Nucleic acid sequences responsive to creatinine in clinically useful ranges

Patent metadata

Field	Value
Publication number	US-2025277800-A1
Application number	US-202418592917-A
Country	US
Kind code	A1
Filing date	Mar 1, 2024
Priority date	Mar 1, 2024
Publication date	Sep 4, 2025
Grant date	—

Abstract

Aptamers and methods for detecting a target molecule/analyte in a sample are disclosed herein. The aptamer can include a single-stranded deoxyribonucleic acid (DNA) strand that includes an oligonucleotide sequence with bases identical at least about 60% to TAATTGTGGTTCGTGTAAA (SEQ ID NO: 1). The aptamer can be configured to bind the target molecule/analyte with a dissociation constant between about 10−9 and about 10−3 M.

First claim

What is claimed is:

1 . An aptamer for detecting a target molecule/analyte in a sample comprising a single-stranded deoxyribonucleic acid (DNA) strand that includes an oligonucleotide sequence with bases identical at least about 60% to TAATTGTGGTTCGTGTAAA (SEQ ID NO: 1), wherein the aptamer is configured to bind the target molecule/analyte with a dissociation constant between about 10 −9 and about 10 −3 M.

2 . The aptamer of claim 1 , wherein the target molecule/analyte is creatinine.

3 . The aptamer of claim 1 , wherein the single-stranded DNA strand comprises at least about fifteen bases.

4 . The aptamer of claim 1 , wherein the aptamer comprises at least one modification.

5 . The aptamer of claim 4 , wherein the at least one modification is selected from the group consisting of atom substitution, neutralization of negative charges, introduction of positive charges, and combinations thereof.

6 . The aptamer of claim 4 , wherein the at least one modification is a modified base, wherein the modified base is selected from the group consisting of a ribonucleic acid (RNA), a modified RNA, a modified DNA, a peptide nucleic acid (PNA), and combinations thereof.

7 . The aptamer of claim 1 , wherein the sample comprises blood, serum, effluent, saliva, sweat, tears, or combinations thereof.

8 . The aptamer of claim 1 , wherein the aptamer comprises a functional group, wherein the functional group comprises thiols, phosphothiols, carboxyl, amines, carbonyls, aldehydes, alkynes, azides, alkenes, strained alkenes, tetrazines, and/or products thereof.

9 . The aptamer of claim 1 , wherein the aptamer is a stem-loop aptamer that includes a capture region and a stem region, wherein the stem region is configured to be positioned to transform a second conformation into a stem-loop structure of the aptamer, or stem-loop structure into a second conformation when the oligonucleotide sequence binds to the target molecule/analyte.

10 . The aptamer of claim 1 , wherein the aptamer is modified or configured to be immobilized to a substrate for sensing the target molecule/analyte.

11 . The aptamer of claim 9 , wherein the stem-loop structure is modified to move away from the substrate upon binding to the target molecule/analyte.

12 . The aptamer of claim 9 , wherein the stem-loop structure is modified to approach to the substrate upon binding to the target molecule/analyte.

13 . The aptamer of claim 1 , wherein the aptamer is configured to be incorporated into a sensor device, wherein the sensor device comprises a field-effect transistor and the aptamer.

14 . The aptamer of claim 1 , wherein the aptamer is configured to be incorporated into a sensor device, wherein the sensor device comprises a gold substrate and the aptamer.

15 . The aptamer of claim 1 , wherein the aptamer is configured to be incorporated into a sensor device, wherein the sensor device comprises a fiber-optical cable and the aptamer.

16 . The aptamer of claim 1 , wherein the aptamer is configured to be incorporated into a sensor device, wherein the sensor device comprises a quartz surface and the aptamer.

17 . The aptamer of claim 1 , wherein the aptamer is configured to the target molecule/analyte without being freely diffused.

18 . The aptamer of claim 13 , wherein the sensor device comprises a freely diffusing molecular with a molecular weight between about 1,000 D and about 1,000,000 D.

