Abstract: The present invention provides fluorescent nucleoside analogs which comprise a fluorescent cyclic compound joined to a carbon of a sugar molecule such as pentose, hexose, ribose or deoxyribose or analogs thereof in either an &agr; or &bgr; configuration. The subject compounds are useful as probes in the study of the structure and dynamics of nucleic acids and their complexes with proteins. In addition, the subject compounds are useful in any technique which uses labeled oligonucleotides for detection. Non-fluorescent spacer molecules in which a cyclohexane, cyclohexene, decalin, or benzene is joined to a carbon of a sugar moiety such as pentose, hexose, ribose or deoxyribose are also provided. Also provided are the 5′ dimethoxytrityl-3′-O-phosphoramidite derivatives, suitable for incorporation into oligonucleotides by automated synthesizers.

Abstract: Telomere-encoding nucleic acid nanocircles, methods for their preparation, and methods for their use are disclosed. The nanocircles can be constructed containing multiple repeats of the complement of telomere repeat sequences. The telomere-encoding nanocircles are useful for extending telomeres both in vitro and in vivo, for treating macular degeneration, the effects of skin aging, liver degeneration, and cancer. The nanocircles are further useful for treating cell cultures to produce long-lived non-cancerous cell populations. This use has wide applicability in scientific research, tissue engineering, and transplantation.

Abstract: The present invention provides methods for synthesis and therapeutic use of DNA and RNA oligonucleotides and analogs. RNA oligonucleotides are synthesized using a small, circular DNA template which lacks an RNA polymerase promoter sequence. The RNA synthesis is performed by combining a circular single-stranded oligonucleotide template with an effective RNA polymerase and at least two types of ribonucleotide triphosphate to form an RNA oligonucleotide multimer comprising multiple copies of the desired RNA oligonucleotide sequence. Preferably, the RNA oligonucleotide multimer is cleaved to produce RNA oligonucleotides having well-defined ends. Preferred RNA oligonucleotide multimers contain ribozymes capable of both cis (autolytic) and trans cleavage.

Abstract: The present invention provides fluorescent nucleoside analogs which comprise a fluorescent cyclic compound joined to a carbon of a sugar molecule such as pentose, hexose, ribose or deoxyribose or analogs thereof in either an &agr; or &bgr; configuration. The subject compounds are useful as probes in the study of the structure and dynamics of nucleic acids and their complexes with proteins. In addition, the subject compounds are useful in any technique which uses labeled oligonucleotides for detection. Non-fluorescent spacer molecules in which a cyclohexane, cyclohexene, decalin, or benzene is joined to a carbon of a sugar moiety such as pentose, hexose, ribose or deoxyribose are also provided. Also provided are the 5′ dimethoxytrityl-3′-O-phosphoramidite derivatives, suitable for incorporation into oligonucleotides by automated synthesizers.

Abstract: The present invention provides fluorescent nucleoside analogs which comprise a fluorescent cyclic compound joined to a carbon of a sugar molecule such as pentose, hexose, ribose or deoxyribose or analogs thereof in either an &agr; or &bgr; configuration. The subject compounds are useful as probes in the study of the structure and dynamics of nucleic acids and their complexes with proteins. In addition, the subject compounds are useful in any technique which uses labeled oligonucleotides for detection. Non-fluorescent spacer molecules in which a cyclohexane, cyclohexene, decalin, or benzene is joined to a carbon of a sugar moiety such as pentose, hexose, ribose or deoxyribose are also provided. Also provided are the 5′ dimethoxytrityl-3′ -O-phosphoramidite derivatives, suitable for incorporation into oligonucleotides by automated synthesizers.

Abstract: The present invention provides methods for synthesis and therapeutic use of DNA and RNA oligonucleotides and analogs. RNA oligonucleotides are synthesized using a small, circular DNA template which lacks an RNA polymerase promoter sequence. The RNA synthesis is performed by combining a circular single-stranded oligonucleotide template with an effective RNA polymerase and at least two types of ribonucleotide triphosphate to form an RNA oligonucleotide multimer comprising multiple copies of the desired RNA oligonucleotide sequence. Preferably, the RNA oligonucleotide multimer is cleaved to produce RNA oligonucleotides having well-defined ends. Preferred RNA oligonucleotide multimers contain ribozymes capable of both cis (autolytic) and trans cleavage.

