U.S. patent application number 14/893645 was filed with the patent office on 2016-05-12 for aptamers for the treatment of sickle cell disease.
This patent application is currently assigned to THE JOHNS HOPKINS UNIVERSITY. The applicant listed for this patent is THE JOHNS HOPKINS UNIVERSITY. Invention is credited to EMILY BARRON-CASELLA, JAMES F. CASELLA, YOLANDA FORTENBERRY, JEFFREY R. KEEFER, SHIRLEY H. PURVIS.
Application Number | 20160130585 14/893645 |
Document ID | / |
Family ID | 51989514 |
Filed Date | 2016-05-12 |
United States Patent
Application |
20160130585 |
Kind Code |
A1 |
CASELLA; JAMES F. ; et
al. |
May 12, 2016 |
APTAMERS FOR THE TREATMENT OF SICKLE CELL DISEASE
Abstract
The present invention provides polynucleotide aptamers that
selectively bind to and inhibit polymerization of sickle hemoglobin
(HbS), pharmaceutical compositions comprising the same, methods of
use for diagnostics and treatment of sickle cell disease, methods
of use as capture reagents, and methods of rational drug
design.
Inventors: |
CASELLA; JAMES F.;
(BALTIMORE, MD) ; BARRON-CASELLA; EMILY;
(BALTIMORE, MD) ; KEEFER; JEFFREY R.; (BALTIMORE,
MD) ; FORTENBERRY; YOLANDA; (BALTIMORE, MD) ;
PURVIS; SHIRLEY H.; (BALTIMORE, MD) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
THE JOHNS HOPKINS UNIVERSITY |
Baltimore |
MD |
US |
|
|
Assignee: |
THE JOHNS HOPKINS
UNIVERSITY
BALTIMORE
MD
|
Family ID: |
51989514 |
Appl. No.: |
14/893645 |
Filed: |
May 27, 2014 |
PCT Filed: |
May 27, 2014 |
PCT NO: |
PCT/US2014/039519 |
371 Date: |
November 24, 2015 |
Related U.S. Patent Documents
|
|
|
|
|
|
Application
Number |
Filing Date |
Patent Number |
|
|
61828142 |
May 28, 2013 |
|
|
|
Current U.S.
Class: |
514/44R ;
435/252.3; 435/254.11; 435/320.1; 435/325; 435/348; 435/419;
435/6.1; 436/501; 530/385; 536/23.1 |
Current CPC
Class: |
G01N 33/721 20130101;
A61P 7/00 20180101; C07K 14/805 20130101; C12N 2320/30 20130101;
C12N 2310/16 20130101; G01N 33/5308 20130101; C12N 15/115
20130101 |
International
Class: |
C12N 15/115 20060101
C12N015/115; G01N 33/53 20060101 G01N033/53; G01N 33/72 20060101
G01N033/72; C07K 14/805 20060101 C07K014/805 |
Claims
1. A polynucleotide aptamer that specifically binds sickle
hemoglobin (HbS).
2. The polynucleotide aptamer of claim 1, wherein the
polynucleotide aptamer is an RNA aptamer.
3. The polynucleotide aptamer of claim 2, wherein the
polynucleotide aptamer inhibits polymerization of HbS.
4. The polynucleotide aptamer of claim 3, wherein the
polynucleotide aptamer specifically binds oxygenated HbS
(oxy-HbS).
5. The polynucleotide aptamer claim 3, wherein the polynucleotide
aptamer specifically binds deoxygenated HbS (deoxy-HbS).
6. The polynucleotide aptamer of claim 3, wherein the
polynucleotide aptamer specifically binds both oxygenated HbS
(oxy-HbS) and deoxygenated HbS (deoxy-HbS).
7. The polynucleotide aptamer of claim 2, comprising a nucleotide
sequence selected from the group consisting of: (a) a nucleotide
sequence at least 80% identical to any one of SEQ ID NOS:2-60; (b)
a nucleotide sequence at least 90% identical to any one of SEQ ID
NOS:2-60; (c) a nucleotide sequence at least 95% identical to any
one of SEQ ID NOS:2-60; (d) a nucleotide sequence at least 99%
identical to any one of SEQ ID NOS:2-60; and (e) the nucleotide
sequence of any one of SEQ ID NOS:2-60.
8. The polynucleotide aptamer of claim 2, comprising a nucleotide
sequence selected from the group consisting of: (a) a nucleotide
sequence at least 80% identical to any one of SEQ ID NOS:2, 4, 31,
and 37; (b) a nucleotide sequence at least 90% identical to any one
of SEQ ID NOS:2, 4, 31, and 37; (c) a nucleotide sequence at least
95% identical to any one of SEQ ID NOS:2, 4, 31, and 37; (d) a
nucleotide sequence at least 99% identical to any one of SEQ ID
NOS:2, 4, 31, and 37; and (e) the nucleotide sequence of any one of
SEQ ID NOS:2, 4, 31, and 37.
9. The polynucleotide aptamer of claim 7 selected from the group
consisting of: (a) wherein when the polynucleotide aptamer is any
one of SEQ ID NOS:2, 4, or 5, the polynucleotide aptamer further
comprises a consensus sequence consisting of SEQ ID NO:61; (b)
wherein when the polynucleotide aptamer is any one of SEQ ID NOS:11
or 14, the polynucleotide aptamer further comprises a consensus
sequence consisting of SEQ ID NO:62; (c) wherein when the
polynucleotide aptamer is any one of SEQ ID NOS: 37, 38, 40, or 49,
the polynucleotide aptamer further comprises a consensus sequence
consisting of SEQ ID NO:63; (d) wherein when the polynucleotide
aptamer is any one of SEQ ID NOS: 31, 37, 38, 40, 42, 45, 46, 47,
48, 49, 53, 56, 59 or 60, the polynucleotide aptamer further
comprises a consensus sequence consisting of SEQ ID NO:64; and (e)
wherein when the polynucleotide aptamer is any one of SEQ ID NOS:
2, 4, 5, 8, 34, or 57, the polynucleotide aptamer further comprises
a consensus sequence consisting of SEQ ID NO:65.
10. The polynucleotide aptamer of claim 2, comprising a consensus
sequence consisting of a nucleotide sequence selected from the
group consisting of SEQ ID NOS:61, 62, 63, 64, and 65.
11. A polynucleotide aptamer of claim 1, wherein the polynucleotide
aptamer is modified to increase its circulating half-life after
administration to a subject.
12. A polynucleotide encoding the polynucleotide aptamer of claim
1.
13. A vector comprising the polynucleotide of claim 12.
14. A cell comprising the polynucleotide aptamer of claim 1.
15. A method of treating or preventing sickle cell disease in a
subject in need thereof, the method comprising administering to the
subject a therapeutically effective amount of a polynucleotide
aptamer that specifically binds sickle hemoglobin (HbS), wherein
the polynucleotide aptamer inhibits polymerization of HbS.
16. The method of claim 15, wherein the polynucleotide aptamer is
an RNA aptamer.
17. The method of claim 16, wherein the polynucleotide aptamer
specifically binds oxygenated HbS (oxy-HbS).
18. The method of claim 16, wherein the polynucleotide aptamer
specifically binds deoxygenated HbS (deoxy-HbS).
19. The method of claim 16, wherein the polynucleotide aptamer
specifically binds both oxygenated HbS (oxy-HbS) and deoxygenated
HbS (deoxy-HbS).
20. The method of claim 16, wherein the polynucleotide aptamer
comprises a nucleotide sequence selected from the group consisting
of: (a) a nucleotide sequence at least 80% identical to any one of
SEQ ID NOS:2-60; (b) a nucleotide sequence at least 90% identical
to any one of SEQ ID NOS:2-60; (c) a nucleotide sequence at least
95% identical to any one of SEQ ID NOS:2-60; (d) a nucleotide
sequence at least 99% identical to any one of SEQ ID NOS:2-60; and
(e) the nucleotide sequence of any one of SEQ ID NOS:2-60.
21. The method of claim 16, wherein the polynucleotide aptamer
comprises a nucleotide sequence selected from the group consisting
of: (a) a nucleotide sequence at least 80% identical to any one of
SEQ ID NOS:2, 4, 31, and 37; (b) a nucleotide sequence at least 90%
identical to any one of SEQ ID NOS:2, 4, 31, and 37; (c) a
nucleotide sequence at least 95% identical to any one of SEQ ID
NOS:2, 4, 31, and 37; (d) a nucleotide sequence at least 99%
identical to any one of SEQ ID NOS:2, 4, 31, and 37; and (e) the
nucleotide sequence of any one of SEQ ID NOS:2, 4, 31, and 37.
22. The method of either of claim 20, wherein the polynucleotide
aptamer is selected from the group consisting of: (a) wherein when
the polynucleotide aptamer is any one of SEQ ID NOS:2, 4, or 5, the
polynucleotide aptamer further comprises a consensus sequence
consisting of SEQ ID NO:61; (b) wherein when the polynucleotide
aptamer is any one of SEQ ID NOS:11 or 14, the polynucleotide
aptamer further comprises a consensus sequence consisting of SEQ ID
NO:62; (c) wherein when the polynucleotide aptamer is any one of
SEQ ID NOS: 37, 38, 40, or 49, the polynucleotide aptamer further
comprises a consensus sequence consisting of SEQ ID NO:63; (d)
wherein when the polynucleotide aptamer is any one of SEQ ID NOS:
31, 37, 38, 40, 42, 45, 46, 47, 48, 49, 53, 56, 59 or 60, the
polynucleotide aptamer further comprises a consensus sequence
consisting of SEQ ID NO:64; and (e) wherein when the polynucleotide
aptamer is any one of SEQ ID NOS: 2, 4, 5, 8, 34, or 57, the
polynucleotide aptamer further comprises a consensus sequence
consisting of SEQ ID NO:65.
23. The method of claim 16, wherein the polynucleotide aptamer
comprises a consensus sequence consisting of a nucleotide sequence
selected from the group consisting of SEQ ID NOS:61, 62, 63, 64,
and 65.
24. The method of claim 16, wherein the polynucleotide aptamer is
modified to increase its circulating half-life after administration
to the subject.
25. The method of claim 16, wherein the polynucleotide aptamer is
in a pharmaceutically acceptable carrier.
26. The method of claim 16, wherein the sickle cell disease is
sickle cell anemia.
27. The method of claim 16, further comprising contacting the
polynucleotide aptamer with an antidote.
28. The method of claim 27, wherein the antidote is an
oligonucleotide comprising a sequence complementary to at least a
portion of the polynucleotide aptamer.
29. A method for diagnosing or predicting a sickle cell disease in
a subject having or at risk of developing a sickle cell disease or
at risk of passing it on to offspring, the method comprising: (a)
obtaining a biological sample from the subject; (b) contacting the
biological sample with a polynucleotide aptamer that specifically
binds to HbS; and (c) detecting binding of the polynucleotide
aptamer with HbS in the biological sample; wherein detection of
binding of the polynucleotide aptamer with HbS in the biological
sample is indicative of the subject having or at risk of developing
a sickle cell disease or at risk of passing it on to offspring.
30. The method of claim 29, wherein the polynucleotide aptamer is
an RNA aptamer.
31. The method of claim 30, wherein the polynucleotide aptamer
specifically binds oxygenated HbS (oxy-HbS).
32. The method of claim 30, wherein the polynucleotide aptamer
specifically binds deoxygenated HbS (deoxy-HbS).
33. The method of claim 30, wherein the polynucleotide aptamer
specifically binds both oxygenated HbS (oxy-HbS) and deoxygenated
HbS (deoxy-HbS).
34. The method of claim 30, wherein the polynucleotide aptamer
comprises a nucleotide sequence selected from the group consisting
of: (a) a nucleotide sequence at least 80% identical to any one of
SEQ ID NOS:2-60; (b) a nucleotide sequence at least 90% identical
to any one of SEQ ID NOS:2-60; (c) a nucleotide sequence at least
95% identical to any one of SEQ ID NOS:2-60; (d) a nucleotide
sequence at least 99% identical to any one of SEQ ID NOS:2-60; and
(e) the nucleotide sequence of any one of SEQ ID NOS:2-60.
35. The method of claim 30, wherein the polynucleotide aptamer
comprises a nucleotide sequence selected from the group consisting
of: (a) a nucleotide sequence at least 80% identical to any one of
SEQ ID NOS:2, 4, 31, and 37; (b) a nucleotide sequence at least 90%
identical to any one of SEQ ID NOS:2, 4, 31, and 37; (c) a
nucleotide sequence at least 95% identical to any one of SEQ ID
NOS:2, 4, 31, and 37; (d) a nucleotide sequence at least 99%
identical to any one of SEQ ID NOS:2, 4, 31, and 37; and (e) the
nucleotide sequence of any one of SEQ ID NOS:2, 4, 31, and 37.
36. The method of claim 34, wherein the polynucleotide aptamer is
selected from the group consisting of: (a) wherein when the
polynucleotide aptamer is any one of SEQ ID NOS:2, 4, or 5, the
polynucleotide aptamer further comprises a consensus sequence
consisting of SEQ ID NO:61; (b) wherein when the polynucleotide
aptamer is any one of SEQ ID NOS:11 or 14, the polynucleotide
aptamer further comprises a consensus sequence consisting of SEQ ID
NO:62; (c) wherein when the polynucleotide aptamer is any one of
SEQ ID NOS: 37, 38, 40, or 49, the polynucleotide aptamer further
comprises a consensus sequence consisting of SEQ ID NO:63; (d)
wherein when the polynucleotide aptamer is any one of SEQ ID NOS:
31, 37, 38, 40, 42, 45, 46, 47, 48, 49, 53, 56, 59 or 60, the
polynucleotide aptamer further comprises a consensus sequence
consisting of SEQ ID NO:64; and (e) wherein when the polynucleotide
aptamer is any one of SEQ ID NOS: 2, 4, 5, 8, 34, or 57, the
polynucleotide aptamer further comprises a consensus sequence
consisting of SEQ ID NO:65.
