In vitro process for producing multiple nucleic acid copies

• US 20050123926A1
• Filed: 11/14/2003
• Published: 06/09/2005
• Est. Priority Date: 01/13/1994
• Status: Abandoned Application

• Current Assignee: Enzo Biochem Incorporated
• Original Assignee: Enzo Diagnostics, Inc.
• Inventors: Stavrianopoulos, Jannis G., Donegan, James J., Rabbani, Elazar, Engelhardt, Dean L.
• Application Number:
  US10/713,183
• Publication Number:
  US 20050123926A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12N 15/10 Processes for the isolation, preparation or purification of DNA or RNA chemical preparation of DNA or RNA C07H21/00; preparation of non-structural polynucleotides from microorganisms or with enzymes C12P19/34
• CPC Class Codes: C12P 19/34 Polynucleotides, e.g. nucleic acids, oligoribonucleotides
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 1/6853 using modified primers or templates
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/6865 Promoter-based amplification, e.g. nucleic acid sequence amplification [NASBA], self-sustained sequence replication [3SR] or transcription-based amplification system [TAS]
• CPC Class Codes: C12Q 2521/119 RNA polymerase
• CPC Class Codes: C12Q 2525/203 incorporating a composite nucleic acid containing a polypeptide sequence other than PNA

Abstract

This invention provides inter alia an in vitro process for producing multiple specific nucleic acid copies in which the copies are produced under isostatic conditions, e.g., temperature, buffer and ionic strength, and independently of any requirement for introducing an intermediate structure for producing the copies. In other aspects, the invention provides in vitro processes for producing multiple specific nucleic acid copies in which the products are substantially free of any primer-coded sequences, such sequences having been substantially or all removed from the product to regenerate a primer binding site, thereby allowing new priming events to occur and multiple nucleic acid copies to be produced. This invention further provides a promoter-independent non-naturally occurring nucleic acid construct that produces a nucleic acid copy or copies without using or relying on any gene product that may be coded by the nucleic acid construct. Another aspect of this invention concerns a protein-nucleic acid construct in the form of a conjugate linked variously, e.g., covalent linkage, complementary nucleic acid base-pairing, nucleic acid binding proteins, or ligand receptor binding. Further disclosed in this invention is an in vivo process for producing a specific nucleic acid in which such a protein-nucleic acid construct conjugate is introduced into a cell. A still further aspect of the invention relates to a construct comprising a host promoter, second promoter and DNA sequence uniquely located on the construct. The host transcribes a sequence in the construct coding for a different RNA polymerase which after translation is capable of recognizing its cognate promoter and transcribing from a DNA sequence of interest in the construct with the cognate promoter oriented such that it does not promote transcription from the construct of the different. RNA polymerase.

Claims

1. (canceled)

119. The process of claim 118, wherein said polymerases derived from thermophilic bacteria comprise Taq DNA polymerase.

120. The process of claim 112, wherein said mixture recited in step (b) comprises nucleic acid precursors, one or more specific labeled polynuclotide primers, or a combination of both.

132. The process of claim 131, wherein said heteroatoms comprise nitrogen or sulfur.

2-90. -90. (canceled)

91. An in vitro process for producing more than one copy of nucleic acids of interest, said process comprising the steps of:

(a) providing a nucleic acid sample containing said nucleic acids of interest;

(b) contacting said sample with a mixture comprising;

(i) nucleic acid precursors;

(ii) one or more specific polynucleotide primers comprising at least one ribonucleic acid segment, each of which primer comprises a sequence complementary to a distinct sequence of said nucleic acids of interest;

(iii) an effective amount of a nucleic acid producing catalyst; and

(iv) RNase H; and

(c) carrying out nucleic acid synthesis, thereby generating multiple copies of said nucleic acids of interest.

92. The process of claim 91, wherein said primers (ii) comprise modified nucleotides, unmodified nucleotides or a combination thereof.

93. The process of claim 91, wherein said primers (ii) comprise sequences noncomplementary to said distinct sequence of said nucleic acids of interest.

94. The process of claim 93, wherein said primers (ii) comprise from about 1 to about 200 noncomplementary nucleotides or nucleotide analogs.

95. The process of claim 91, wherein said primers (ii) further comprise deoxyribonucleotides.

96. The process of claim 91, wherein said nucleic acid producing catalyst (iii) comprises DNA polymerase, RNA polymerase, reverse transcriptase or a combination thereof.