Abstract: The present invention provides fluorescent nucleosides carrying polycyclic aromatic hydrocarbons such as anthracene, phenanthrene, pyrene stilbene, tetracene or pentacene. The subject nucleosides may be synthesized using a C-glycosidic bond formation method employing organocadmium or organozinc derivatives of the aromatic compounds and coupling with a 1-&agr;-chlororibose or deoxyribose synthon. The &agr;-anomers of the coupling reaction may be epimerized to the &bgr;-anomers by acid-catalyzed equilibration. The fluorescent nucleosides act as DNA or RNA base analogs and can be incorporated into nucleic acids. Resultant fluorescently tagged nucleic acids are useful as probes for target nucleic acids in tissues, solutions or immobilized on membranes.

Abstract: The present invention provides fluorescent nucleosides carrying polycyclic aromatic hydrocarbons such as anthracene, phenanthrene, pyrene stilbene, tetracene or pentacene. The subject nucleosides may be synthesized using a C-glycosidic bond formation method employing organocadium or organozinc derivatives of the aromatic compounds and coupling with a 1-.alpha.-chlororibose or deoxyribose synthon. The .alpha.-anomers of the coupling reaction may be epimerized to the .beta.-anomers by acid-catalyzed equilibration. The fluorescent nucleosides act as DNA or RNA base analogs and can be incorporated into nucleic acids. Resultant fluorescently tagged nucleic acids are useful as probes for target nucleic acids in tissues, solutions or immobilized on membranes.

Abstract: The present invention provides methods for synthesis, and therapeutic use of DNA and RNA oligonucleotides and analogs. RNA oligonucleotides arc synthesized using a small, circular DNA template which lacks an RNA polymerase promoter sequence. The RNA synthesis is performed by combining a circular single-stranded oligonucleotide template with an effective RNA polymerase and at least two types of ribonucleotide triphosphate to form an RNA oligonucleotide multimer comprising multiple copies of the desired RNA oligonucleotide sequence. Preferably, the RNA oligonucleotide multimer is cleaved to produce RNA oligonucleotides having well-defined ends. Preferred RNA oligonucleotide multimers contain ribozymes capable of both cis (autolytic) and trans cleavage.

Abstract: The present invention provides detectably labeled RNA and DNA oligonucleotide multimers useful as diagnostic probes in medical, biological and chemical applications. A method for synthesizing DNA and RNA oligonucleotides, oligonucleotide multimers, and analogs, preferably those that are detectably labeled, is also provided. Oligonucleotide synthesis is performed by combining a circular single-stranded oligonucleotide template with an effective polymerase and at least two types of nucleotide triphosphate, without the addition of auxiliary proteins, to yield an oligonucleotide multimer comprising multiple copies of a repeated oligonucleotide sequence.

Abstract: The present invention provides single-stranded circular oligonucleotides each with at least one parallel binding (P) domain and/or at least one corresponding anti-parallel binding (AP) domain separated from each other by loop domains. When more than one P or AP domain is included in a circular oligonucleotide of the present invention, the additional P or AP domains can constitute loop domains for a pair of corresponding P and AP domains, and vice versa. The present invention further provides single-stranded circular oligonucleotides with at least one Hoogsten antiparallel (HAP) domain. Each P, AP and HAP domain has sufficient complementarity to bind to one strand of a defined nucleic acid target wherein the P domain binds in a parallel manner to the target and the HAP or AP domain binds in an anti-parallel manner to the target. Moreover, the present single-stranded circular oligonucleotides can bind to both single-stranded and double-stranded target nucleic acids.

Abstract: The present invention provides stem-loop oligonucleotides containing a double-stranded stem domain of at least about 2 base pairs and a single-stranded loop domain. The loop domains of the present oligonucleotides include at least one parallel binding (P) domain separated by at least about 3 nucleotides from a corresponding anti-parallel binding (AP) domain. Each P and corresponding AP domain of the present oligonucleotides can bind detectably to one strand of a defined nucleic acid target wherein the P domain binds in a parallel manner to the target and the corresponding AP domain binds in an anti-parallel manner to the target. The present stem-loop oligonucleotides can bind to both single-stranded and double-stranded target nucleic acids. The present invention also provides methods of using these oligonucleotides as well as kits and pharmaceutical compositions containing these oligonucleotides.

