Short Optimally Capped Duplex DNA as Conformationally Restricted Analogue of B‐DNA

Abstract

We describe the synthesis of short double-stranded DNA fragments (see 4 and 13) which are capped on both ends by an optimally designed linker molecule. The new structures are stable with respect to hybrid dissociation and should have implications in physical studies involving double-stranded DNA as well as in the antisense area for the specific modulation of gene expressions.1. Introduction. -Physical studies on DNA and DNA complexes with proteins/peptides or small molecules are mainly performed on oligonucleotide duplexes in order to decrease complexity. A drawback with oligonucleotides is that they often show a dynamic behavior with respect to hybridization, oligomer formation, and stem loop structures. One way to overcome these limitations is by cross-linking the two single-stranded DNA fragments. This may be achieved oiu internal disulfide cross-links, but this approach might disturb the instrinsic properties of the oligonucleotide double strand [ 11. Another possible solution is cyclic DNA with a complementary region. However, this creates dumbbell-like structures with loop formation on both sides adjacent to the complementary region thus hampering optimal hybridization [2] [3] (Fig. l a ) . A recently described stabilization of duplex DNA makes use of a hairpin structure which is cross-linked at the end by a disulfide bridge [4].

Nucleic Acid Selection and the Challenge of Combinatorial Chemistry

“…Alternatively, dumbbells can be made chemically by phosphorylating during solidphase synthesis and ligating using either 1-[3-(dimethylamino)propyl]-3-ethylcarbodiimide hydrochloride (EDC) 87 or CNBr. 88 alkyl tethers of varying lengths (3-to 5-atoms) are positioned at the N 6 of adenosine (26), 105 the N 2 of guanosine (27), 106 or the N 4 of cytosine (28). 107,108 The resultant disulfides occupy the grooves of the helix (Figure 7).…”

NMR studies of DNA duplexes singly cross-linked by different synthetic linkers

“…Other approaches involve the incorporation of a covalently-closed base pair (bp) at one end of the duplex (3,4) or cross-linking steps after the oligonucleotide synthesis (5-10). More recently several groups have proposed introducing synthetic linkers as phosphoramidite building blocks during DNA synthesis, with linkers of hexaethylene glycol (11), triethylene glycol (12), 1,3-dihydroxy-propane or 1,9-dihydroxynonane (12), alkyl chains containing the terephthalamide group (13) or two 1,3-dipropanol units connected by a phosphate group (14). This technique was also used to synthesize DNA dumbbells with two synthetic linkers at each end of a duplex, with the linkers being 1,3-dihydroxy-dodecane (15) or two 1,3-dihydroxy-propane moieties connected by a phosphate group (14).…”

“…More recently several groups have proposed introducing synthetic linkers as phosphoramidite building blocks during DNA synthesis, with linkers of hexaethylene glycol (11), triethylene glycol (12), 1,3-dihydroxy-propane or 1,9-dihydroxynonane (12), alkyl chains containing the terephthalamide group (13) or two 1,3-dipropanol units connected by a phosphate group (14). This technique was also used to synthesize DNA dumbbells with two synthetic linkers at each end of a duplex, with the linkers being 1,3-dihydroxy-dodecane (15) or two 1,3-dihydroxy-propane moieties connected by a phosphate group (14). For the hexaethylene glycol linker it has been qualitatively demonstrated that no large structural perturbations are introduced since the lac repressor and its N-terminal headpiece bind with similar characteristics to a mini-operator linked by hexaethylene glycol or to the operator fragment containing no linker (16).…”

High definition polyphosphoesters: between nucleic acids and plastics

“…This was first performed using 2 x C3 units to create 'sausage DNA' which showed a Tm 40 °C higher than the uncapped version. 33 HEG has been used to link two T-rich sequences into an elongated cyclic structure which then bound a third strand, raising Tm of the triplex by 16 °C. HEG also shows benefits for linear, folded, triplex structures, giving an 18 °C increase in Tm.…”