US 2003/0073078 A1Published application

Method for the recognition of translating genetic coding sequences

OwnerDavid Ian Rosnick, Donald L. Bitzer +2inventors

InventorsDavid Ian Rosnick, Donald L. Bitzer, Mladen A. Vouk, Eleboba Eni May

Life of this patent

Estimating the term…

Loading patent…

Abstract

Computer-based methods are useful for screening a nucleic acid sequence for efficient translation in a predetermined host. These methods involve providing a 3′-end terminal ribosomal nucleic acid (rRNA) sequence, providing a substrate nucleic acid sequence, and detecting the presence or absence of a three-base binding strength (i.e., binding energy) periodic cycle and/or phase between the ribosomal nucleic acid sequence and the substrate nucleic acid sequence through the substrate nucleic acid sequence. The presence of the three base periodic binding strength cycle and/or correct phase through the substrate nucleic acid sequence indicates that the substrate nucleic acid sequence is a candidate for efficient translation in the host.

Claims37

Dependent claims

A computer-based method for screening a nucleic acid sequence for efficient translation in a predetermined host, said method comprising the steps of:

(a) providing a ribosomal nucleic acid sequence, said ribosomal nucleic acid sequence comprising a continuous segment of from 6 to 15 bases of the first 15 bases closest to the 3′ end of the 16S or 18S rRNA ribosomal subunit of said host;
(b) providing a substrate nucleic acid sequence;
(c) determining a first binding strength of said ribosomal nucleic acid sequence to said substrate nucleic acid sequence at a first alignment of interest in the substrate;
(d) determining a second binding strength of said ribosomal nucleic acid sequence to said substrate nucleic acid sequence at a second alignment of interest;
wherein said second substrate alignment of interest is one base downstream from said first alignment of interest;
(e) determining a third binding strength of said ribosomal nucleic acid sequence to said substrate nucleic acid sequence at a third alignment of interest, wherein said third substrate alignment of interest is two bases downstream from said first alignment of interest;
(f) successively repeating steps (c) through (e) along said substrate nucleic acid sequence, wherein the first alignment of interest in each successive step (c) is three bases downstream of the first alignment of interest in the immediately preceding step (c), until a binding strength is determined at every alignment of said substrate nucleic acid sequence;
(g) generating a binding strength pattern from said first through third binding strengths determined in said successively repeated steps (c) through (e);
and
(h) detecting the presence or absence of a three-base binding strength periodic cycle and phase through said substrate nucleic acid sequence from said binding strength pattern, the presence of said three base periodic binding strength cycle and correct phase through said substrate nucleic acid sequence indicating said substrate nucleic acid sequence is a candidate for efficient translation in said host.

7 more elements

A system for screening a nucleic acid sequence for efficient translation in a predetermined host, comprising:

(a) means for providing a ribosomal nucleic acid sequence, said ribosomal nucleic acid sequence comprising a continuous segment of from 6 to 15 bases of the first 15 bases closest to the 3′ end of the 16S or 18S rRNA ribosomal subunit of said host;
(b) means for providing a substrate nucleic acid sequence;
(c) means for determining a first binding strength of said ribosomal nucleic acid sequence to said substrate nucleic acid sequence at a first alignment of interest in the substrate;
(d) means for determining a second binding strength of said ribosomal nucleic acid sequence to said substrate nucleic acid sequence at a second alignment of interest;
wherein said second substrate alignment of interest is one base downstream from said first alignment of interest;
(e) means for determining a third binding strength of said ribosomal nucleic acid sequence to said substrate nucleic acid sequence at a third alignment of interest, wherein said third substrate alignment of interest is two bases downstream from said first alignment of interest;
(f) means for successively repeating steps (c) through (e) along said substrate nucleic acid sequence, wherein the first alignment of interest in each successive step (c) is three bases downstream of the first alignment of interest in the immediately preceding step (c), until a binding strength is determined at every alignment of said substrate nucleic acid sequence;
(g) means generating a binding strength pattern from said first through third binding strengths determined in said successively repeated steps (c) through (e);
and
(h) means for detecting the presence or absence of a three-base binding strength periodic cycle and phase through said substrate nucleic acid sequence from said binding strength pattern, the presence of said three base periodic binding strength cycle and correct phase through said substrate nucleic acid sequence indicating said substrate nucleic acid sequence is a candidate for efficient translation in said host.