97. The process of claim 96, wherein said DNA polymerase comprises E. coli DNA polymerase I, Klenow polymerase, polymerases derived from thermophilic bacteria or a combination thereof.

98. The process of claim 97, wherein said polymerases derived from thermophilic bacteria comprise Taq DNA polymerase.

99. The process of claim 91, wherein said mixture recited in step (b) comprises nucleic acid precursors, one or more specific labeled polynucleotide primers or a combination of both.

100. The process of claim 91, wherein said primers comprise a 3′

-hydroxyl group or an isosteric configuration of heteroatoms.

101. The process of claim 100, wherein said heteroatoms comprise nitrogen or sulfur.

141. The process of claim 91, wherin said mixture recited in step (b) comprises nucleic acid precursors, one or more specific labeled polynuclotide primers or a combination of both.

142. The process of claim 141, wherein said primers comprise from about 1 to 200 noncomplementary nucleotides or nucleotide analogs.

102. An in vitro process for producing more than one copy of nucleic acids of interest, said process comprising the steps of:

(a) providing a nucleic acid sample containing or suspected of containing said nucleic acids of interest;

(b) contacting said sample with a mixture comprising;

(i) nucleic acid precursors;

(ii) one or more specific polynucleotide primers comprising at least one ribonucleic acid segment and at least one deoxyribonucleic acid segment, each of which primer comprises a sequence complementary to a distinct sequence of said nucleic acids of interest;

(iii) an effective amount of a nucleic acid producing catalyst; and

(iv) RNase H; and

(c) allowing nucleic acid synthesis to be carried out, thereby generating multiple copies of said nucleic acids of interest.

103. The process of claim 102, wherein said primers comprise modified nucleotides, unmodified nucleotides or a combination of both.

104. The process of claim 102, wherein said primers comprise sequences noncomplementary to said distinct sequence of said nucleic acids of interest.

105. The process of claim 104, wherein said primers comprise from about 1 to about 200 noncomplementary nucleotides or nucleotide analogs.

106. The process of claim 102, wherein said nucleic acid producing catalyst (iii) comprises DNA polymerase, RNA polymerase, reverse transcriptase or a combination theerof.

107. The process of claim 106, wherein said DNA polymerase comprises E. coli DNA polymerase I, Klenow polymerase, polymerases derived from thermophilic bacteria, or a combination thereof.

108. The process of claim 107, wherein said polymerases derived from thermophilic bacteria comprise Taq DNA polymerase.

109. The process of claim 102, wherin said mixture recited in step (b) comprises nucleic acid precursors, one or more specific labeled polynuclotide primers, or a combination of both.

110. The process of claim 102, wherein said primers (ii) contain a 3′

-hydroxyl group or an isosteric configuration of heteroatoms.

111. The process of claim 110, wherein said heteroatoms comprise nitrogen or sulfur.

112. An in vitro process for producing more than one copy of nucleic acids of interest, said process comprising the steps of:

(a) providing a nucleic acid sample containing said nucleic acids of interest;

(b) contacting said sample with a mixture comprising;

(i) nucleic acid precursors;

(ii) one or more specific polynucleotide primers comprising at least one ribonucleic acid segment, each of which primer comprises a sequence complementary to a distinct sequence of said nucleic acids of interest;

(iii) an effective amount of a nucleic acid producing catalyst; and

(iv) RNase H; and

(c) carrying out nucleic acid synthesis to produce a polynucleotide comprising an RNA/DNA hybrid, thereby generating a substrate for RNase H;

(d) digesting said substrate with RNase H to remove said ribonucleic acid segment and allow another primer binding event to occur, thereby producing multiple copies of said nucleic acids of interest.

113. The process of claim 112, wherein said primers (ii) comprise modified nucleotides, unmodified nucleotides or a combination thereof.

114. The process of claim 112, wherein said primers (ii) comprise sequences noncomplementary to said distinct sequence of said nucleic acids of interest.

115. The process of claim 114, wherein said primers (ii) comprise from about 1 to 200 noncomplementary nucleotides or nucleotide analogs.