37. The method of claim 30, wherein the polynucleotide aptamer
comprises a consensus sequence consisting of a nucleotide sequence
selected from the group consisting of SEQ ID NOS:61, 62, 63, 64,
and 65.
38. The method of claim 30, wherein the sickle cell disease is
sickle cell anemia.
39. The method of claim 30, wherein the biological sample comprises
whole blood, hemocytes, serum, or plasma.
40. The methods of claim 30, wherein the polynucleotide aptamer is
labeled for detection with a fluorescent, luminescent,
phosphorescent, radioactive, or colorimetric compound.
41. A method of purifying hemoglobin from a biological sample, the
method comprising: (a) providing a biological sample containing
hemoglobin; (b) contacting the biological sample with a
polynucleotide aptamer that specifically binds to HbS under
conditions effective to bind hemoglobin to the aptamer; and (c)
recovering the hemoglobin bound to the aptamer.
42. The method of claim 41, wherein the step of contacting the
biological sample with the polynucleotide aptamer that specifically
binds to HbS under conditions effective to bind hemoglobin to the
polynucleotide aptamer comprises providing a solid support
comprising an aptamer that specifically binds to HbS immobilized
onto the solid support through a spacer.
43. The method of claim 41, wherein the polynucleotide aptamer is
an RNA aptamer.
44. The method of claim 43, wherein the polynucleotide aptamer
specifically binds oxygenated HbS (oxy-HbS).
45. The method of claim 43, wherein the polynucleotide aptamer
specifically binds deoxygenated HbS (deoxy-HbS).
46. The method of claim 43, wherein the polynucleotide aptamer
specifically binds both oxygenated HbS (oxy-HbS) and deoxygenated
HbS (deoxy-HbS).
47. The method of claim 43, wherein the polynucleotide aptamer
comprises a nucleotide sequence selected from the group consisting
of: (a) a nucleotide sequence at least 80% identical to any one of
SEQ ID NOS:2-60; (b) a nucleotide sequence at least 90% identical
to any one of SEQ ID NOS:2-60; (c) a nucleotide sequence at least
95% identical to any one of SEQ ID NOS:2-60; (d) a nucleotide
sequence at least 99% identical to any one of SEQ ID NOS:2-60; and
(e) the nucleotide sequence of any one of SEQ ID NOS:2-60.
48. The method of claim 43, wherein the polynucleotide aptamer
comprises a nucleotide sequence selected from the group consisting
of: (a) a nucleotide sequence at least 80% identical to any one of
SEQ ID NOS:2, 4, 31, and 37; (b) a nucleotide sequence at least 90%
identical to any one of SEQ ID NOS:2, 4, 31, and 37; (c) a
nucleotide sequence at least 95% identical to any one of SEQ ID
NOS:2, 4, 31, and 37; (d) a nucleotide sequence at least 99%
identical to any one of SEQ ID NOS:2, 4, 31, and 37; and (e) the
nucleotide sequence of any one of SEQ ID NOS:2, 4, 31, and 37.
49. The method of claim 47, wherein the polynucleotide aptamer is
selected from the group consisting of: (a) wherein when the
polynucleotide aptamer is any one of SEQ ID NOS:2, 4, or 5, the
polynucleotide aptamer further comprises a consensus sequence
consisting of SEQ ID NO:61; (b) wherein when the polynucleotide
aptamer is any one of SEQ ID NOS:11 or 14, the polynucleotide
aptamer further comprises a consensus sequence consisting of SEQ ID
NO:62; (c) wherein when the polynucleotide aptamer is any one of
SEQ ID NOS: 37, 38, 40, or 49, the polynucleotide aptamer further
comprises a consensus sequence consisting of SEQ ID NO:63; (d)
wherein when the polynucleotide aptamer is any one of SEQ ID NOS:
31, 37, 38, 40, 42, 45, 46, 47, 48, 49, 53, 56, 59 or 60, the
polynucleotide aptamer further comprises a consensus sequence
consisting of SEQ ID NO:64; and (e) wherein when the polynucleotide
aptamer is any one of SEQ ID NOS: 2, 4, 5, 8, 34, or 57, the
polynucleotide aptamer further comprises a consensus sequence
consisting of SEQ ID NO:65.
50. The method of claim 43, wherein the polynucleotide aptamer
comprises a consensus sequence consisting of a nucleotide sequence
selected from the group consisting of SEQ ID NOS:61, 62, 63, 64,
and 65.
51. The method of claim 43, wherein the polynucleotide aptamer is
modified to enable covalent immobilization or to prevent enzymatic
degradation.
52. The method of claim 43, wherein the biological sample comprises
whole blood, hemocytes, serum, or plasma.
53. A method of using a three-dimensional structure of a
polynucleotide aptamer that specifically binds to HbS and inhibits
polymerization of HbS in a drug screening assay comprising: (a)
selecting a potential drug by performing rational drug design with
the three-dimensional structure of the polynucleotide aptamer that
specifically binds to HbS and inhibits polymerization of HbS
determined from one or more sets of atomic coordinates; wherein
said selecting is performed in conjunction with computer modeling;
(b) contacting the potential drug with HbS; (c) detecting the
binding of the potential drug with the HbS; and (d) detecting the
inhibition of polymerization of HbS by the potential drug; wherein
a potential drug is selected as a drug if the potential drug binds
to HbS and inhibits polymerization of HbS.
54. The method of claim 53, wherein the polynucleotide aptamer is
an RNA aptamer.
55. The method of claim 54, wherein the polynucleotide aptamer
specifically binds oxygenated HbS (oxy-HbS).
56. The method of claim 54, wherein the polynucleotide aptamer
specifically binds deoxygenated HbS (deoxy-HbS).
57. The method of claim 54, wherein the polynucleotide aptamer
specifically binds both oxygenated HbS (oxy-HbS) and deoxygenated
HbS (deoxy-HbS).
58. The method of claim 54, wherein the polynucleotide aptamer
comprises a nucleotide sequence selected from the group consisting
of: (a) a nucleotide sequence at least 80% identical to any one of
SEQ ID NOS:2-60; (b) a nucleotide sequence at least 90% identical
to any one of SEQ ID NOS:2-60; (c) a nucleotide sequence at least
95% identical to any one of SEQ ID NOS:2-60; (d) a nucleotide
sequence at least 99% identical to any one of SEQ ID NOS:2-60; and
(e) the nucleotide sequence of any one of SEQ ID NOS:2-60.
59. The method of claim 54, wherein the polynucleotide aptamer
comprises a nucleotide sequence selected from the group consisting
of: (a) a nucleotide sequence at least 80% identical to any one of
SEQ ID NOS:2, 4, 31, and 37; (b) a nucleotide sequence at least 90%
identical to any one of SEQ ID NOS:2, 4, 31, and 37; (c) a
nucleotide sequence at least 95% identical to any one of SEQ ID
NOS:2, 4, 31, and 37; (d) a nucleotide sequence at least 99%
identical to any one of SEQ ID NOS:2, 4, 31, and 37; and (e) the
nucleotide sequence of any one of SEQ ID NOS:2, 4, 31, and 37.
60. The method of claim 58, wherein the polynucleotide aptamer is
selected from the group consisting of: (a) wherein when the
polynucleotide aptamer is any one of SEQ ID NOS:2, 4, or 5, the
polynucleotide aptamer further comprises a consensus sequence
consisting of SEQ ID NO:61; (b) wherein when the polynucleotide
aptamer is any one of SEQ ID NOS:11 or 14, the polynucleotide
aptamer further comprises a consensus sequence consisting of SEQ ID
NO:62; (c) wherein when the polynucleotide aptamer is any one of
SEQ ID NOS: 37, 38, 40, or 49, the polynucleotide aptamer further
comprises a consensus sequence consisting of SEQ ID NO:63; (d)
wherein when the polynucleotide aptamer is any one of SEQ ID NOS:
31, 37, 38, 40, 42, 45, 46, 47, 48, 49, 53, 56, 59 or 60, the
polynucleotide aptamer further comprises a consensus sequence
consisting of SEQ ID NO:64; and (e) wherein when the polynucleotide
aptamer is any one of SEQ ID NOS: 2, 4, 5, 8, 34, or 57, the
polynucleotide aptamer further comprises a consensus sequence
consisting of SEQ ID NO:65.
61. The method of claim 54, wherein the polynucleotide aptamer
comprises a consensus sequence consisting of a nucleotide sequence
selected from the group consisting of SEQ ID NOS: 61, 62, 63, 64,
and 65.
Description
CROSS-REFERENCE TO RELATED APPLICATION
[0001] This application claims the benefit of U.S. Provisional
Application No. 61/828,142, filed May 28, 2013; which is
incorporated herein by reference in its entirety.
BACKGROUND
[0002] Sickle cell anemia (SCA), a genetic disorder affecting 1 in
400 African Americans and up to 2% of the population in some areas
of Africa, results from the production of an abnormal type of
hemoglobin that polymerizes (aggregates) leading to detrimental
shape changes in red blood cells (sickling) and significant
morbidity and mortality in patients.
[0003] Polymerization of sickle hemoglobin (HbS) in the red blood
cells of patients with SCA leads to rigid red cells which occlude
blood vessels, leading to pain, strokes, organ damage,
susceptibility to infection and early death. Present methods known
in the art that have been shown to alter the severity of the
disorder are complex and labor intensive therapies: 1) bone marrow
transplantation; 2) routine blood transfusions; or 3) hydroxyurea,
a drug which indirectly (and incompletely) prevents HbS
polymerization by inducing the production of another type of
hemoglobin (fetal hemoglobin). Accordingly, treatments for SCA are
lacking and focus mainly on palliative or symptomatic therapy.
SUMMARY
[0004] In some aspects, the presently disclosed subject matter
provides polynucleotide aptamers that specifically bind sickle
hemoglobin (HbS) in such a way that polymerization of HbS is
inhibited without a deleterious effect on hemoglobin's functional
capabilities. In certain aspects, the polynucleotide aptamers are
RNA aptamers. In other aspects, polynucleotide aptamers inhibit
polymerization of HbS. The polynucleotide aptamers may specifically
bind oxygenated HbS (oxy-HbS), deoxygenated HbS (deoxy-HbS), or may
bind both oxy-HbS and deoxy-HbS. In certain aspects, the
polynucleotide aptamers comprise a nucleotide sequence that is at
least 70% identical, e.g., at least 75%, 80%, 85%, 90%, 91%, 92%,
93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to any one of SEQ ID
NOS:2-60, particularly SEQ ID NOS:2, 4, 31, and 37 or fragments or
analogs thereof, more particularly: (a) any one of SEQ ID NOS:2, 4,
or 5 wherein the polynucleotide aptamer further comprises a
consensus sequence consisting of SEQ ID NO:61; (b) any one of SEQ
ID NOS:11 or 14 or wherein the polynucleotide aptamer further
comprises a consensus sequence consisting of SEQ ID NO:62; (c) any
one of SEQ ID NOS:37, 38, 40, or 49 wherein the polynucleotide
further comprises a consensus sequence consisting of SEQ ID NO:63;
(d) any one of SEQ ID NOS:31, 37, 38, 40, 42, 45, 46, 47, 48, 49,
53, 56, 59, or 60 wherein the polynucleotide aptamer further
comprises a consensus sequence consisting of SEQ ID NO:64; or (e)
any one of SEQ ID NOS:2, 4, 5, 8, 34, or 57 wherein the
polynucleotide aptamer further comprises a consensus sequence
consisting of SEQ ID NO:65. In another aspect, the polynucleotide
aptamer of the presently disclosed subject matter comprises a
consensus sequence consisting of a nucleotide sequence selected
from the group consisting of SEQ ID NOS:61, 62, 63, 64, and 65.
Other aspects of the presently disclosed subject matter relate to
polynucleotides encoding the polynucleotide aptamers of the
invention, vectors comprising the polynucleotide aptamers, and
cells comprising the polynucleotide aptamers.
[0005] In other aspects, the presently disclosed subject matter
provides a method of treating or preventing sickle cell disease in
a subject in need thereof, the method comprising administering to
the subject a therapeutically effective amount of a polynucleotide
aptamer that specifically binds sickle hemoglobin (HbS), where the
polynucleotide aptamer inhibits polymerization of HbS. In certain
aspects, the polynucleotide aptamers are modified to increase the
circulating half-life of the aptamer after administration to a
subject. In another aspect, the polynucleotide aptamer is
administered in a pharmaceutically acceptable carrier. In other
aspects, the sickle cell disease is sickle cell anemia. In yet
another aspect, the method of treating or preventing sickle cell
disease further comprises contacting the polynucleotide aptamer
with an antidote, particularly an oligonucleotide comprising a
sequence complementary to at least a portion of the polynucleotide
aptamer.
[0006] In other aspects, the presently disclosed subject matter
provides a method for diagnosing or predicting sickle cell disease
in a subject having or at risk of developing sickle cell disease or
at risk of passing it on to offspring, the method comprising: (a)
obtaining a biological sample from the subject; (b) contacting the
biological sample with a polynucleotide aptamer that specifically
binds to HbS; and (c) detecting binding of the polynucleotide
aptamer with HbS in the biological sample; where detection of
binding of the polynucleotide aptamer with HbS in the biological
sample is indicative of the subject having or at risk of developing
sickle cell disease or at risk of passing it on to offspring. In
one aspect, the sickle cell disease is sickle cell anemia. In
another aspect, the biological sample comprises whole blood,
hemocytes, serum, or plasma. In other aspects, the polynucleotide
aptamer is labeled for detection with a fluorescent, luminescent,
phosphorescent, radioactive, or colorimetric compound.