7 more elements

A computer program product for screening a nucleic acid sequence for efficient translation in a predetermined host, said computer program product comprising a computer usable storage medium having computer readable program code means embodied in the medium, the computer readable program code means comprising:

(a) means for providing a ribosomal nucleic acid sequence, said ribosomal nucleic acid sequence comprising a continuous segment of from 6 to 15 bases of the first 15 bases closest to the 3′ end of the 16S or 18S rRNA ribosomal subunit of said host;
(b) means for providing a substrate nucleic acid sequence;
(c) means for determining a first binding strength of said ribosomal nucleic acid sequence to said substrate nucleic acid sequence at a first alignment of interest in the substrate;
(d) means for determining a second binding strength of said ribosomal nucleic acid sequence to said substrate nucleic acid sequence at a second alignment of interest;
wherein said second substrate alignment of interest is one base downstream from said first alignment of interest;
(e) means for determining a third binding strength of said ribosomal nucleic acid sequence to said substrate nucleic acid sequence at a third alignment of interest, wherein said third substrate alignment of interest is two bases downstream from said first alignment of interest;
(f) means for successively repeating steps (c) through (e) along said substrate nucleic acid sequence, wherein the first alignment of interest in each successive step (c) is three bases downstream of the first alignment of interest in the immediately preceding step (c), until a binding strength is determined at every alignment of said substrate nucleic acid sequence;
(g) means for generating a binding strength pattern from said first through third binding strengths determined in said successively repeated steps (c) through (e);
and
(h) means for detecting the presence or absence of a three-base binding strength periodic cycle and phase through said substrate nucleic acid sequence from said binding strength pattern, the presence of said three base periodic binding strength cycle and correct phase through said substrate nucleic acid sequence indicating said substrate nucleic acid sequence is a candidate for efficient translation in said host.

7 more elements

A computer-based method for screening a nucleic acid sequence for the presence of at least one coding sequence therein, said method comprising the steps of:

(a) providing a substrate nucleic acid sequence from a predetermined host;
(b) providing a ribosomal nucleic acid sequence, said ribosomal nucleic acid sequence comprising a continuous segment of from 6 to 15 bases of the first 15 bases closest to the 3′ end of the 16S or 18S rRNA ribosomal subunit of said host;
(c) determining a first binding strength of said ribosomal nucleic acid sequence to said substrate nucleic acid sequence at a first alignment of interest;
(d) determining a second binding strength of said ribosomal nucleic acid sequence to said substrate nucleic acid sequence at a second alignment of interest;
wherein said second alignment of interest is one base downstream from said first alignment of interest;
(e) determining a third binding strength of said ribosomal nucleic acid sequence to said substrate nucleic acid sequence at a third alignment of interest, wherein said third alignment of interest is two bases downstream from said first alignment of interest;
(f) successively repeating steps (c) through (e) along said substrate nucleic acid sequence, wherein the first alignment of interest in each successive step (c) is three bases downstream of the first alignment of interest in the immediately preceding step (c), until a binding strength is determined at every alignment of said substrate nucleic acid sequence;
(g) generating a binding strength pattern from said first through third binding strengths determined in said successively repeated steps (c) through (e);
and
(h) detecting the presence or absence of a three-base binding strength periodic cycle and phase in at least one portion of the said substrate nucleic acid sequence from said binding strength pattern, the presence of said three base periodic binding strength cycle through said substrate nucleic acid sequence indicating said at least one portion of said nucleic acid sequence is a coding portion in said host.