Abstract: The present invention provides methods for synthesis, selection, and amplification of DNA and RNA oligonucleotides and analogs. The method for synthesizing an oligonucleotide involves: providing an effective amount of an isolated circular oligonucleotide template which comprises at least one copy of the desired oligonucleotide sequence linked to a cleavage site; providing an effective amount of an isolated oligonucleotide primer; annealing the primer to the circular template to form a primed circular template; and combining the primed circular template with an effective amount of at least two types of nucleotide triphosphates and an effective amount of a polymerase enzyme to form a nucleotide multimer complementary to the circular oligonucleotide template, wherein the nucleotide multimer comprises multiple copies of the oligonucleotide sequence joined end to end. Preferably, the nucleotide multimer is cleaved to produce oligonucleotides having well-defined ends.

Abstract: The present invention provides single-stranded circular oligonucleotides each with at least one parallel binding (P) domain and/or at least one corresponding anti-parallel binding (AP) domain separated from each other by loop domains. When more than one P or AP domain is included in a circular oligonucleotide of the present invention, the additional P or AP domains can constitute loop domains for a pair of corresponding P and AP domains, and vice versa. The present invention further provides single-stranded circular oligonucleotides with at least one Hoogsten antiparallel (HAP) domain. Each P, AP and HAP domain has sufficient complementarity to bind to one strand of a defined nucleic acid target wherein the P domain binds in a parallel manner to the target and the HAP or AP domain binds in an anti-parallel manner to the target. Moreover, the present single-stranded circular oligonucleotides can bind to both single-stranded and double-stranded target nucleic acids.

Abstract: The present invention provides stem-loop and circular oligonucleotides each with at least one Watson-Crick binding (WC) domain and at least one corresponding Hoogsteen binding (H) domain separated from each other by linker domains. Each WC domain has sufficient complementarity to bind to one strand of a defined nucleic acid target by Watson-Crick base pairing in an anti-parallel orientation. Each corresponding H domain is capable of binding to the WC domain by Hoogsteen base pairing in an anti-parallel manner. The present invention also provides methods of making and using these oligonucleotides as well as kits and pharmaceutical compositions containing these oligonucleotides.

Abstract: The present invention provides stem-loop oligonucleotides containing a double-stranded stem domain of at least about 2 base pairs and a single-stranded loop domain. The loop domains of the present oligonucleotides include at least one parallel binding (P) domain separated by at least about 3 nucleotides from a corresponding anti-parallel binding (AP) domain. Each P and corresponding AP domain of the present oligonucleotides can bind detectably to one strand of a defined nucleic acid target wherein the P domain binds in a parallel manner to the target and the corresponding AP domain binds in an anti-parallel manner to the target. The present stem-loop oligonucleotides can bind to both single-stranded and double-stranded target nucleic acids. The present invention also provides methods of using these oligonucleotides as well as kits and pharmaceutical compositions containing these oligonucleotides.

Abstract: The present invention provides single-stranded circular oligonucleotides each with at least one parallel binding (P) domain and at least one corresponding anti-parallel binding (AP) domain separated from each other by loop domains. When more than one P or AP domain is included in a circular oligonucleotide of the present invention, the additional P or AP domains can constitute loop domains for a pair of corresponding P and AP domains, and vice versa. Each P and AP domain has sufficient complementarity to bind to one strand of a defined nucleic acid target wherein the P domain binds in a parallel manner to the target and the corresponding AP domain binds in an anti-parallel manner to the target. Moreover, the present single-stranded circular oligonucleotides can bind to both single-stranded and double-stranded target nucleic acids. The present invention also provides methods of making and using these oligonucleotides as well as kits and pharmaceutical compositions containing these oligonucleotides.

Abstract: Hydrogen sulfide and mercaptans are scavenged from materials, especially fluids, by contacting the fluids with maleimides.