[0007] In yet other aspects, the presently disclosed subject matter
provides a method of purifying hemoglobin from a biological sample,
the method comprising: (a) providing a biological sample containing
hemoglobin; (b) contacting the biological sample with a
polynucleotide aptamer that specifically binds to HbS under
conditions effective to bind hemoglobin to the aptamer; and (c)
recovering the hemoglobin bound to the aptamer. In one aspect, the
step of contacting the biological sample with the polynucleotide
aptamer that specifically binds to HbS comprises providing a solid
support comprising an aptamer that specifically binds to HbS
immobilized onto the solid support through a spacer. In other
aspects, the polynucleotide aptamer is modified to enable covalent
immobilization or to prevent enzymatic degradation. In another
aspect, the biological sample comprises whole blood, hemocytes,
serum, or plasma.
[0008] In other aspects, the presently disclosed subject matter
provides a method of using a three-dimensional structure of a
polynucleotide aptamer that specifically binds to HbS and inhibits
polymerization of HbS in a drug screening assay comprising: (a)
selecting a potential drug by performing rational drug design with
the three-dimensional structure of the polynucleotide aptamer that
specifically binds to HbS and inhibits polymerization of HbS
determined from one or more sets of atomic coordinates; wherein
said selecting is performed in conjunction with computer modeling;
(b) contacting the potential drug with HbS; (c) detecting the
binding of the potential drug with the HbS; and (d) detecting the
inhibition of polymerization of HbS by the potential drug; wherein
a potential drug is selected as a drug if the potential drug binds
to HbS and inhibits polymerization of HbS.
[0009] Certain aspects of the presently disclosed subject matter
having been stated hereinabove, which are addressed in whole or in
part by the presently disclosed subject matter, other aspects will
become evident as the description proceeds when taken in connection
with the accompanying Examples and Figures as best described herein
below.
BRIEF DESCRIPTION OF THE FIGURES
[0010] Having thus described the presently disclosed subject matter
in general terms, reference will now be made to the accompanying
Figures, which are not necessarily drawn to scale, and wherein:
[0011] FIG. 1 shows dose-dependent saturable binding of deoxy
aptamer to deoxy sickle hemoglobin (HbS);
[0012] FIG. 2 shows inhibition of HbS polymerization by deoxy 3-A
aptamer (SEQ ID NO:4) in a polymerization assay;
[0013] FIG. 3 shows inhibition of HbS polymerization by deoxy 1
aptamer (SEQ ID NO:2) in one of two runs of a polymerization
assay;
[0014] FIG. 4 shows inhibition of HbS polymerization by deoxy EM8-A
aptamer (SEQ ID NO:31) in a polymerization assay;
[0015] FIG. 5 shows inhibition of HbS polymerization by oxy 3-B
aptamer (SEQ ID NO:37) in a polymerization assay;
[0016] FIGS. 6A-6B show the concentration-dependent inhibition of
HbS polymerization by deoxy 3-A aptamer: A) polymerization curves
as a function of deoxy 3-A aptamer concentration; and B) slope of
polymerization curves;
[0017] FIG. 7 shows that lipofectin facilitates entry of deoxy 3-A
aptamer into sickle red blood cells; and
[0018] FIG. 8 shows that HbS retains the ability to form new
polymer when growing filament ends are provided by mechanical
disruption.
DETAILED DESCRIPTION
[0019] The presently disclosed subject matter now will be described
more fully hereinafter with reference to the accompanying Figures,
in which some, but not all embodiments of the presently disclosed
subject matter are shown. Like numbers refer to like elements
throughout. The presently disclosed subject matter may be embodied
in many different forms and should not be construed as limited to
the embodiments set forth herein; rather, these embodiments are
provided so that this disclosure will satisfy applicable legal
requirements. Indeed, many modifications and other embodiments of
the presently disclosed subject matter set forth herein will come
to mind to one skilled in the art to which the presently disclosed
subject matter pertains having the benefit of the teachings
presented in the foregoing descriptions and the associated Figures.
Therefore, it is to be understood that the presently disclosed
subject matter is not to be limited to the specific embodiments
disclosed and that modifications and other embodiments are intended
to be included within the scope of the appended claims.
I. Hemoglobins and Sickle Cell Disease
[0020] Normally, hemoglobin is a tetrameric protein composed of two
pairs of two different subunits. Hemoglobin A (hereinafter
abbreviated as HbA) has .alpha.-chain and .beta.-chain subunits.
Binding of glucose to N-terminal amino acid(s) of this/these
.beta.-chain results in hemoglobin A.sub.1c (hereinafter
abbreviated as HbA.sub.1c). HbA.sub.1c, if produced via a
reversible reaction therebetween, is called labile HbA.sub.1c and,
if produced via an irreversible reaction involving the labile
HbA.sub.1c, is called stable HbA.sub.1c.
[0021] The separation of hemoglobins present in a hemolyzed sample
by means of cation exchange liquid chromatography, if performed
over a sufficiently long period of time, generally results in the
sequential elution of hemoglobin A.sub.1a (hereinafter abbreviated
as HbA.sub.1a) and hemoglobin A.sub.1b (hereinafter abbreviated as
HbA.sub.1b), hemoglobin F (hereinafter abbreviated as HbF), labile
HbA.sub.1c, stable HbA.sub.1c and hemoglobin A.sub.0 (hereinafter
abbreviated as HbA.sub.0). HbA.sub.1a, HbA.sub.1b and HbA.sub.1c
each is a glycated HbA. HbF is fetal hemoglobin composed of .alpha.
and .gamma. chains. HbA.sub.0 consists of a group of hemoglobin
components, includes HbA as its primary component and is retained
more strongly to a column than HbA.sub.1c.
[0022] Hemoglobin S or sickle hemoglobin (hereinafter abbreviated
as HbS) and hemoglobin C (hereinafter abbreviated as HbC) are known
as "abnormal hemoglobins." HbS and HbC result from substitution of
glutamic acid located in a sixth position from an N-terminal of the
.beta. chain of HbA for valine and lysine, respectively. Hemoglobin
A.sub.2 (hereinafter abbreviated as HbA.sub.2) is composed of a and
.delta. chains and, like HbF, its elevated level is interpreted as
evidence of Mediterranean anemia (thalassemia). In the normal
determination of hemoglobins by cation exchange liquid
chromatography, they are eluted in the sequence of HbA.sub.0,
HbA.sub.2, HbS and HbC.
[0023] Sickle-cell disease (SCD), or sickle-cell anemia (or
drepanocytosis), is a life-long blood disorder characterized by red
blood cells (erythrocytes: RBC) that assume an abnormal, rigid,
sickle shape. Sickling decreases flexibility of RBC and results in
a risk of various complications. RBC sickling occurs because of a
mutation in the hemoglobin gene. SCD is an inherited disorder and
SCD is an autosomal recessive disease. Although, some people who
inherit one sickle cell gene and one other defective hemoglobin
gene may experience a similar sickle-cell disorder. Sickle cell
disease includes but is not limited to sickle cell anemia, sickle
.beta.-thalassemia, sickle cell-hemoglobin C disease and any other
sickle hemoglobinopathy in which HbS interacts with a hemoglobin
other than HbS. "Sickle hemoglobinopathy" is an abnormality of
hemoglobin which results in sickle cell disease or sickle
variants.
II. Polynucleotide Aptamers
[0024] A. Aptamers
[0025] In some embodiments, the presently disclosed subject matter
relates to the generation of aptamers that specifically bind sickle
hemoglobin (HbS) in such a way that polymerization of HbS is
inhibited without a deleterious effect on hemoglobin's functional
capabilities. Aptamers are small single-stranded nucleic acid
molecules (.about.5-25 kDa) that fold into unique structures,
allowing them to bind to molecular targets with high specificity
and affinity. This specific binding confers the potential for
aptamers to be used in a wide variety of diagnostic or therapeutic
applications and have emerged as viable alternatives to
small-molecule and antibody-based therapy (Que-Gewirth et al.
(2007) Gene Ther. 14:283; Ireson et al. (2006) Mol. Cancer Ther.
5:2957). Like antibodies, aptamers possess binding affinities in
the low nanomolar to picomolar range. However, aptamers are
advantageous in that they are easily synthesized and stored, can
bind very small targets, are non-immunogenic, are heat stable,
possess minimal interbatch variability, and can be
antidote-controlled. In addition, in contrast to antisense
oligonucleotides, RNA aptamers can effectively target extracellular
targets, such as HbS. Furthermore, chemical modifications, such as
amino or fluoro substitutions at the 2' position of pyrimidines,
may reduce degradation by nucleases. The biodistribution and
clearance of aptamers can also be altered by chemical addition of
moieties such as polyethylene glycol and cholesterol.
[0026] An aptamer's small size also maximizes its ability to bind
to a specific site on a protein, altering the function of that
site, without affecting the functions of other sites on the
protein. For example, Fortenberry and colleagues have developed
aptamers that bind specifically to plasminogen activator
inhibitor-1 (PAI-1), a serine protease inhibitor that has a role in
the pathophysiology of several diseases, including cancer and
cardiovascular disease. PAI-1 binds to vitronectin, preventing
vitronectin's interaction with integrin, thereby resulting in a
decrease in cell adhesion and migration. These aptamers bind
specifically to PAI-1's vitronectin binding site, affecting PAI-1's
interaction with vitronectin, but having no affect on its
proteolytic activity.
[0027] Specific aptamers are typically selected from very large
libraries of more than 10.sup.14 random sequence oligonucleotides
in a process called the "systematic evolution of ligands by
exponential enrichment" (SELEX). This is an iterative selection
process, which begins with a protein or other target of interest
being incubated with the oligonucleotide library. A small fraction
of the oligonucleotides bind the target and the rest are separated
out by a suitable separation technique. The small population that
bound the target is then amplified and used in the next round of
incubation with the target. This cycle is repeated multiple times,
with increasingly stringent incubation and separation conditions at
each round in order to enrich for high affinity binders. This
process will be referred to herein as "positive selection."
However, in certain cases the aptamers that do not bind to the
target protein will be amplified, and the binders will be
discarded. This process will be referred to herein as "negative
selection." Both positive and negative selection may be used,
including experiments where the bound aptamers are recovered from
the target--positive selection, and experiments where the aptamers
that recognized more than one target are removed from the pool (for
example, by absorbing pools of molecules that bind both HbA and HbS
to HbA, allowing the molecules that specifically bind only to HbS
to "flow through"--negative selection).
[0028] Accordingly, in one embodiment, the presently disclosed
subject matter relates to polynucleotide aptamers that specifically
bind to sickle hemoglobin (HbS). In some embodiments, the
polynucleotide aptamers inhibit the polymerization of HbS,
particularly without a deleterious effect on hemoglobin's
functional capabilities. Preventing the polymerization of HbS is
essentially a cure for sickle cell anemia, since the complications
of the disease arise directly as a result of red blood cell changes
brought about by HbS polymerization.
[0029] As used herein, "polymerization" includes the process of
forming a polymer from many monomeric units of hemoglobin. A
polymer may be formed by any chemical bonding interaction between
or among molecules, i.e. covalent, ionic, or van der Waals. As used
herein, "aggregation" and "polymerization" may be used
interchangeably. In particular embodiments, the presently disclosed
aptamers inhibit polymerization of HbS. However, it is understood
by those of skill in the art that 100% inhibition of polymerization
of HbS is not required within the presently disclosed methods. In
some embodiments, the presently disclosed methods produce at least
about a 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%,
70%, 75%, 80%, 85%, 90%, 95%, or even 100% inhibition of
polymerization of HbS relative to polymerization of HbS measured in
absence of aptamers or modified aptamers described herein that
specifically bind HbS and inhibit polymerization of HbS, i.e., a
control sample, in an assay.
[0030] Thus, one embodiment of the presently disclosed subject
matter relates to polynucleotide aptamers that specifically bind to
HbS and inhibit polymerization of HbS, particularly without a
deleterious effect on hemoglobin's functional capabilities. In
another embodiment, the presently disclosed subject matter relates
to polynucleotide aptamers that specifically bind to oxygenated HbS
(oxy-HbS) or to deoxygenated HbS (deoxy-HbS), or that specifically
bind to both oxy-HbS and deoxy-HbS. In one embodiment, the aptamers
are DNA or RNA aptamers or hybrid DNA/RNA aptamers. In a particular
embodiment, the aptamers are RNA aptamers.
[0031] The term "specifically binds," as used herein, refers to a
molecule (e.g., an aptamer) that binds to a target (e.g., a protein
such as HbS) with at least five-fold greater affinity as compared
to any non-targets, e.g., at least 10-, 20-, 50-, or 100-fold
greater affinity. The aptamers of the presently disclosed subject
matter may bind HbS, including oxy-HbS and/or deoxy-HbS, as well as
HbA and other types of hemoglobin, with a K.sub.d of less than
about 1000 nM, e.g., less than about 500, 200, 100, 50, or 20
nM.
[0032] The sequence of the polynucleotide aptamers of the invention
may be selected by any method known in the art. In one embodiment,
aptamers are selected by the SELEX process. In another embodiment,
aptamers may be selected by starting with the sequences and
structural requirements of the aptamers disclosed herein and
modifying the sequences to produce other aptamers.