19 . The aptamer of claim 1 , wherein the aptamer is attached to a fluorophore, a quencher, an enzyme, a redox dye, or combinations thereof.

20 . The aptamer of claim 1 , wherein the sample is a diluted sample, wherein the diluted sample is a sample diluted up to about 1%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 90%, 100%, 200%, 300%, 400%, 500%, 600%, 700%, 800%, 900%, or 1000% with a solution.

21 . The aptamer of claim 1 , wherein the sample is a non-diluted sample.

22 . A method for detecting a target molecule/analyte in a sample, comprising:
contacting at least a portion of the sample with effective amounts of an aptamer, wherein the aptamer comprises a single-stranded deoxyribonucleic acid (DNA) strand that includes an oligonucleotide sequence with bases identical at least about 60% to TAATTGTGGTTCGTGTAAA (SEQ ID NO: 1), wherein the aptamer is configured to bind the target molecule/analyte with a dissociation constant between about 10 −9 and about 10 −3 M, detecting a change after the contacting.

23 . The method of claim 22 , wherein the change comprises a change of conductance, fluorescence, and/or any electrochemical readouts.

24 . The method of claim 22 , wherein the target molecule/analyte is creatinine.

25 . The method of claim 22 , wherein the sample comprises blood, plasma, serum, effluent, saliva, sweat, tears, or combinations thereof.

26 . The method of claim 22 , wherein the aptamer is a stem-loop aptamer that includes a capture region and a stem region, wherein the stem region is configured to be positioned to transform a stem-loop structure of the aptamer to a second conformation when the oligonucleotide sequence binds to the target molecule/analyte.

27 . The method of claim 22 , wherein the aptamer is configured to be immobilized to a substrate for sensing the target molecule/analyte.

28 . The method of claim 27 , wherein the substrate comprises gold and/or quartz.

29 . The method of claim 26 , wherein the stem-loop structure is modified to move away from the substrate upon binding to the target molecule/analyte so the conductance of the substrate changes.

30 . The method of claim 26 , wherein the stem-loop structure is modified to approach to the substrate upon binding to the target molecule/analyte so the conductance of the substrate changes.

31 . The method of claim 22 , wherein the aptamer is attached to a fluorophore, a quencher, an enzyme, a redox dye, or combinations thereof.

32 . The method of claim 22 , wherein the sample is a diluted sample, wherein the sample is a diluted sample, wherein the diluted sample is a sample diluted up to about 1%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 90%, 100%, 200%, 300%, 400%, 500%, 600%, 700%, 800%, 900%, or 1000% with a solution.

33 . The method of claim 22 , wherein the sample is a non-diluted sample.

34 . The method of claim 22 , further comprising
diagnosing a kidney disease based on the detected level of creatinine in the sample, and providing a subject with a treatment based on the detected level of creatinine in the sample.

35 . The method of claim 34 , wherein a level of the treatment is enhanced with an increased creatinine level detected by the aptamer.

36 . The method of claim 34 , wherein a level of the treatment is lowered with a decreased creatinine level detected by the aptamer.

37 . The method of claim 22 , further comprising sensing the target molecule/analyte at a predetermined frequency.

38 . The method of claim 37 , the predetermined frequency comprises once every hour, once every ten minutes, once every minute, once every second, or any predetermined period in between.

Assignees

• Univ Columbia

Inventors

• Stojanovic Milan
• Milosavic Nenad
• Mohan Sumit
• Jovicic Jovan
• Stevens Jacob

Classifications

• G01N33/5308

  for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites · CPC title

• C12N2310/16

  Aptamers · CPC title

• C12N2310/531

  Stem-loop; Hairpin · CPC title

• C12N15/115

  Aptamers, i.e. nucleic acids binding a target molecule specifically and with high affinity without hybridising therewith {; Nucleic acids binding to non-nucleic acids, e.g. aptamers} · CPC title

• G01N33/70 Primary

  involving creatine or creatinine · CPC title