Double-stranded DNA molecule for the detecting and characterizing molecular interactions

Patent metadata

Field	Value
Publication number	US-12455284-B2
Application number	US-201816955596-A
Country	US
Kind code	B2
Filing date	Dec 21, 2018
Priority date	Dec 21, 2017
Publication date	Oct 28, 2025
Grant date	Oct 28, 2025

Abstract

The present application relates to a double-stranded DNA molecule comprising a first double-stranded DNA molecule (1) connected to a second double-stranded DNA molecule (2) by at least one covalent bond which is not a phosphodiester, phosphorothioate, phosphoramidate or phosphorodiamidate bond, preferably by a tether, said tether preferably being a double-stranded DNA molecule.

First claim

The invention claimed is:

1. A double-stranded DNA molecule comprising a first double-stranded DNA molecule (1) connected to a second double-stranded DNA molecule (2) by a tether comprising double-stranded DNA, wherein the tether is attached by
(i) at least one covalent bond to a first nucleotide in the first double-stranded DNA molecule (1), and by
(ii) at least one covalent bond to a second nucleotide in the second double-stranded DNA molecule (2),

wherein
the at least one covalent bond of (i) and the at least one covalent bond of (ii) are not phosphodiester bonds, phosphorothioate bonds, phosphoramidate bonds or phosphorodiamidate bonds,
the first nucleotide in the first double-stranded DNA molecule (1) is neither the 5′-terminal nor the 3′-terminal nucleotide of either strand of the first double-stranded DNA molecule (1), and
the second nucleotide in the second double-stranded DNA molecule (1) is neither the 5′-terminal nor the 3′-terminal nucleotide of either strand of the second double-stranded DNA molecule (2);

and wherein
the first double-stranded DNA molecule (1) and the second double-stranded DNA molecule (2) are in linear form;
the first double-stranded DNA molecule (1) and/or the second double-stranded DNA molecule (2) has a length of 300 to 5000 base pairs; and
the tether has a length of 300 to 50,000 base pairs.

2. The double-stranded DNA molecule according to claim 1 , wherein the tether consists of a double-stranded DNA molecule.

3. The double-stranded DNA molecule according to claim 1 ,
wherein the tether is attached to
the first double-stranded DNA molecule (1) by first covalent bond(s) between at least one nucleotide of a first double-stranded DNA extremity of the tether and at least one nucleotide of an intermediate region of the first double-stranded DNA molecule (1),

and to
the second double-stranded DNA molecule (2) by second covalent bond(s) between at least one nucleotide of a second double-stranded DNA extremity of the tether and at least one nucleotide of an intermediate region of the second double-stranded DNA molecule (2).

4. The double-stranded DNA molecule according to claim 1 , wherein
a first test molecule is linked to a nucleotide of a first double-stranded DNA extremity of the first double-stranded DNA molecule (1) and
a second test molecule is linked to a nucleotide of a first double-stranded DNA extremity of the second double-stranded DNA molecule (2),
wherein the first extremity of the first double-stranded DNA molecule (1) and/or the first extremity of the second double-stranded DNA molecule (2) has a length of 10 to 150 base pair.

5. The double-stranded DNA molecule according to claim 4 , wherein
the second double-stranded DNA extremity of the first double-stranded DNA molecule (1) is linked to a first support and
the second double-stranded DNA extremity of the second double-stranded DNA molecule (2) is linked to a second support,
wherein said supports are surface or solid substrates, at least one of them being a moveable support.

6. The double-stranded DNA molecule according to claim 4 , wherein the first and/or second test molecule
is selected from the group consisting
of amino acids, peptides, polypeptides, and proteins.

7. A device comprising the double-stranded DNA molecule according to claim 1 , wherein the first and second double-stranded DNA molecules (1) and (2) are specifically attached to supports which are surface or solid substrates, and wherein at least one of the supports is a moveable support.

8. A double-stranded DNA molecule comprising a first double-stranded DNA molecule (A) and a second double-stranded DNA molecule (B), wherein
the first double-stranded DNA molecule (A) comprises a cleavage site which is present only in the first double-stranded DNA molecule (A),
the first double-stranded DNA molecule (A) is connected to the second double-stranded DNA molecule (B) by two covalent bonds which are not phosphodiester bonds, phosphorothioate bonds, phosphoramidate bonds or phosphorodiamidate bonds, and
the two covalent bonds are located on either side of the cleavage site.

9. A process for manufacturing a double-stranded DNA molecule according to claim 1 , comprising a step of:
a) cleaving a precursor molecule of the first and second double-stranded DNA molecules (1) and (2) at a cleavage site that is present only in the precursor molecule, thereby generating a double-stranded DNA molecule comprising a first double-stranded DNA molecule (1) and a second double-stranded DNA molecule (2).

10. The double-stranded DNA molecule according to claim 5 , wherein at least one of the two supports is a movable support.

11. The double-stranded DNA molecule according to claim 1 , wherein the first double-stranded DNA molecule (1) and/or the second double-stranded DNA molecule (2) has a length of 650 to 1500 base pairs.

12. The double-stranded DNA molecule according to claim 4 , wherein the first extremity of the first double-stranded DNA molecule (1) and/or the first extremity of the second double-stranded DNA molecule (2) has a length of 30 to 50 base pairs.

13. The double-stranded DNA molecule according to claim 4 , wherein the first and/or second test molecule is selected from the group consisting of nucleosides, nucleotides, polynucleotides, and oligonucleotides.

Assignees

• Paris Sciences Et Lettres—Quartier Latin
• Centre Nat Rech Scient
• Ecole Normale Superieure
• Univ Paris
• Inst Nat Sante Rech Med

Inventors

• Strick Térence
• Gosse Charlie
• Kostrz Dorota
• Wang Jinglong
• Nadal Marc

Classifications

• G01Q60/24

  AFM [Atomic Force Microscopy] or apparatus therefor, e.g. AFM probes · CPC title

• G01N33/6803

  General methods of protein analysis not limited to specific proteins or families of proteins · CPC title

• C12Q1/6825

  Nucleic acid detection involving sensors · CPC title

• G01N33/54373 Primary

  involving physiochemical end-point determination, e.g. wave-guides, FETS, gratings · CPC title

• C12Q1/6806 Primary

  Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay (C12Q1/6804 takes precedence) · CPC title