[0033] The length of the aptamers of the presently disclosed
subject matter is not limited, but typical aptamers have a length
of about 10 to about 120 nucleotides, particularly about 80
nucleotides. In certain embodiments, the aptamer may have
additional nucleotides attached to the 5'- and/or 3' end. The
additional nucleotides may be, e.g., part of primer sequences,
restriction endonuclease sequences, or vector sequences useful for
producing the aptamer.
[0034] The polynucleotide aptamers of the present invention may be
comprised of ribonucleotides only (RNA aptamers),
deoxyribonucleotides only (DNA aptamers), or a combination of
ribonucleotides and deoxyribonucleotides. The nucleotides may be
naturally occurring nucleotides (e.g., ATP, TTP, GTP, CTP, UTP) or
modified nucleotides. Modified nucleotides refers to nucleotides
comprising bases such as, for example, adenine, guanine, cytosine,
thymine, and uracil, xanthine, inosine, and queuosine that have
been modified by the replacement or addition of one or more atoms
or groups. Some examples of types of modifications that can
comprise nucleotides that are modified with respect to the base
moieties, include but are not limited to, alkylated, halogenated,
thiolated, aminated, amidated, or acetylated bases, in various
combinations. More specific examples include 5-propynyluridine,
5-propynylcytidine, 6-methyladenine, 6-methylguanine,
N,N,-dimethyladenine, 2-propyladenine, 2-propylguanine,
2-aminoadenine, 1-methylinosine, 3-methyluridine, 5-methylcytidine,
5-methyluridine and other nucleotides having a modification at the
5 position, 5-(2-amino)propyl uridine, 5-halocytidine,
5-halouridine, 4-acetylcytidine, 1-methyladenosine,
2-methyladenosine, 3-methylcytidine, 6-methyluridine,
2-methylguanosine, 7-methylguanosine, 2,2-dimethylguanosine,
5-methylaminoethyluridine, 5-methyloxyuridine, deazanucleotides
such as 7-deaza-adenosine, 6-azouridine, 6-azocytidine,
6-azothymidine, 5-methyl-2-thiouridine, other thio bases such as
2-thiouridine and 4-thiouridine and 2-thiocytidine, dihydrouridine,
pseudouridine, queuosine, archaeosine, naphthyl and substituted
naphthyl groups, any 0- and N-alkylated purines and pyrimidines
such as N6-methyladenosine, 5-methylcarbonylmethyluridine, uridine
5-oxyacetic acid, pyridine-4-one, pyridine-2-one, phenyl and
modified phenyl groups such as aminophenol or 2,4,6-trimethoxy
benzene, modified cytosines that act as G-clamp nucleotides,
8-substituted adenines and guanines, 5-substituted uracils and
thymines, azapyrimidines, carboxyhydroxyalkyl nucleotides,
carboxyalkylaminoalkyl nucleotides, and alkylcarbonylalkylated
nucleotides. Modified nucleotides also include those nucleotides
that are modified with respect to the sugar moiety (e.g., 2'-fluoro
or 2'-O-methyl nucleotides), as well as nucleotides having sugars
or analogs thereof that are not ribosyl. For example, the sugar
moieties may be, or be based on, mannoses, arabinoses,
glucopyranoses, galactopyranoses, 4'-thioribose, and other sugars,
heterocycles, or carbocycles. The term nucleotide is also meant to
include what are known in the art as universal bases. By way of
example, universal bases include but are not limited to
3-nitropyrrole, 5-nitroindole, or nebularine. Modified nucleotides
include labeled nucleotides such as radioactively, enzymatically,
or chromogenically labeled nucleotides).
[0035] In one embodiment, the presently disclosed subject matter
relates to an RNA aptamer and comprises a nucleotide sequence that
is identical to any one of SEQ ID NOS:2-60 as shown in Table 1 (see
Example 1). In another embodiment, the RNA aptamer consists of a
nucleotide sequence that is identical to any one of SEQ ID
NOS:2-60. In a further embodiment, the RNA aptamer comprises a
nucleotide sequence that is at least 70% identical, e.g., at least
75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%
identical to any one of SEQ ID NOS:2-60. In another embodiment, the
aptamer consists of a nucleotide sequence that is at least 70%
identical, e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%,
95%, 96%, 97%, 98%, or 99% identical to any one of SEQ ID NOS:2-60.
In yet another embodiment, the aptamer comprises a nucleotide
sequence that is identical to a fragment of any one of SEQ ID
NOS:2-60 of at least 10 contiguous nucleotides, e.g., at least
about 15, 20, 25, 30, or 35 contiguous nucleotides. In another
embodiment, the aptamer comprises a nucleotide sequence that is at
least 70% identical, e.g., at least 75%, 80%, 85%, 90%, 91%, 92%,
93%, 94%, 95%; 96%, 97%, 98%, or 99% identical to a fragment of any
one of SEQ ID NOS: 2-60 of at least contiguous 10 nucleotides,
e.g., at least about 15, 20, 25, 30, or 35 contiguous nucleotides.
In one embodiment, one or more ribonucleotides in the RNA aptamers
described above are substituted by a deoxyribonucleotide. In
another embodiment, the fragments and/or analogs of the aptamers of
SEQ ID NOS:2-60 have a substantially similar activity as one or
more of the aptamers of SEQ ID NOS:2-60. "Substantially similar,"
as used herein, refers to specific binding to HbS, and in some
embodiments also refers to an inhibitory activity on the
polymerization of HbS, particularly without a deleterious effect on
hemoglobin's functional capabilities, that is at least about 20% of
the inhibitory activity of one or more of the aptamers of SEQ ID
NOS:2-60.
[0036] Changes to the aptamer sequences, such as SEQ ID NOS:2-60,
may be made based on structural requirements for binding of the
aptamers to HbS, including oxy-HbS and/or deoxy-HbS. The structural
requirements may be readily determined by one of skill in the art
by analyzing common sequences between the disclosed aptamers and/or
by mutagenizing the disclosed aptamers and measuring HbS binding
affinity.
[0037] When a number of individual, distinct aptamer sequences for
a single target molecule have been obtained and sequenced as
described herein, the sequences can be examined for "consensus
sequences." As used herein, "consensus sequence" refers to a
nucleotide sequence or region (which might or might not be made up
of contiguous nucleotides) that is found in one or more regions of
at least two aptamers, the presence of which can be correlated with
aptamer-to-target-binding or with aptamer structure.
[0038] A consensus sequence can be as short as three nucleotides
long. It also can be made up of one or more noncontiguous sequences
with nucleotide sequences or polymers of hundreds of bases long
interspersed between the consensus sequences. Consensus sequences
can be identified by sequence comparisons between individual
aptamer species, which comparisons can be aided by computer
programs and other tools for modeling secondary and tertiary
structure from sequence information. Generally, the consensus
sequence will contain at least about 5 to 20 nucleotides, more
commonly from 11 to 15 nucleotides.
[0039] In one embodiment, wherein when the RNA aptamer of the
presently disclosed subject matter comprises a nucleotide sequence
that is at least 70% identical, e.g., at least 75%, 80%, 85%, 90%,
91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to any one
of SEQ ID NOS:2, 4, or 5 or fragments or analogs thereof, the RNA
aptamer further comprises a consensus sequence consisting of
GAACUGGGCUG (SEQ ID NO:61).
[0040] In another embodiment, wherein when the RNA aptamer of the
presently disclosed subject matter comprises a nucleotide sequence
that is at least 70% identical, e.g., at least 75%, 80%, 85%, 90%,
91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to any one
of SEQ ID NOS:11 or 14 or fragments or analogs thereof, the RNA
aptamer further comprises a consensus sequence consisting of
CACCCCAACGCGGAG (SEQ ID NO:62).
[0041] In another embodiment, wherein when the RNA aptamer of the
presently disclosed subject matter comprises a nucleotide sequence
that is at least 70% identical, e.g., at least 75%, 80%, 85%, 90%,
91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to any one
of SEQ ID NOS:37, 38, 40, or 49, or fragments or analogs thereof,
the RNA aptamer further comprises a consensus sequence consisting
of GUCUAUUAGGAC (SEQ ID NO:63).
[0042] In another embodiment, wherein when the RNA aptamer of the
presently disclosed subject matter comprises a nucleotide sequence
that is at least 70% identical, e.g., at least 75%, 80%, 85%, 90%,
91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to any one
of SEQ ID NOS:31, 37, 38, 40, 42, 45, 46, 47, 48, 49, 53, 56, 59,
or 60 or fragments or analogs thereof, the RNA aptamer further
comprises a consensus sequence consisting of CUAUUAGGACCAG (SEQ ID
NO:64).
[0043] In another embodiment, wherein when the RNA aptamer of the
presently disclosed subject matter comprises a nucleotide sequence
that is at least 70% identical, e.g., at least 75%, 80%, 85%, 90%,
91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to any one
of SEQ ID NOS:2, 4, 5, 8, 34, or 57, or fragments or analogs
thereof, the RNA aptamer further comprises a consensus sequence
consisting of CGAUUAGAACUGG (SEQ ID NO:65).
[0044] In another embodiment, the RNA aptamer of the presently
disclosed subject matter comprises a consensus sequence consisting
of a nucleotide sequence selected from the group consisting of SEQ
ID NOS:61, 62, 63, 64, and 65.
[0045] As used herein, a "nucleic acid" or "polynucleotide" refers
to the phosphate ester polymeric form of ribonucleosides
(adenosine, guanosine, uridine or cytidine; "RNA molecules") or
deoxyribonucleosides (deoxyadenosine, deoxyguanosine,
deoxythymidine, or deoxycytidine; "DNA molecules"), or any
phosphoester anologs thereof, such as phosphorothioates and
thioesters, in either single stranded form, or a double-stranded
helix. Double stranded DNA-DNA, DNA-RNA and RNA-RNA helices are
possible. The term nucleic acid molecule, and in particular DNA or
RNA molecule, refers only to the primary and secondary structure of
the molecule, and does not limit it to any particular tertiary
forms. Thus, this term includes double-stranded DNA found, inter
alia, in linear or circular DNA molecules (e.g., restriction
fragments), plasmids, and chromosomes. In discussing the structure
of particular double-stranded DNA molecules, sequences may be
described herein according to the normal convention of giving only
the sequence in the 5' to 3' direction along the non-transcribed
strand of DNA (i.e., the strand having a sequence homologous to the
mRNA). A "recombinant DNA molecule" is a DNA molecule that has
undergone a molecular biological manipulation.
[0046] The term "fragment" refers to a nucleotide sequence of
reduced length relative to the reference nucleic acid and
comprising, over the common portion, a nucleotide sequence
identical to the reference nucleic acid. Such a nucleic acid
fragment according to the presently disclosed subject matter may
be, where appropriate, included in a larger polynucleotide of which
it is a constituent. Such fragments comprise, or alternatively
consist of, oligonucleotides ranging in length from at least 6, 8,
9, 10, 12, 15, 18, 20, 21, 22, 23, 24, 25, 30, 39, 40, 42, 45, 48,
50, 51, 54, 57, 60, 63, 66, 70, 75, 78, 80, 90, 100, 105, 120, 135,
150, 200, 300, 500, 720, 900, 1000 or 1500 consecutive nucleotides
of a nucleic acid according to the presently disclosed subject
matter.
[0047] The term "percent identity," as known in the art, is a
relationship between two or more polypeptide sequences or two or
more polynucleotide sequences, as determined by comparing the
sequences. In the art, "identity" also means the degree of sequence
relatedness between polypeptide or polynucleotide sequences, as the
case may be, as determined by the match between strings of such
sequences. "Identity" and "similarity" can be readily calculated by
known methods, including but not limited to those described in:
Computational Molecular Biology (Lesk, A. M., ed.) Oxford
University Press, New York (1988); Biocomputing: Informatics and
Genome Projects (Smith, D. W., ed.) Academic Press, New York
(1993); Computer Analysis of Sequence Data, Part I (Griffin, A. M.,
and Griffin, H. G., eds.) Humana Press, New Jersey (1994); Sequence
Analysis in Molecular Biology (von Heinje, G., ed.) Academic Press
(1987); and Sequence Analysis Primer (Gribskov, M. and Devereux,
J., eds.) Stockton Press, New York (1991). Preferred methods to
determine identity are designed to give the best match between the
sequences tested. Methods to determine identity and similarity are
codified in publicly available computer programs. Sequence
alignments and percent identity calculations may be performed using
the Megalign program of the LASERGENE bioinformatics computing
suite (DNASTAR Inc., Madison, Wis.). Multiple alignment of the
sequences may be performed using the Clustal method of alignment
(Higgins and Sharp (1989) CABIOS. 5:151-153) with the default
parameters, including default parameters for pairwise
alignments.
[0048] The term "sequence analysis software" refers to any computer
algorithm or software program that is useful for the analysis of
nucleotide or amino acid sequences. "Sequence analysis software"
may be commercially available or independently developed. Typical
sequence analysis software will include but is not limited to the
GCG suite of programs (Wisconsin Package Version 9.0, Genetics
Computer Group (GCG), Madison, Wis.), BLASTP, BLASTN, BLASTX
(Altschul et al. (1990) J. Mol. Biol. 215:403-410, and DNASTAR
(DNASTAR, Inc., Madison, Wis.). Within the context of this
application it will be understood that where sequence analysis
software is used for analysis, that the results of the analysis
will be based on the "default values" of the program referenced,
unless otherwise specified. As used herein "default values" will
mean any set of values or parameters which originally load with the
software when first initialized.
