In vitro processes for producing multiple copies of primer sequence-free specific nucleic acid

• US 20050123927A1
• Filed: 11/19/2003
• Published: 06/09/2005
• Est. Priority Date: 01/13/1994
• Status: Abandoned Application

• Current Assignee: Enzo Diagnostics, Inc.
• Original Assignee: Enzo Diagnostics, Inc.
• Inventors: Stavrianopoulos, Jannis G., Donegan, James J., Rabbani, Elazar, Engelhardt, Dean L.
• Application Number:
  US10/718,391
• Publication Number:
  US 20050123927A1
• 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)

2-90. -90. (canceled)

91. An in vitro process for producing more than one copy of a specific nucleic acid, said products being substantially free of any primer sequences, said process comprising the steps of:

(a) providing a nucleic acid sample containing or suspected of containing the sequence of said specific nucleic acid;

(b) contacting said sample with a mixture comprising;

(i) unmodified nucleic acid precursors,

(ii) one or more specific chemically-modified primers each of which primer is substantially complementary to a distinct sequence of said specific nucleic acid, and

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

(c) allowing said mixture to react under isostatic conditions of temperature, buffer and ionic strength to produce at least one copy of said specific nucleic acid; and

(d) removing all primer sequences from the product produced in step (c) to regenerate a primer binding site, thereby allowing a new priming event to occur and producing more than one copy of said specific nucleic acid.

92. The process of claim 91, wherein said removing step (d) is carried out by digestion with an enzyme.

93. The process of claim 92, wherein said enzyme comprises ribonuclease H.

94. The process of claim 91, wherein said specific chemically modified primers comprise ribonucleic acid, deoxyribonucleic acid, a DNA.RNA copolymer, a polymer capable of hybridizing or forming a base-specific pairing complex and initiating nucleic acid polymerization, or a combination of any of the foregoing.

95. The process of claim 91, wherein said specific chemically modified primers comprise a 3′

-hydroxyl group or an isosteric configuration of heteroatoms.

96. The process of claim 95, wherein said heteroatoms comprise nitrogen or sulfur.

97. The process of claim 91, wherein said specific chemically modified primers comprise nucleoside triphosphates, nucleoside triphosphate analogs, or a combination thereof, wherein at least one of said nucleoside triphosphates or analogs is modified on the sugar, phosphate or base.

98. The process of claim 91, wherein said specific chemically modified primers further comprise from about 1 to about 200 noncomplementary nucleotide or nucleotide analogs.

99. An in vitro process for producing more than one copy of a specific nucleic acid, said products being free of any primer sequences, said process comprising the steps of:

(a) providing a nucleic acid sample containing or suspected of containing the sequence of said specific nucleic acid;

(b) contacting said sample with a mixture comprising;

(i) unmodified nucleic acid precursors,

(ii) one or more specific unmodified primers each of which primer comprises at lease one non-complementary sequence to a distinct sequence of said specific nucleic acid, such that upon hybridization to said specific nucleic acid at least one loop structure is formed, and

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

(c) allowing said mixture to react under isostatic conditions of temperature, buffer and ionic strength, thereby producing at least one copy of said specific nucleic acid; and

(d) removing primer sequences from the product produced in step (c) to regenerate a primer binding site, to allow a new priming event to occur and produce more than one copy of said specific nucleic acid.

100. The process of claim 99, wherein said removing step (d) is carried out by digestion with an enzyme.

101. The process of claim 100, wherein said enzyme comprises ribonuclease H.

102. The process of claim 99, wherein said specific unmodified primers comprise ribonucleic acid, deoxyribonucleic acid, a DNA.RNA copolymer, a polymer capable of hybridizing or forming a base-specific pairing complex and initiating nucleic acid polymerization, or a combination of any of the foregoing.

103. The process of claim 99, wherein said specific unmodified primers further comprise from about 1 to about 200 noncomplementary nucleotide or nucleotide analogs.