Lynx Therapeutics, Inc.

Geron Corporation

Ronald G Schultz

Sergei M Gryaznov

Jer-Kang Chen

Karen L Fearon

Bernard L Hirschbein

Sarah N McCurdy

Jeffery S Nelson

Jeffrey S Nelson

Oligonucleotides with a novel sugar-phosphate backbone containing at least one 2'-arabino-fluoronucleoside and an internucleoside 3&#x2032;-NH&#x2014;P(&#x2014;O)(OR)&#x2014;O-5&#x2032; linkage, where R is a positively charged counter ion or hydrogen, and methods of synthesizing and using the inventive oligonucleotides are provided. The inventive phosphoramidate 2&#x2032;-arabino-fluorooligonucleotides have a high RNA binding affinity to complementary nucleic acids and are base and acid stable.

2'-arabino-fluorooligonucleotide N3&#x2032;&#x2dc;P5&#x2032; phosphoramidates: their synthesis and use

2'-arabino-fluorooligonucleotide N3&#x2032;&#x2192;P5&#x2032; phosphoramidates: their synthesis and use

Oligonucleotides with a novel sugar-phosphate backbone containing at least one 2'-arabino-fluoronucleoside and an internucleoside 3&#x2032;-NH&#x2014;P(&#x2550;O)(OR)&#x2014;O-5&#x2032; linkage, where R is a positively charged counter ion or hydrogen, and methods of synthesizing and using the inventive oligonucleotides are provided. The inventive phosphoramidate 2&#x2032;-aribino-fluorooligonucleotides have a high RNA binding affinity to complementary nucleic acids and are base and acid stable.

Oligonucleotides with a novel sugar-phosphate backbone containing at least one 2'-arabino-fluoronucleoside and an internucleoside 3&#x2032;-NH&#x2014;P(&#x2550;O)(OR)&#x2014;O-5&#x2032; linkage, where R is a positively charged counter ion or hydrogen, and methods of synthesizing and using the inventive oligonucleotides are provided. The inventive phosphoramidate 2&#x2032;-arabino-fluorooligonucleotides have a high RNA binding affinity to complementary nucleic acids and are base and acid stable.

2'-arabino-fluorooligonucleotide N3&#x2032;-P5&#x2032; phosphoramidates: their synthesis and use

Modified oligonucleotides 3&prime;-NHP(O)(O,)O-5&prime; phosphoramidates were synthesized on a solid phase support. The phosphoramidate analogs were found to have significantly increased resistance toward phosphodiesterase digestion. Thermal dissociation experiments demonstrated that these compounds form more stable duplexes than phosphodiesters with complementary DNA and particularly RNA strands. Further, the phosphoramidate analogs can also form stable triplexes with double-stranded DNA target, where under similar conditions parent phosphodiester compounds failed to do so.

Oligonucleotide N3&prime;&rarr;N5&prime;Phosphoramidate Duplexes

Oligonucleotide N3'.fwdarw.P5' phosphoramidates

The invention provides a method of synthesizing oligonucleotide N3'.fwdarw.P5' phosphoramidates using an amine-exchange reaction of phosphoramidites in which a -deprotected 3'-amino group of a solid phase supported oligonucleotide chain is exhanged for the amino portion of a 5'-phosphoramidite of an incoming monomer which has a protected 3'-amino group. The resulting internucleotide phosphoramidite linkage is then oxidized to form a stable protected phosphoramidate linkage. The method of the invention greatly improves product yields and reduces reagent usage over currently available methods for synthesizing the above class of compound.

Synthons for synthesis of oligonucleotide N3-P5 phosphoramidates

Modified oligonucleotides 3'-NHP(O)(O.sup.-)O-5' phosphoramidates were synthesized on a solid phase support. The phosphoramidate analogs were found to have significantly increased resistance toward phosphodiesterase digestion. Thermal dissociation experiments demonstrated that these compounds form more stable duplexes than phosphodiesters with complementary DNA and particularly RNA strands. Further, the phosphoramidate analogs can also form stable triplexes with double-stranded DNA target, where under similar conditions parent phosphodiester compounds failed to do so.

Oligonucleotide N3'-P5' phosphoramidates: hybridization and nuclease

The invention provides a method of synthesizing oligonucleotide N3'.fwdarw.P5' phosphoramidates using an amine-exchange reaction of phosphoramidites in which a deprotected 3'-amino group of a solid phase supported oligonucleotide chain is exhanged for the amino portion of a 5'-phosphoramidite of an incoming monomer which has a protected 3'-amino group. The resulting internucleotide phosphoramidite linkage is then oxidized to form a stable protected phosphoramidate linkage. The method of the invention greatly improves product yields and reduces reagent usage over currently available methods for synthesizing the above class of compound.

Solid phase synthesis of oligonucleotide N3'-P5' phosphoramidates

Modified oligodeoxyribonucleotide 3'--NHP (O) (O.sup.-) O-5' phosphoramidates were synthesized on a solid phase support. The phosphoramidate analogs were found to have significantly increased resistance toward phosphodiesterase digestion. Thermal dissociation experiments demonstrated that these compounds form more stable duplexes than phosphodiesters with complementary DNA and particularly RNA strands. Further, the phosphoramidate analogs can also form stable triplexes with double-stranded DNA target, where under similar conditions parent phosphodiester compounds failed to do so.

Oligodeoxyribonucleotide N3' P5' phosphoramidates

A new class of oligonucleotide N3'.fwdarw.P5' phosphoramidates having 2' fluoro substituents are provided that have superior acid stability. The invention includes oligo-2'-fluoronucleotide N3'.fwdarw.P5' phosphoramidates, methods of synthesis, and duplexes and triplexes formed with DNA and RNA. Compounds of the invention are useful where the formation of stable and specific duplex and/or triplex structures is desired, including antisense and/or anti-gene pharmaceuticals, branched DNA components, DNA and/or RNA capture agents, components of DNA-based diagnostic assays, and the like.

Oligo-2'-fluoronucleotide N3'-&gt;P5' phosphoramidates

Oligonucleotide N3'.fwdarw.P5' phosphoramidates: hybridization and

Modified oligonucleotide 3'-NHP(O)(O.sup.-)O-5' phosphoramidates were synthesized on a solid phase support. The phosphoramidate analogs were found to have significantly increased resistance toward phosphodiesterase digestion. Thermal dissociation experiments demonstrated that these compounds form more stable duplexes than phosphodiesters with complementary DNA and particularly RNA strands. Further, the phosphoramidate analogs can also form stable triplexes with double-stranded DNA target, where under similar conditions parent phosphodiester compounds failed to do so.

Growing community of inventors

Urbana, MO, United States of America

Ronald G Schultz