[0049] The term "isolated" designates a biological material
(nucleic acid or protein) that has been removed from its original
environment (the environment in which it is naturally present). For
example, a polynucleotide present in the natural state in a plant
or an animal is not isolated, however the same polynucleotide
separated from the adjacent nucleic acids in which it is naturally
present, is considered "isolated". The term "purified" does not
require the material to be present in a form exhibiting absolute
purity, exclusive of the presence of other compounds.
[0050] B. Polynucleotides Encoding Aptamers, Vectors, and Cells
[0051] Once an aptamer sequence according to the presently
disclosed subject matter is identified, the aptamer may by
synthesized by any method known to those of skill in the art. In
one embodiment, aptamers may be produced by chemical synthesis of
oligonucleotides and/or ligation of shorter oligonucleotides.
Accordingly, another embodiment of the present invention relates to
polynucleotides encoding the aptamers of the invention. The
polynucleotides may be used to express the aptamers, e.g., by in
vitro transcription, polymerase chain reaction amplification, or
cellular expression. The polynucleotide may be DNA and/or RNA and
may be single-stranded or double-stranded. In one embodiment, the
polynucleotide is a vector which may be used to express the
aptamer. The vector may be, e.g., a plasmid vector or a viral
vector and may be suited for use in any type of cell, such as
mammalian, insect, plant, fungal, or bacterial cells. The vector
may comprise one or more regulatory elements necessary for
expressing the aptamers, e.g., a promoter, enhancer, transcription
control elements, etc. Another embodiment of the invention relates
to a cell comprising a polynucleotide encoding the aptamers of the
invention. In another embodiment, the invention relates to a cell
comprising the aptamers of the invention. The cell may be any type
of cell, e.g., mammalian, insect, plant, fungal, or bacterial
cells.
[0052] Several methods known in the art may be used to propagate a
polynucleotide according to the presently disclosed subject matter.
Once a suitable host system and growth conditions are established,
recombinant expression vectors can be propagated and prepared in
quantity. As described herein, the expression vectors which can be
used include, but are not limited to, the following vectors or
their derivatives: human or animal viruses such as vaccinia virus
or adenovirus; insect viruses such as baculovirus; yeast vectors;
bacteriophage vectors (e.g., lambda), and plasmid and cosmid DNA
vectors, to name but a few.
[0053] A "vector" is any means for the cloning of and/or transfer
of a nucleic acid into a host cell. A vector may be a replicon to
which another DNA segment may be attached so as to bring about the
replication of the attached segment. A "replicon" is any genetic
element (e.g., plasmid, phage, cosmid, chromosome, virus) that
functions as an autonomous unit of DNA replication in vivo, i.e.,
capable of replication under its own control. The term "vector"
includes both viral and nonviral means for introducing the nucleic
acid into a cell in vitro, ex vivo or in vivo. A large number of
vectors known in the art may be used to manipulate nucleic acids,
incorporate response elements and promoters into genes, etc.
Possible vectors include, for example, plasmids or modified viruses
including, for example bacteriophages such as lambda derivatives,
or plasmids such as pBR322 or pUC plasmid derivatives, or the
Bluescript vector. For example, the insertion of the DNA fragments
corresponding to response elements and promoters into a suitable
vector can be accomplished by ligating the appropriate DNA
fragments into a chosen vector that has complementary cohesive
termini. Alternatively, the ends of the DNA molecules may be
enzymatically modified or any site may be produced by ligating
nucleotide sequences (linkers) into the DNA termini Such vectors
may be engineered to contain selectable marker genes that provide
for the selection of cells that have incorporated the marker into
the cellular genome. Such markers allow identification and/or
selection of host cells that incorporate and express the proteins
encoded by the marker.
[0054] Viral vectors, and particularly retroviral vectors, have
been used in a wide variety of gene delivery applications in cells,
as well as living animal subjects. Viral vectors that can be used
include but are not limited to retrovirus, adeno-associated virus,
pox, baculovirus, vaccinia, herpes simplex, Epstein-Barr,
adenovirus, geminivirus, and caulimovirus vectors. Non-viral
vectors include plasmids, liposomes, electrically charged lipids
(cytofectins), DNA-protein complexes, and biopolymers. In addition
to a nucleic acid, a vector may also comprise one or more
regulatory regions, and/or selectable markers useful in selecting,
measuring, and monitoring nucleic acid transfer results (transfer
to which tissues, duration of expression, etc.).
[0055] Vectors may be introduced into the desired host cells by
methods known in the art, e.g., transfection, electroporation,
microinjection, transduction, cell fusion, DEAE dextran, calcium
phosphate precipitation, lipofection (lysosome fusion), use of a
gene gun, or a DNA vector transporter (see, e.g., Wu et al. (1992)
J. Biol. Chem. 267:963; Wu et al. (1988) J. Biol. Chem. 263:14621).
Aptamers may also be targeted to cells of interest by coupling
aptamers to other aptamers that are known to specifically enter
cells of interest, which can be screened for, or by attachment to
other ligands for red cell receptors that are internalized (e.g.,
transferrin-transferrin receptors), as described more fully
below.
[0056] A polynucleotide according to the presently disclosed
subject matter can also be introduced in vivo by lipofection. For
the past decade, there has been increasing use of liposomes for
encapsulation and transfection of nucleic acids in vitro. Synthetic
cationic lipids designed to limit the difficulties and dangers
encountered with liposome-mediated transfection can be used to
prepare liposomes for in vivo transfection of a gene encoding a
marker (Feigner et al. (1988) Proc. Natl. Acad. Sci. USA 84:7413;
Mackey et al. (1988) Proc. Natl. Acad. Sci. U.S.A. 85:8027; and
Ulmer et al. (1993) Science 259:1745). The use of cationic lipids
may promote encapsulation of negatively charged nucleic acids, and
also promote fusion with negatively charged cell membranes (Feigner
et al. (1989) Science 337:387). Particularly useful lipid compounds
and compositions for transfer of nucleic acids are described in PCT
Patent Pubs. WO95/18863 and WO96/17823, and in U.S. Pat. No.
5,459,127. The use of lipofection to introduce exogenous genes into
the specific organs in vivo has certain practical advantages.
Molecular targeting of liposomes to specific cells represents one
area of benefit. It is clear that directing transfection to
particular cell types would be particularly preferred in a tissue
with cellular heterogeneity, such as pancreas, liver, kidney, and
the brain. Lipids may be chemically coupled to other molecules for
the purpose of targeting (Mackey et al. (1988) Proc. Natl. Acad.
Sci. U.S.A. 85:8027). Targeted peptides, e.g., hormones or
neurotransmitters, and proteins such as antibodies, or non-peptide
molecules could be coupled to liposomes chemically.
[0057] Other molecules are also useful for facilitating
transfection of a nucleic acid in vivo, such as a cationic
oligopeptide (e.g., PCT Patent Pub. WO95/21931), peptides derived
from DNA binding proteins (e.g., PCT Patent Pub. WO96/25508), or a
cationic polymer (e.g., PCT Patent Pub. WO95/21931).
[0058] It is also possible to introduce a vector in vivo as a naked
DNA plasmid (see U.S. Pat. Nos. 5,693,622, 5,589,466 and
5,580,859). Receptor-mediated DNA delivery approaches can also be
used (Curiel et al. (1992) Hum. Gene Ther. 3:147; Wu et al. (1987)
J. Biol. Chem. 262:4429).
[0059] The term "transfection" means the uptake of exogenous or
heterologous RNA or DNA by a cell. A cell has been "transfected" by
exogenous or heterologous RNA or DNA when such RNA or DNA has been
introduced inside the cell. A cell has been "transformed" by
exogenous or heterologous RNA or DNA when the transfected RNA or
DNA effects a phenotypic change. The transforming RNA or DNA can be
integrated (covalently linked) into chromosomal DNA making up the
genome of the cell.
[0060] The term "promoter" refers to a DNA sequence capable of
controlling the expression of a coding sequence or functional RNA.
In general, a coding sequence is located 3' to a promoter sequence.
Promoters may be derived in their entirety from a native gene, or
be composed of different elements derived from different promoters
found in nature, or even comprise synthetic DNA segments. It is
understood by those skilled in the art that different promoters may
direct the expression of a gene in different tissues or cell types,
or at different stages of development, or in response to different
environmental or physiological conditions. Promoters that cause a
gene to be expressed in most cell types at most times are commonly
referred to as "constitutive promoters." Promoters that cause a
gene to be expressed in a specific cell type are commonly referred
to as "cell-specific promoters" or "tissue-specific promoters."
Promoters that cause a gene to be expressed at a specific stage of
development or cell differentiation are commonly referred to as
"developmentally-specific promoters" or "cell
differentiation-specific promoters." Promoters that are induced and
cause a gene to be expressed following exposure or treatment of the
cell with an agent, biological molecule, chemical, ligand, light,
or the like that induces the promoter are commonly referred to as
"inducible promoters" or "regulatable promoters." It is further
recognized that since in most cases the exact boundaries of
regulatory sequences have not been completely defined, DNA
fragments of different lengths may have identical promoter
activity.
[0061] A "promoter sequence" is a DNA regulatory region capable of
binding RNA polymerase in a cell and initiating transcription of a
downstream (3' direction) coding sequence. For purposes of defining
the presently disclosed subject matter, the promoter sequence is
bounded at its 3' terminus by the transcription initiation site and
extends upstream (5' direction) to include the minimum number of
bases or elements necessary to initiate transcription at levels
detectable above background. Within the promoter sequence will be
found a transcription initiation site (conveniently defined for
example, by mapping with nuclease S1), as well as protein binding
domains (consensus sequences) responsible for the binding of RNA
polymerase.
[0062] A coding sequence is "under the control" of transcriptional
and translational control sequences in a cell when RNA polymerase
transcribes the coding sequence into mRNA, which is then trans-RNA
spliced (if the coding sequence contains introns) and translated
into the protein encoded by the coding sequence.
[0063] "Transcriptional and translational control sequences" are
DNA regulatory sequences, such as promoters, enhancers,
terminators, and the like, that provide for the expression of a
coding sequence in a host cell. In eukaryotic cells,
polyadenylation signals are control sequences.
[0064] The term "operably linked" refers to the association of
nucleic acid sequences on a single nucleic acid fragment so that
the function of one is affected by the other. For example, a
promoter is operably linked with a coding sequence when it is
capable of affecting the expression of that coding sequence (i.e.,
that the coding sequence is under the transcriptional control of
the promoter). Coding sequences can be operably linked to
regulatory sequences in sense or antisense orientation.
[0065] Enhancers that may be used in embodiments of the presently
disclosed subject matter include but are not limited to: an SV40
enhancer, a cytomegalovirus (CMV) enhancer, an elongation factor I
(EF1) enhancer, yeast enhancers, viral gene enhancers, and the
like.
[0066] Termination control regions, i.e., terminator or
polyadenylation sequences, may also be derived from various genes
native to the preferred hosts. In one embodiment of the presently
disclosed subject matter, the termination control region may
comprise or be derived from a synthetic sequence, synthetic
polyadenylation signal, an SV40 late polyadenylation signal, an
SV40 polyadenylation signal, a bovine growth hormone (BGH)
polyadenylation signal, viral terminator sequences, or the
like.
[0067] The terms "3' non-coding sequences" or "3' untranslated
region (UTR)" refer to DNA sequences located downstream (3') of a
coding sequence and may comprise polyadenylation [poly(A)]
recognition sequences and other sequences encoding regulatory
signals capable of affecting mRNA processing or gene expression.
The polyadenylation signal is usually characterized by affecting
the addition of polyadenylic acid tracts to the 3' end of the mRNA
precursor.
[0068] The term "regulatory region" means a nucleic acid sequence
that regulates the expression of a second nucleic acid sequence. A
regulatory region may include sequences which are naturally
responsible for expressing a particular nucleic acid (a homologous
region) or may include sequences of a different origin that are
responsible for expressing different proteins or even synthetic
proteins (a heterologous region). In particular, the sequences can
be sequences of prokaryotic, eukaryotic, or viral genes or derived
sequences that stimulate or repress transcription of a gene in a
specific or non-specific manner and in an inducible or
non-inducible manner. Regulatory regions include origins of
replication, RNA splice sites, promoters, enhancers,
transcriptional termination sequences, and signal sequences which
direct the polypeptide into the secretory pathways of the target
cell.
[0069] C. Modified Aptamers
[0070] In one embodiment of the presently disclosed subject matter,
the aptamers are modified to increase the circulating half-life of
the aptamer after administration to a subject. In one embodiment,
the nucleotides of the aptamers are linked by phosphate linkages.
In another embodiment, one or more of the internucleotide linkages
are modified linkages, e.g., linkages that are resistant to
nuclease degradation. The term "modified internucleotide linkage"
includes all modified internucleotide linkages known in the art or
that come to be known and that, from reading this disclosure, one
skilled in the art will conclude is useful in connection with the
present invention. Internucleotide linkages may have associated
counterions, and the term is meant to include such counterions and
any coordination complexes that can form at the internucleotide
linkages. Modifications of internucleotide linkages include,
without limitation, phosphorothioates, phosphorodithioates,
methylphosphonates, 5'-alkylenephosphonates, 5'-methylphosphonate,
3'-alkylene phosphonates, borontrifluoridates, borano phosphate
esters and selenophosphates of 3'-5' linkage or 2'-5' linkage,
phosphotriesters, thionoalkylphosphotriesters, hydrogen phosphonate
linkages, alkyl phosphonates, alkylphosphonothioates,
arylphosphonothioates, phosphoroselenoates, phosphorodiselenoates,
phosphinates, phosphoramidates, 3'-alkylphosphoramidates,
aminoalkylphosphoramidates, thionophosphoramidates,
phosphoropiperazidates, phosphoroanilothioates,
phosphoroanilidates, ketones, sulfones, sulfonamides, carbonates,
carbamates, methylenehydrazos, methylenedimethylhydrazos,
formacetals, thioformacetals, oximes, methyleneiminos,
methylenemethyliminos, thioamidates, linkages with riboacetyl
groups, aminoethyl glycine, silyl or siloxane linkages, alkyl or
cycloalkyl linkages with or without heteroatoms of, for example, 1
to 10 carbons that can be saturated or unsaturated and/or
substituted and/or contain heteroatoms, linkages with morpholino
structures, amides, polyamides wherein the bases can be attached to
the aza nitrogens of the backbone directly or indirectly, and
combinations of such modified internucleotide linkages. In another
embodiment, the aptamers comprise 5'- or 3'-terminal blocking
groups to prevent nuclease degradation (e.g., an inverted
deoxythymidine or hexylamine).