116. The process of claim 112, wherein said primers (ii) further comprise deoxyribonucleotides,

117. The process of claim 112, wherein said nucleic acid producing catalysts (iii) comprise DNA polymerase, RNA polymerase, reverse transcriptase or a combination thereof.

118. The process of claim 117, wherein said DNA polymerase comprises E. coli DNA polymerase I, Klenow polymerase, polymerases derived from thermophilic bacteria or a combination thereof.

121. The process of claim 112, wherein said primers (ii) contain a 3′

-hydroxyl group or an isosteric configuration of heteroatoms.

122. The process of claim 121, wherein said heteroatoms comprise nitrogen or sulfur.

123. A process for multiply initiating polynucleotide or oligonucleotide synthesis comprising:

(a) providing nucleic acids of interest;

(b) contacting said sample with a mixture comprising;

(i) nucleic acid precursors;

(ii) one or more specific copolymer primers comprising at least one DNA segment and at least one RNA segment, each of which primer comprises a sequence complementary to a distinct sequence of said nucleic acid of interest;

(iii) an effective amount of a nucleic acid producing catalyst; and

(iv) RNase H; and

(c) producing at least one copy of said nucleic acid of interest by using said nucleic acid producing catalyst (iii) and said nucleic acids of interest as templates; and

d) removing said RNA segment from said template by digesting with RNase H to bind another primer and initiate synthesis, thereby mulitiply initiating polynucleotide or oligonucleotide synthesis.

124. The process of claim 123, wherein said primers comprise modified nucleotides, unmodified nucleotides or a combination thereof.

125. The process of claim 123, wherein said primers further comprise sequences that are noncomplementary to said distinct sequence of said nucleic acids of interest.

126. The process of claim 125, wherein said primers comprise from about 1 to 200 noncomplementary nucleotides or nucleotide analogs.

127. The process of claim 123, wherein the nucleic acid producing catalyst (iii) comprises DNA polymerase, RNA polymerase, reverse transcriptase or a combination thereof.

128. The process of claim 127, wherein said DNA polymerase comprises E. coli DNA polymerase I, Klenow polymerase, polymerases derived from thermophilic bacteria or a combination thereof.

129. The process of claim 128, wherein said polymerases derived from thermophilic bacteria comprise Taq DNA polymerase.

130. The process of claim 123, wherein said mixture recited in step (b) comprises nucleic acid precursors, one or more specific labeled polynucleotide primers or a combination of both.

131. The process of claim 123, wherein said primers contain a 3′

-hydroxyl group or an isosteric configuration of heteroatoms.

133. An in vitro process for producing more than one copy of RNA of interest, said process comprising the steps of:

(a) providing a nucleic acid sample containing said RNA of interest;

(b) contacting said sample containing with a mixture comprising;

(i) nucleic acid precursors;

(ii) one or more polynucleotide primers wherein said primers comprise (A) at least one ribonucleic acid segment and (B) a sequence complementary to a distinct sequence in said RNA of interest;

(iii) an effective amount of a nucleic acid producing catalyst; and

(iv) RNase H;

(c) producing at least one DNA copy from said RNA of interest;

(d) using said DNA copy as a template to produce a double-stranded copy comprising a second copy complementary to said DNA copy produced in step (c); and

(e) removing said ribonucleic acid segment of said primers with RNase H from said double-stranded copy produced in step (d) to regenerate a primer binding site, thereby allowing a new priming event to occur and producing more than one copy of said RNA of interest.

134. The process of claim 133, wherein said primers (ii) comprise modified nucleotides, unmodified nucleotides or a combination thereof.

135. The process of claim 133, wherein said primers (ii) further comprise sequences noncomplementary to said distinct sequence of said RNA of interest.

136. The process of claim 135, wherein said primers (ii) further comprise from about 1 to 200 noncomplementary nucleotides or nucleotide analogs.

137. The process of claim 133, wherein said primers (ii) further comprise deoxyribonucleotides.

138. The process of claim 133, wherein said nucleic acid producing catalysts (iii) comprise DNA polymerase, RNA polymerase, reverse transcriptase or a combination thereof.

139. The process of claim 138, wherein said DNA polymerase comprises E. coli DNA polymerase I, Klenow polymerase, polymerases derived from thermophilic bacteria, or a combination thereof.

140. The process of claim 139, wherein said polymerases derived from thermophilic bacteria comprise Taq DNA polymerase.