Oligonucleotides form a duplex with non-helical properties on a positively charged surface

@article{Lemeshko2001, abstract = {The double helix is known to form as a result of hybridization of complementary nucleic acid strands in aqueous solution. In the helix the negatively charged phosphate groups of each nucleic acid strand are distributed helically on the outside of the duplex and are available for interaction with cationic groups. Cation-coated glass surfaces are now widely used in biotechnology, especially for covalent attachment of cDNAs and oligonucleotides as surface-bound probes on microarrays. These cationic surfaces can bind the nucleic acid backbone electrostatically through the phosphate moiety. Here we describe a simple method to fabricate DNA microarrays based upon adsorptive rather than covalent attachment of oligonucleotides to a positively charged surface. We show that such adsorbed oligonucleotide probes form a densely packed monolayer, which retains capacity for base pair-specific hybridization with a solution state DNA target strand to form the duplex. However, both strand dissociation kinetics and the rate of DNase digestion suggest, on symmetry grounds, that the target DNA binds to such adsorbed oligonucleotides to form a highly asymmetrical and unwound duplex. Thus, it is suggested that, at least on a charged surface, a non-helical DNA duplex can be the preferred structural isomer under standard biochemical conditions. 10.1093/nar/29.14.3051}, author = {Lemeshko, S. V. and Powdrill, T. and Belosludtsev, Y. Y. and Hogan, M. }, citeulike-article-id = {2414037}, doi = {http://dx.doi.org/10.1093/nar/29.14.3051}, journal = {Nucl. Acids Res.}, keywords = {background, mica-dna-afm, non-helical-dna, origami}, month = {July}, number = {14}, pages = {3051--3058}, posted-at = {2008-02-22 11:58:08}, priority = {2}, title = {Oligonucleotides form a duplex with non-helical properties on a positively charged surface}, url = {http://dx.doi.org/10.1093/nar/29.14.3051}, volume = {29}, year = {2001} }

TY - JOUR ID - Lemeshko2001 L3 - citeulike-article-id:2414037 TI - Oligonucleotides form a duplex with non-helical properties on a positively charged surface JF - Nucl. Acids Res. VL - 29 IS - 14 SP - 3051 EP - 3058 N2 - The double helix is known to form as a result of hybridization of complementary nucleic acid strands in aqueous solution. In the helix the negatively charged phosphate groups of each nucleic acid strand are distributed helically on the outside of the duplex and are available for interaction with cationic groups. Cation-coated glass surfaces are now widely used in biotechnology, especially for covalent attachment of cDNAs and oligonucleotides as surface-bound probes on microarrays. These cationic surfaces can bind the nucleic acid backbone electrostatically through the phosphate moiety. Here we describe a simple method to fabricate DNA microarrays based upon adsorptive rather than covalent attachment of oligonucleotides to a positively charged surface. We show that such adsorbed oligonucleotide probes form a densely packed monolayer, which retains capacity for base pair-specific hybridization with a solution state DNA target strand to form the duplex. However, both strand dissociation kinetics and the rate of DNase digestion suggest, on symmetry grounds, that the target DNA binds to such adsorbed oligonucleotides to form a highly asymmetrical and unwound duplex. Thus, it is suggested that, at least on a charged surface, a non-helical DNA duplex can be the preferred structural isomer under standard biochemical conditions. 10.1093/nar/29.14.3051 KW - background KW - mica-dna-afm KW - non-helical-dna KW - origami AU - Lemeshko, SV AU - Powdrill, T AU - Belosludtsev, YY AU - Hogan, M PY - 2001/07/15/ UR - http://dx.doi.org/10.1093/nar/29.14.3051 ER -