[0071] In a further embodiment, the aptamers are linked to
conjugates that increase the circulating half-life, e.g., by
decreasing nuclease degradation or renal filtration of the aptamer.
Conjugates may include, for example, amino acids, peptides,
polypeptides, proteins, antibodies, antigens, toxins, hormones,
lipids, nucleotides, nucleosides, sugars, carbohydrates, polymers
such as polyethylene glycol and polypropylene glycol, as well as
analogs or derivatives of all of these classes of substances.
Additional examples of conjugates also include steroids, such as
cholesterol, phospholipids, di- and tri-acylglycerols, fatty acids,
hydrocarbons that may or may not contain unsaturation or
substitutions, enzyme substrates, biotin, digoxigenin, and
polysaccharides. Further examples include thioethers such as
hexyl-S-tritylthiol, thiocholesterol, acyl chains such as
dodecandiol or undecyl groups, phospholipids such as
di-hexadecyl-rac-glycerol, triethylammonium
1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate, polyamines,
polyethylene glycol, adamantane acetic acid, palmityl moieties,
octadecylamine moieties, hexylaminocarbonyl-oxycholesterol,
farnesyl, geranyl and geranylgeranyl moieties, such as polyethylene
glycol, cholesterol, lipids, or fatty acids. Conjugates can also be
detectable labels. For example, conjugates can be fluorophores.
Conjugates can include fluorophores such as TAMRA, BODIPY, cyanine
derivatives such as Cy3 or Cy5 Dabsyl, or any other suitable
fluorophore known in the art. A conjugate may be attached to any
position on the terminal nucleotide that is convenient and that
does not substantially interfere with the desired activity of the
aptamer that bears it, for example the 3' or 5' position of a
ribosyl sugar. A conjugate substantially interferes with the
desired activity of an aptamer if it adversely affects its
functionality such that the ability of the aptamer to bind HbS,
including oxy-HbS and/or deoxy-HbS, is reduced by greater than 80%
in a binding assay.
[0072] In a further embodiment, the aptamers as described herein
that specifically bind HbS are linked to conjugates to mediate
intracellular delivery into a cell of interest. Accordingly another
embodiment of the presently disclosed subject matter relates to
compositions and methods for intracellular delivery of aptamers as
described herein that specifically bind HbS into a cell of
interest. "Cell of interest" as used herein refers to red blood
cells (RBCs or erythrocytes) and include nucleated or non-nucleated
adult and/or fetal red blood cells, but may also refer to
erythroblasts, reticulocytes, and/or normoblasts. Such conjugates
that mediate intracellular delivery of the aptamers as described
herein that specifically bind HbS into a cell of interest include
other aptamers that are known to specifically enter cells of
interest (referred to herein as "delivery aptamers") or other
ligands that bind receptors on a cell of interest and are
internalized by the cell (e.g., transferrin and transferrin
receptors (CD71) on red blood cells). Such conjugates may further
include detectable labels such as fluorophores to facilitate
methods of screening cells of interest containing the aptamers as
described herein that specifically bind HbS. Where the conjugates
are delivery aptamers, the delivery aptamers and the aptamers as
described herein that specifically bind HbS may be linked, for
example, covalently or functionally through nucleic acid duplex
formation. At least one of the linked aptamers may be partly or
wholly comprised of 2'-modified RNA or DNA such as 2'F, 2'OH,
2'OMe, 2'allyl, 2'MOE (methoxy-O-methyl) substituted nucleotides,
and may contain polyethylene glycol (PEG)-spacers and abasic
residues. Covalent linkages for delivery aptamers and other ligands
may include, for example, a linking moiety such as a nucleic acid
moiety, a PNA moiety, a peptidic moiety, a disulfide bond or a
polyethylene glycol (PEG) moiety.
III. Methods of Treatment
[0073] A. Methods for Treating Sickle Cell Disease
[0074] In one embodiment, the presently disclosed subject matter
relates to a method of treating or preventing sickle cell disease
in a subject in need thereof, the method comprising administering
to the subject a therapeutically effective amount of a
polynucleotide aptamer that specifically binds to sickle hemoglobin
(HbS) and inhibits polymerization of HbS. In a particular
embodiment, the polynucleotide aptamer inhibits polymerization of
HbS without a substantial or intolerable deleterious effect on
hemoglobin's functional capabilities (e.g., a mild shift in Hb
oxygen affinity might be associated with mild to moderate, but
tolerable side effects).
[0075] As used herein, "sickle cell disease" means that the subject
has at least one sickle cell. As used herein, a "sickle cell"
includes a cell which is an abnormal, crescent-shaped erythrocyte
that contains sickle cell hemoglobin from a subject with sickle
cell disease. "Sickling" includes the process whereby a
normal-shaped cell becomes crescent-shaped. As described herein,
sickle cell disease includes but is not limited to sickle cell
anemia, sickle .beta.-thalassemia, sickle cell-hemoglobin C disease
and any other sickle hemoglobinopathy in which HbS interacts with a
hemoglobin other than HbS. "Sickle hemoglobinopathy" is an
abnormality of hemoglobin which results in sickle cell disease or
sickle variants.
[0076] Any of the aptamers or modified aptamers described herein
that specifically bind HbS and inhibit polymerization of HbS,
including oxy-HbS and/or deoxy-HbS, may be used within these
methods of treating sickle cell disease in a subject in need
thereof. In one embodiment, the polynucleotide aptamer that
specifically binds to HbS and inhibits polymerization of HbS for
use within the methods for treating or preventing sickle cell
disease in a subject in need thereof is an RNA aptamer that
comprises a nucleotide sequence that is at least 70%, 75%, 80%,
85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%
identical to any one of SEQ ID NOS:2-60, or a fragment or analog
thereof. In a particular embodiment, the polynucleotide aptamer
that specifically binds to HbS and inhibits polymerization of HbS
for use within the methods for treating or preventing sickle cell
disease in a subject in need thereof is an RNA aptamer that
comprises a nucleotide sequence that is at least 70%, 75%, 80%,
85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%
identical to any one of SEQ ID NOS:2, 4, 31, and 37, or, a fragment
or analog thereof.
[0077] In some embodiments, the presently disclosed methods produce
at least about a 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%,
60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or even 100% inhibition of
polymerization of HbS relative to polymerization of HbS measured in
the absence of aptamers or modified aptamers described herein that
specifically bind HbS and inhibit polymerization of HbS, i.e., a
control sample, in an assay.
[0078] In any of the above-described methods, the administering of
any of aptamers or modified aptamers described herein that
specifically bind HbS and inhibit polymerization of HbS can result
in at least about a 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%,
55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or even 100% decrease
in one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) symptoms of
sickle cell disease, compared to a subject that is not administered
the aptamers or modified aptamers described herein that
specifically bind HbS and inhibit polymerization of HbS.
[0079] In any of the above-described methods, the administering of
the aptamers or modified aptamers described herein that
specifically bind HbS and inhibit polymerization of HbS results in
at least about a 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%,
60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or even 100% decrease in
the likelihood of developing sickle cell disease in a subject,
compared to a control population of subjects that are not
administered the aptamers or modified aptamers described herein
that specifically bind HbS and inhibit polymerization of HbS.
[0080] As used herein, the term "inhibit" or "inhibits" means to
decrease, suppress, attenuate, diminish, arrest, or stabilize the
development or progression of a disease, disorder, or condition,
the activity of a biological pathway, or a biological activity such
as polymerization of HbS, e.g., by at least 10%, 20%, 30%, 40%,
50%, 60%, 70%, 80%, 90%, 95%, 98%, 99%, or even 100% compared to an
untreated control subject, cell, biological pathway, or biological
activity. By the term "decrease" is meant to inhibit, suppress,
attenuate, diminish, arrest, or stabilize a symptom of a sickle
cell disease, disorder, or condition. Sickle cell disease
associated symptoms include, but are not limited to, erythrocyte
(RBC) sickling, oxygen release, increased HbS polymerization,
hemolysis, tissue congestion and organ damage or dysfunction. It
will be appreciated that, although not precluded, treating a
disease, disorder or condition does not require that the disease,
disorder, condition or symptoms associated therewith be completely
eliminated.
[0081] The method described above for treating or preventing sickle
cell disease in a subject in need thereof may be carried out using
a single aptamer targeted to HbS, or may be carried out using two
or more different aptamers targeted to HbS, e.g., three, four,
five, or six different aptamers.
[0082] For use within the methods for treating or preventing sickle
cell disease in a subject in need thereof, the aptamers described
herein that specifically bind to HbS and inhibit polymerization of
HbS may optionally be administered in conjunction with other
compounds (e.g., therapeutic agents) or treatments (e.g.,
hydroxyurea or blood transfusions) useful in treating sickle cell
disease. The other compounds or treatments may optionally be
administered concurrently. As used herein, the word "concurrently"
means sufficiently close in time to produce a combined effect (that
is, concurrently may be simultaneously, or it may be two or more
events occurring within a short time period before or after each
other). The other compounds may be administered separately from the
aptamers as disclosed herein, or may be combined together with the
aptamers as disclosed herein in a single composition.
[0083] As used herein, the terms "treat," treating," "treatment,"
and the like, are meant to decrease, suppress, attenuate, diminish,
arrest, the underlying cause of a disease, disorder, or condition,
or to stabilize the development or progression of a disease,
disorder, condition, and/or symptoms associated therewith. The
terms "treat," "treating," "treatment," and the like, as used
herein can refer to curative therapy, prophylactic therapy, and
preventative therapy. Accordingly, as used herein, "treating" means
either slowing, stopping or reversing the progression of the
sickling of a cell, including reversing the progression to the
point of eliminating the presence of sickled cells and/or reducing
or eliminating the amount of polymerization of hemoglobin, or the
amelioration of symptoms associated with sickle cell disease.
Sickle cell disease associated symptoms include, but are not
limited to, erythrocyte (RBC) sickling, oxygen release, increased
HbS polymerization, hemolysis, tissue congestion and organ damage
or dysfunction. The treatment, administration, or therapy can be
consecutive or intermittent. Consecutive treatment, administration,
or therapy refers to treatment on at least a daily basis without
interruption in treatment by one or more days. Intermittent
treatment or administration, or treatment or administration in an
intermittent fashion, refers to treatment that is not consecutive,
but rather cyclic in nature. Treatment according to the presently
disclosed methods can result in complete relief or cure from a
disease, disorder, or condition, or partial amelioration of one or
more symptoms of the disease, disease, or condition, and can be
temporary or permanent. The term "treatment" also is intended to
encompass prophylaxis, therapy and cure.
[0084] As used herein, the terms "prevent," "preventing,"
"prevention," "prophylactic treatment" and the like refer to
reducing the probability of developing a disease, disorder, or
condition in a subject, who does not have, but is at risk of or
susceptible to developing a disease, disorder, or condition. Thus,
in some embodiments, an agent can be administered prophylactically
to prevent the onset of a disease, disorder, or condition, or to
prevent the recurrence of a disease, disorder, or condition.
[0085] The subject treated by the presently disclosed methods in
their many embodiments is desirably a human subject, although it is
to be understood that the methods described herein are effective
with respect to all vertebrate species, which are intended to be
included in the term "subject." Accordingly, a "subject" can
include a human subject for medical purposes, such as for the
treatment of an existing disease, disorder, condition or the
prophylactic treatment for preventing the onset of a disease,
disorder, or condition or an animal subject for medical, veterinary
purposes, or developmental purposes. Suitable animal subjects
include mammals including, but not limited to, primates, e.g.,
humans, monkeys, apes, gibbons, chimpanzees, orangutans, macaques
and the like; bovines, e.g., cattle, oxen, and the like; ovines,
e.g., sheep and the like; caprines, e.g., goats and the like;
porcines, e.g., pigs, hogs, and the like; equines, e.g., horses,
donkeys, zebras, and the like; felines, including wild and domestic
cats; canines, including dogs; lagomorphs, including rabbits,
hares, and the like; and rodents, including mice, rats, guinea
pigs, and the like. An animal may be a transgenic animal. In some
embodiments, the subject is a human including, but not limited to,
fetal, neonatal, infant, juvenile, and adult subjects. Further, a
"subject" can include a patient afflicted with or suspected of
being afflicted with a disease, disorder, or condition. Thus, the
terms "subject" and "patient" are used interchangeably herein.
Subjects also include animal disease models (e.g., rats or mice
used in experiments, and the like).