7 more elements

A system for screening a nucleic acid sequence for the presence of at least one coding sequence therein, comprising:

(a) means for providing a substrate nucleic acid sequence from a predetermined host;
(b) means for providing a ribosomal nucleic acid sequence, said ribosomal nucleic acid sequence comprising a continuous segment of from 6 to 15 bases of the first 15 bases closest to the 3′ end of the 16S or 18S rRNA ribosomal subunit of said host;
(c) means for determining a first binding strength of said ribosomal nucleic acid sequence to said substrate nucleic acid sequence at a first alignment of interest;
(d) means for determining a second binding strength of said ribosomal nucleic acid sequence to said substrate nucleic acid sequence at a second alignment of interest;
wherein said second alignment of interest is one base downstream from said first alignment of interest;
(e) means for determining a third binding strength of said ribosomal nucleic acid sequence to said substrate nucleic acid sequence at a third alignment of interest, wherein said third alignment of interest is two bases downstream from said first alignment of interest;
(f) means for successively repeating steps (c) through (e) along said substrate nucleic acid sequence, wherein the first alignment of interest in each successive step (c) is three bases downstream of the first alignment of interest in the immediately preceding step (c), until a binding strength is determined at every alignment of said substrate nucleic acid sequence;
(g) means for generating a binding strength pattern from said first through third binding strengths determined in said successively repeated steps (c) through (e);
and
(h) means for detecting the presence or absence of a three-base binding strength periodic cycle and phase in at least one portion of the said substrate nucleic acid sequence from said binding strength pattern, the presence of said three base periodic binding strength cycle through said substrate nucleic acid sequence indicating said at least one portion of said nucleic acid sequence is a coding portion in said host.

7 more elements

A computer program product for screening a nucleic acid sequence for the presence of at least one coding sequence therein, said computer program product comprising a computer usable storage medium having computer readable program code means embodied in the medium, the computer readable program code means comprising:

(a) means for providing a substrate nucleic acid sequence from a predetermined host;
(b) means for providing a ribosomal nucleic acid sequence, said ribosomal nucleic acid sequence comprising a continuous segment of from 6 to 15 bases of the first 15 bases closest to the 3′ end of the 16S or 18S rRNA ribosomal subunit of said host;
(c) means for determining a first binding strength of said ribosomal nucleic acid sequence to said substrate nucleic acid sequence at a first alignment of interest;
(d) means for determining a second binding strength of said ribosomal nucleic acid sequence to said substrate nucleic acid sequence at a second alignment of interest;
wherein said second alignment of interest is one base downstream from said first alignment of interest;
(e) means for determining a third binding strength of said ribosomal nucleic acid sequence to said substrate nucleic acid sequence at a third alignment of interest, wherein said third alignment of interest is two bases downstream from said first alignment of interest;
(f) means for successively repeating steps (c) through (e) along said substrate nucleic acid sequence, wherein the first alignment of interest in each successive step (c) is three bases downstream of the first alignment of interest in the immediately preceding step (c), until a binding strength is determined at every alignment of said substrate nucleic acid sequence;
(g) means for generating a binding strength pattern from said first through third binding strengths determined in said successively repeated steps (c) through (e);
and
(h) means for detecting the presence or absence of a three-base binding strength periodic cycle and phase in at least one portion of the said substrate nucleic acid sequence from said binding strength pattern, the presence of said three base periodic binding strength cycle through said substrate nucleic acid sequence indicating said at least one portion of said nucleic acid sequence is a coding portion in said host.

7 more elements

Dependencies are inferred from the claim text.

Facts

Application: 09/905,289Filed 13 Jul 2001
Priority: 21 Jul 2000
Published: 17 Apr 2003
Term ends: Not estimatedThe source records don’t support an estimate.

Classification5 codes

G16B 35/20
ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides: screening of libraries
G16B 35/00
Ict specially adapted for in silico combinatorial libraries of nucleic acids, proteins
G16C 20/60
Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds…
G16B
Bioinformatics, i.e. information and communication technology [ict] specially adapted for genetic or

Family

Application60/219,887Us provisional application · filed 21 Jul 2000
US 2003/0073078 A1This patent

From the US filing history. Foreign family members aren’t listed.

Timeline

Citations

Open elsewhere

Building an agent or pulling many patents? Use the API or MCP server instead of scraping pages. Get an API key