
• wherein the biomolecular hybridization device comprises:
• a substrate having an aminosilanized surface permanently and covalently attached thereto;
• and
• an adsorbed monolayer of unmodified single-stranded oligonucleotides all of which comprise 10 to 24 bases in length adsorbed to the aminosilanized surface as a saturated film of constrained oligonucleotides on the surface via direct non-covalent phosphate-surface adsorptive contact of substantially all phosphate groups of each oligonucleotide at a density of one phosphate group per about 0.5 square nanometers to less than about 1 square nanometer of surface, wherein each constrained oligonucleotide base plane is presented from the surface in a manner effective to dissociably hybridize to a complementary single-stranded nucleic acid with asymmetric, non-helical base pairing without alteration of the oligonucleotide base plane presentation and without oligonucleotide phosphate group dissociation from the surface;
• a single-stranded nucleic acid reversibly hybridized to at least one of said single-stranded oligonucleotides as a non-helical duplex of 10 to about 24 base pairs long adsorbed to the surface;
• eluting formed duplex-protein complex(es) from the surface with a salt solution with an ionic strength of an aqueous solution of from about 1 M to about 5 M NaCl;
• and
• sequencing at least one strand of the eluted nucleic acid duplex.