[0086] B. Pharmaceutical Compositions
[0087] The presently disclosed pharmaceutical compositions and
formulations include pharmaceutical compositions of aptamers that
specifically bind to HbS and inhibit polymerization of HbS as
disclosed herein, alone or in combination with one or more
additional therapeutic agents, in admixture with a physiologically
compatible carrier, which can be administered to a subject, for
example, a human subject, for therapeutic or prophylactic
treatment. As used herein, "physiologically compatible carrier"
refers to a physiologically acceptable diluent including, but not
limited to water, phosphate buffered saline, or saline, and, in
some embodiments, can include an adjuvant. Acceptable carriers,
excipients, or stabilizers are nontoxic to recipients at the
dosages and concentrations employed, and can include buffers such
as phosphate, citrate, and other organic acids; antioxidants
including ascorbic acid, BHA, and BHT; low molecular weight (less
than about 10 residues) polypeptides; proteins, such as serum
albumin, gelatin or immunoglobulins; hydrophilic polymers, such as
polyvinylpyrrolidone, amino acids such as glycine, glutamine,
asparagine, arginine, or lysine; monosaccharides, disaccharides,
and other carbohydrates including glucose, mannose, or dextrins;
chelating agents such as EDTA; sugar alcohols such as mannitol or
sorbitol; salt-forming counter-ions such as sodium; and/or nonionic
surfactants such as Tween, Pluronics, or PEG. Adjuvants suitable
for use with the presently disclosed compositions include adjuvants
known in the art including, but not limited to, incomplete Freund's
adjuvant, aluminum phosphate, aluminum hydroxide, and alum.
[0088] Compositions to be used for in vivo administration must be
sterile, which can be achieved by filtration through sterile
filtration membranes, prior to or following lyophilization and
reconstitution. Therapeutic compositions may be placed into a
container having a sterile access port, for example, an intravenous
solution bag or vial having a stopper pierceable by a hypodermic
injection needle.
[0089] In certain embodiments, the presently disclosed subject
matter also includes combination therapies. Additional therapeutic
agents, which are normally administered to treat or prevent sickle
cell disease, may be administered in combination with aptamers that
specifically bind to HbS and inhibit polymerization of HbS as
disclosed herein. These additional agents may be administered
separately, as part of a multiple dosage regimen, from the
composition comprising aptamers that specifically bind to HbS and
inhibit polymerization of HbS as disclosed herein. Alternatively,
these agents may be part of a single dosage form, mixed together
with the aptamers that specifically bind to HbS and inhibit
polymerization of HbS as disclosed herein, in a single
composition.
[0090] By "in combination with" is meant the administration of a
aptamers that specifically bind to HbS and inhibit polymerization
of HbS as disclosed herein, with one or more therapeutic agents
either simultaneously, sequentially, or a combination thereof.
Therefore, a subject administered a combination of aptamers that
specifically bind to HbS and inhibit polymerization of HbS as
disclosed herein, can receive an aptamer that specifically binds to
HbS and inhibits polymerization of HbS as disclosed herein, and one
or more therapeutic agents at the same time (i.e., simultaneously)
or at different times (i.e., sequentially, in either order, on the
same day or on different days), so long as the effect of the
combination of both agents is achieved in the subject. When
administered sequentially, the agents can be administered within 1,
5, 10, 30, 60, 120, 180, 240 minutes or longer of one another. In
other embodiments, agents administered sequentially, can be
administered within 1, 5, 10, 15, 20 or more days of one another.
Where the aptamer that specifically binds to HbS and inhibits
polymerization of HbS as disclosed herein, and one or more
therapeutic agents are administered simultaneously, they can be
administered to the subject as separate pharmaceutical
compositions, each comprising either an aptamer that specifically
binds to HbS and inhibits polymerization of HbS as disclosed
herein, or one or more therapeutic agents, or be administered to a
subject as a single pharmaceutical composition comprising both
agents.
[0091] When administered in combination, the effective
concentration of each of the agents to elicit a particular
biological response may be less than the effective concentration of
each agent when administered alone, thereby allowing a reduction in
the dose of one or more of the agents relative to the dose that
would be needed if the agent was administered as a single agent.
The effects of multiple agents may, but need not be, additive or
synergistic. The agents may be administered multiple times. In such
combination therapies, the therapeutic effect of the first
administered agent is not diminished by the sequential,
simultaneous or separate administration of the subsequent
agent(s).
[0092] C. Dosage and Mode of Administration
[0093] The presently disclosed pharmaceutical compositions can be
administered using a variety of methods known in the art depending
on the subject and the particular disease, disorder, or condition
being treated. The administering can be carried out by, for
example, intravenous infusion; injection by intravenous,
intraperitoneal, intracerebral, intramuscular, intraocular,
intraarterial or intralesional routes; or topical or ocular
application.
[0094] More particularly, as described herein, the presently
disclosed aptamers that specifically bind to HbS and inhibit
polymerization of HbS can be administered to a subject for therapy
by any suitable route of administration, including orally, nasally,
transmucosally, ocularly, rectally, intravaginally, parenterally,
including intramuscular, subcutaneous, intramedullary injections,
as well as intrathecal, direct intraventricular, intravenous,
intra-articular, intra-sternal, intra-synovial, intra-hepatic,
intralesional, intracranial, intraperitoneal, intranasal, or
intraocular injections, intracisternally, topically, as by powders,
ointments or drops (including eyedrops), including buccally and
sublingually, transdermally, through an inhalation spray, or other
modes of delivery known in the art.
[0095] The phrases "systemic administration," "administered
systemically," "peripheral administration" and "administered
peripherally" as used herein mean the administration of an aptamer
that specifically binds to HbS and inhibits polymerization of HbS,
a compound, drug or other material other than directly into the
central nervous system, such that it enters the patient's system
and, thus, is subject to metabolism and other like processes, for
example, subcutaneous administration.
[0096] The phrases "parenteral administration" and "administered
parenterally" as used herein mean modes of administration other
than enteral and topical administration, usually by injection, and
includes, without limitation, intravenous, intramuscular,
intarterial, intrathecal, intracapsular, intraorbital, intraocular,
intracardiac, intradermal, intraperitoneal, transtracheal,
subcutaneous, subcuticular, intraarticular, subcapsular,
subarachnoid, intraspinal and intrasternal injection and
infusion.
[0097] The presently disclosed pharmaceutical compositions can be
manufactured in a manner known in the art, e.g. by means of
conventional mixing, dissolving, granulating, dragee-making,
levitating, emulsifying, encapsulating, entrapping or lyophilizing
processes.
[0098] More particularly, pharmaceutical compositions for oral use
can be obtained through combination of an aptamer that specifically
binds to HbS and inhibits polymerization of HbS with a solid
excipient, optionally grinding a resulting mixture, and processing
the mixture of granules, after adding suitable auxiliaries, if
desired, to obtain tablets or dragee cores. Suitable excipients
include, but are not limited to, carbohydrate or protein fillers,
such as sugars, including lactose, sucrose, mannitol, or sorbitol;
starch from corn, wheat, rice, potato, or other plants; cellulose,
such as methyl cellulose, hydroxypropylmethyl-cellulose, or sodium
carboxymethyl cellulose; and gums including arabic and tragacanth;
and proteins, such as gelatin and collagen; and
polyvinylpyrrolidone (PVP:povidone). If desired, disintegrating or
solubilizing agents, such as cross-linked polyvinyl pyrrolidone,
agar, alginic acid, or a salt thereof, such as sodium alginate,
also can be added to the compositions.
[0099] Dragee cores are provided with suitable coatings, such as
concentrated sugar solutions, which also can contain gum arabic,
talc, polyvinylpyrrolidone, carbopol gel, polyethylene glycol
(PEG), and/or titanium dioxide, lacquer solutions, and suitable
organic solvents or solvent mixtures. Dyestuffs or pigments can be
added to the tablets or dragee coatings for product identification
or to characterize the quantity of an aptamer that specifically
binds to HbS and inhibits polymerization of HbS, e.g., dosage, or
different combinations of aptamer doses.
[0100] Pharmaceutical compositions suitable for oral administration
include push-fit capsules made of gelatin, as well as soft, sealed
capsules made of gelatin and a coating, e.g., a plasticizer, such
as glycerol or sorbitol. The push-fit capsules can contain active
ingredients admixed with a filler or binder, such as lactose or
starches, lubricants, such as talc or magnesium stearate, and,
optionally, stabilizers. In soft capsules, the aptamer that
specifically binds to HbS and inhibits polymerization of HbS can be
dissolved or suspended in suitable liquids, such as fatty oils,
liquid paraffin, or liquid polyethylene glycols (PEGs), with or
without stabilizers. Stabilizers can be added as warranted.
[0101] In some embodiments, the presently disclosed pharmaceutical
compositions can be administered by rechargeable or biodegradable
devices. For example, a variety of slow-release polymeric devices
have been developed and tested in vivo for the controlled delivery
of drugs, including proteinacious biopharmaceuticals. Suitable
examples of sustained release preparations include semipermeable
polymer matrices in the form of shaped articles, e.g., films or
microcapsules. Sustained release matrices include polyesters,
hydrogels, polylactides (U.S. Pat. No. 3,773,919; EP 58,481),
copolymers of L-glutamic acid and gamma ethyl-L-glutamate (Sidman
et al., Biopolymers 22:547, 1983), poly
(2-hydroxyethyl-methacrylate) (Langer et al., J. Biomed. Mater.
Res. 15:167, 1981; Langer, Chem. Tech. 12:98, 1982), ethylene vinyl
acetate (Langer et al., Id), or poly-D-(-)-3-hydroxybutyric acid
(EP 133,988A). Sustained release compositions also include
liposomally entrapped aptamers, which can be prepared by methods
known per se (Epstein et al., Proc. Natl. Acad. Sci. U.S.A.
82:3688, 1985; Hwang et al., Proc. Natl. Acad. Sci. U.S.A. 77:4030,
1980; U.S. Pat. Nos. 4,485,045 and 4,544,545; and EP 102,324A).
Ordinarily, the liposomes are of the small (about 200-800
Angstroms) unilamelar type in which the lipid content is greater
than about 30 mol % cholesterol, the selected proportion being
adjusted for the optimal therapy. Such materials can comprise an
implant, for example, for sustained release of the presently
disclosed aptamers that specifically bind to HbS and inhibit
polymerization of HbS, which, in some embodiments, can be implanted
at a particular, pre-determined target site.
[0102] Pharmaceutical compositions for parenteral administration
include aqueous solutions of aptamers that specifically bind to HbS
and inhibit polymerization of HbS. For injection, the presently
disclosed pharmaceutical compositions can be formulated in aqueous
solutions, for example, in some embodiments, in physiologically
compatible buffers, such as Hank's solution, Ringer's solution, or
physiologically buffered saline. Aqueous injection suspensions can
contain substances that increase the viscosity of the suspension,
such as sodium carboxymethyl cellulose, sorbitol, or dextran.
Additionally, suspensions of the aptamers that specifically bind to
HbS and inhibit polymerization of HbS or vehicles include fatty
oils, such as sesame oil, or synthetic fatty acid esters, such as
ethyl oleate or triglycerides, or liposomes. Optionally, the
suspension also can contain suitable stabilizers or agents that
increase the solubility of the aptamers that specifically bind to
HbS and inhibit polymerization of HbS to allow for the preparation
of highly concentrated solutions.
[0103] For nasal or transmucosal administration generally,
penetrants appropriate to the particular barrier to be permeated
are used in the formulation. Such penetrants are generally known in
the art.
[0104] For inhalation delivery, the agents of the disclosure also
can be formulated by methods known to those of skill in the art,
and may include, for example, but not limited to, examples of
solubilizing, diluting, or dispersing substances such as, saline,
preservatives, such as benzyl alcohol, absorption promoters, and
fluorocarbons.
[0105] Additional ingredients can be added to compositions for
topical administration, as long as such ingredients are
pharmaceutically acceptable and not deleterious to the epithelial
cells or their function. Further, such additional ingredients
should not adversely affect the epithelial penetration efficiency
of the composition, and should not cause deterioration in the
stability of the composition. For example, fragrances, opacifiers,
antioxidants, gelling agents, stabilizers, surfactants, emollients,
coloring agents, preservatives, buffering agents, and the like can
be present. The pH of the presently disclosed topical composition
can be adjusted to a physiologically acceptable range of from about
6.0 to about 9.0 by adding buffering agents thereto such that the
composition is physiologically compatible with a subject's
skin.
[0106] In other embodiments, the pharmaceutical composition can be
a lyophilized powder, optionally including additives, such as 1
mM-50 mM histidine, 0.1%-2% sucrose, 2%-7% mannitol at a pH range
of 4.5 to 5.5 that is combined with buffer prior to use.
[0107] The presently disclosed subject matter also includes the use
of aptamers that specifically bind to HbS and inhibit
polymerization of HbS disclosed herein, in the manufacture of a
medicament for sickle cell disease.
[0108] Regardless of the route of administration selected, the
presently disclosed aptamers that specifically bind to HbS and
inhibit polymerization of HbS, which may be used in a suitable
hydrated form, and/or the pharmaceutical compositions are
formulated into pharmaceutically acceptable dosage forms such as
described below or by other conventional methods known to those of
skill in the art.
[0109] The term "effective amount," as in "a therapeutically
effective amount," of a therapeutic agent refers to the amount of
the agent necessary to elicit the desired biological response. As
will be appreciated by those of ordinary skill in this art, the
effective amount of an agent may vary depending on such factors as
the desired biological endpoint, the agent to be delivered, the
composition of the pharmaceutical composition, the target tissue or
cell, and the like. More particularly, the term "effective amount"
refers to an amount sufficient to produce the desired effect, e.g.,
to reduce or ameliorate the severity, duration, progression, or
onset of a disease, disorder, or condition (e.g., a disease,
condition, or disorder related to polymerization of HbS such as
sickle cell disease), or one or more symptoms thereof; prevent the
advancement of a disease, disorder, or condition, cause the
regression of a disease, disorder, or condition; prevent the
recurrence, development, onset or progression of a symptom
associated with a disease, disorder, or condition, or enhance or
improve the prophylactic or therapeutic effect(s) of another
therapy.
[0110] Actual dosage levels of the active ingredients in the
presently disclosed pharmaceutical compositions can be varied so as
to obtain an amount of the active ingredient that is effective to
achieve the desired therapeutic response for a particular subject,
composition, route of administration, and disease, disorder, or
condition without being toxic to the subject. The selected dosage
level will depend on a variety of factors including the activity of
the particular aptamer employed, the route of administration, the
time of administration, the rate of excretion of the particular
aptamer being employed, the duration of the treatment, other drugs,
aptamers and/or materials used in combination with the particular
aptamer employed, the age, sex, weight, condition, general health
and prior medical history of the patient being treated, and like
factors well known in the medical arts.
[0111] A physician or veterinarian having ordinary skill in the art
can readily determine and prescribe the effective amount of the
pharmaceutical composition required. For example, the physician or
veterinarian could start doses of the aptamers that specifically
bind to HbS and inhibit polymerization of HbS, employed in the
pharmaceutical composition at levels lower than that required to
achieve the desired therapeutic effect and gradually increase the
dosage until the desired effect is achieved. Accordingly, the
dosage range for administration will be adjusted by the physician
as necessary. It will be appreciated that an amount of an aptamer
required for achieving the desired biological response, e.g.,
inhibition of polymerization of HbS, may be different from the
amount of compound effective for another purpose.
[0112] In general, a suitable daily dose of aptamers that
specifically bind to HbS and inhibit polymerization of HbS, will be
that amount of the aptamer that is the lowest dose effective to
produce a therapeutic effect. Such an effective dose will generally
depend upon the factors described above. Generally, doses of the
aptamers that specifically bind to HbS and inhibit polymerization
of HbS will range from about 0.0001 to about 1000 mg per kilogram
of body weight of the subject per day. In certain embodiments, the
dosage is between about 1 .mu.g/kg and about 500 mg/kg, more
preferably between about 0.01 mg/kg and about 50 mg/kg. For
example, in certain embodiments, a dose can be about 1, 5, 10, 15,
20, or 40 mg/kg/day.
[0113] If desired, the effective daily dose of the aptamers that
specifically bind to HbS and inhibit polymerization of HbS can be
administered as two, three, four, five, six or more sub-doses
administered separately at appropriate intervals throughout the
day, optionally, in unit dosage forms.
[0114] D. Kits or Pharmaceutical Systems
[0115] The presently disclosed aptamers that specifically bind to
HbS and inhibit polymerization of HbS disclosed herein and
compositions can be assembled into kits or pharmaceutical systems
for use in treating or preventing neurodegenerative diseases,
disorders, or conditions. In some embodiments, the presently
disclosed kits or pharmaceutical systems include aptamers that
specifically bind to HbS and inhibit polymerization of HbS as
disclosed herein. In particular embodiments, the aptamers that
specifically bind to HbS and inhibit polymerization of HbS as
disclosed herein, are in unit dosage form. In further embodiments,
the aptamers that specifically bind to HbS and inhibit
polymerization of HbS as disclosed herein, can be present together
with a pharmaceutically acceptable solvent, carrier, excipient, or
the like, as described herein.
[0116] In some embodiments, the presently disclosed kits comprise
one or more containers, including, but not limited to a vial, tube,
ampule, bottle and the like, for containing the compound. The one
or more containers also can be carried within a suitable carrier,
such as a box, carton, tube or the like. Such containers can be
made of plastic, glass, laminated paper, metal foil, or other
materials suitable for holding medicaments.
[0117] In some embodiments, the container can hold a composition
that is by itself or when combined with another composition
effective for treating or preventing the condition and may have a
sterile access port (for example the container may be an
intravenous solution bag or a vial having a stopper pierceable by a
hypodermic injection needle). Alternatively, or additionally, the
article of manufacture may further include a second (or third)
container including a pharmaceutically-acceptable buffer, such as
bacteriostatic water for injection (BWFI), phosphate-buffered
saline, Ringer's solution and dextrose solution. It may further
include other materials desirable from a commercial and user
standpoint, including other buffers, diluents, filters, needles,
and syringes.
[0118] The presently disclosed kits or pharmaceutical systems also
can include associated instructions for using the aptamers that
specifically bind to HbS and inhibit polymerization of HbS as
disclosed herein for treating or sickle cell disease. In some
embodiments, the instructions include one or more of the following:
a description of the aptamer that specifically binds to HbS and
inhibits polymerization of HbS as disclosed herein; a dosage
schedule and administration for treating or preventing sickle cell
disease; precautions; warnings; indications; counter-indications;
overdosage information; adverse reactions; animal pharmacology;
clinical studies; and references. The instructions can be printed
directly on a container (when present), as a label applied to the
container, as a separate sheet, pamphlet, card, or folder supplied
in or with the container.
IV. Antidotes
[0119] The presently disclosed subject matter also relates to
antidotes for the aptamers that specifically bind to HbS and
inhibit polymerization of HbS as disclosed herein. Such antidotes
can comprise oligonucleotides that are reverse complements of
segments of the aptamers that specifically bind to HbS and inhibit
polymerization of HbS as disclosed herein. In accordance with the
presently disclosed subject matter, the antidote is contacted with
a targeted aptamer under conditions such that it binds to the
aptamer and modifies the interaction between the aptamer and its
target molecule (e.g., HbS). Modification of that interaction can
result from modification of the aptamer structure as a result of
binding by the antidote. The antidote can bind free aptamer and/or
aptamer bound to its target molecule. In certain embodiments, the
aptamer that specifically binds to HbS and inhibits polymerization
of HbS as disclosed herein is provided in alternation with an
antidote.
[0120] Antidotes of the presently disclosed subject matter can be
designed so as to bind any particular aptamer with a high degree of
specificity and a desired degree of affinity. The antidote can be
designed so that upon binding to the targeted aptamer, the
three-dimensional structure of that aptamer is altered such that
the aptamer can no longer bind to its target molecule or binds to
its target molecule with less affinity.
[0121] Antidotes of the presently disclosed subject matter include
any pharmaceutically acceptable agent that can bind an aptamer and
modify the interaction between that aptamer and its target molecule
(e.g., by modifying the structure of the aptamer) in a desired
manner. Examples of such antidotes include oligonucleotides
complementary to at least a portion of the aptamers that
specifically bind to HbS and inhibit polymerization of HbS as
disclosed herein (including ribozymes or DNAzymes or peptide
nucleic acids), nucleic acid binding peptides, polypeptides or
proteins including nucleic acid binding tripeptides (see generally,
Hwang et al. (1999) Proc. Natl. Acad. Sci. USA 96:12997), and
oligosaccharides such as aminoglycosides (see, generally, Davies et
al. (1993) Chapter 8, p. 185, RNA World, Cold Spring Harbor
Laboratory Press, eds Gestlaad and Atkins; Werstuck et al. (1998)
Science 282:296; U.S. Pat. Nos. 5,935,776 and 5,534,408; Chase et
al. (1986) Ann. Rev. Biochem. 56:103; Eichhorn et al. (1968) J. Am.
Chem. Soc. 90:7323; Dale et al. (1975) Biochemistry 14:2447; and
Lippard et al. (1978) Acc. Chem. Res. 11:211).
[0122] Standard binding assays can be used to screen for antidotes
of the presently disclosed subject matter (e.g., using BIACORE
assays). Candidate antidotes can be contacted with the aptamer to
be targeted under conditions favoring binding and a determination
made as to whether the candidate antidote in fact binds the
aptamer. Candidate antidotes that are found to bind the aptamer can
then be analyzed in an appropriate bioassay (which will vary
depending on the aptamer and its target molecule) to determine if
the candidate antidote can affect the binding of the aptamer to its
target molecule.
[0123] Where the antidote is an oligonucleotide, the antidote
oligonucleotide does not need to be completely complementary to the
aptamer that specifically binds to HbS and inhibits polymerization
of HbS as disclosed herein as long as the antidote sufficiently
binds to or hybridizes to the aptamer to neutralize its activity.
In one embodiment, the antidote of the presently disclosed subject
matter is an oligonucleotide that comprises a sequence
complementary to at least a portion of the targeted aptamer
sequence. In one embodiment, the antidote oligonucleotide comprises
a sequence complementary to up to 80, 75, 70, 65, 60, 55, 50, 45,
40, 35, 30, 25, 20, 15, 10, or 5 consecutive nucleotides of the
targeted aptamer.
V. Diagnostic Methods
[0124] In one embodiment, the presently disclosed subject matter
provides a method for diagnosing or predicting a sickle cell
disease in a subject having or at risk of developing a sickle cell
disease or at risk of passing it on to offspring. The method
includes contacting a biological sample from the subject with an
aptamer that specifically binds to HbS and inhibits polymerization
of HbS as disclosed herein.
[0125] The aptamers that specifically bind to HbS and inhibit
polymerization of HbS as disclosed herein are particularly well
suited for diagnostic applications. Aptamers represent a class of
molecules that may be used in place of antibodies for in vitro or
in vivo diagnostic purposes. The aptamers of the presently
disclosed subject matter are therefore particularly useful as
diagnostic reagents to detect the presence or absence of the target
substances to which they specifically bind, i.e., HbS. Such
diagnostic tests are conducted by contacting a biological sample
with the specifically binding oligonucleotide to obtain a complex
which is then detected by conventional means. For example, the
aptamers may be labeled using radioactive, fluorescent, or
chromogenic labels and the presence of label bound to solid support
to which the target substance has been bound through a specific or
nonspecific binding means detected. Alternatively, the specifically
binding oligonucleotides may be used to effect initial complexation
to the support. Means for conducting assays using such oligomers as
specific binding partners will track those for standard specific
binding partner based assays.
[0126] Accordingly, in one embodiment, the presently disclosed
subject matter provides a method for diagnosing or predicting a
sickle cell disease in a subject having or at risk of developing a
sickle cell disease or at risk of passing it on to offspring, the
method comprising: (a) obtaining a biological sample from the
subject; (b) contacting the biological sample with a polynucleotide
aptamer that specifically binds to HbS as disclosed herein; and (c)
detecting binding of the polynucleotide aptamer with HbS in the
biological sample, wherein detection of binding of the
polynucleotide aptamer with HbS in the biological sample is
indicative of the subject having or at risk of developing a sickle
cell disease or at risk of passing it on to offspring. The aptamers
can be labeled for detection using methods and labels known in the
art including, but not limited to, fluorescent, luminescent,
phosphorescent, radioactive, and/or colorimetric compounds.
[0127] As used herein, the phrase "biological sample" encompasses a
variety of sample types obtained from a subject and useful in the
procedure of the presently disclosed subject matter. In one
embodiment of the presently disclosed subject matter, the
biological sample comprises whole blood, hemocytes, serum, or
plasma. However, biological samples may include, but are not
limited to, solid tissue samples, liquid tissue samples, biological
fluids, aspirates, cells and cell fragments. Specific examples of
biological samples include, but are not limited to, solid tissue
samples obtained by surgical removal, pathology specimens, archived
samples, or biopsy specimens, tissue cultures or cells derived
therefrom and the progeny thereof, and sections or smears prepared
from any of these sources. Non-limiting examples of biological
samples include samples obtained from breast tissue, lymph nodes,
and breast tumors. Biological samples also include any material
derived from the body of a vertebrate animal, including, but not
limited to, blood, cerebrospinal fluid, serum, plasma, urine,
nipple aspirate, fine needle aspirate, tissue lavage such as ductal
lavage, saliva, sputum, ascites fluid, liver, kidney, breast, bone,
bone marrow, testes, brain, ovary, skin, lung, prostate, thyroid,
pancreas, cervix, stomach, intestine, colorectal, brain, bladder,
colon, nares, uterine, semen, lymph, vaginal pool, synovial fluid,
spinal fluid, head and neck, nasopharynx tumors, amniotic fluid,
breast milk, pulmonary sputum or surfactant, urine, fecal matter
and other liquid samples of biologic origin.
VI. Capture Reagents
[0128] In another embodiment, the presently disclosed subject
matter relates to the use of aptamers that specifically bind to HbS
as capture reagents for clearing clear HbS or other hemoglobins
(including normal hemoglobin) from a biological sample. Within
these methods of the invention, the aptamers that specifically bind
to HbS do not necessarily need to also inhibit polymerization of
HbS.
[0129] Accordingly, in one embodiment the presently disclosed
subject matter is directed to a method of purifying hemoglobin from
a biological sample comprising providing a biological sample
containing hemoglobin, contacting the biological sample with an
aptamer that specifically binds to HbS as disclosed herein under
conditions effective to bind hemoglobin to the aptamer, and
recovering the hemoglobin bound to the aptamer. In certain
embodiments, the hemoglobin is HbS. In other embodiments, the
biological sample comprises whole blood, hemocytes, serum, or
plasma.
[0130] The methods for purifying hemoglobin from a biological
sample may include the use of a solid support comprising an
immobilized aptamer. Thus, in one embodiment of the method of
purifying hemoglobin from a biological sample, the step of
contacting the biological sample with an aptamer that specifically
binds to HbS as disclosed herein under conditions effective to bind
hemoglobin to the aptamer comprises providing a solid support
comprising an aptamer that specifically binds to HbS as disclosed
herein immobilized onto the solid support through a spacer.
[0131] As used herein, a "spacer" is intended to mean a molecule
which is inserted between the aptamer and the solid support.
Advantageously, the spacer is bound both to one end of the aptamer
and to the solid support. Advantageously, such structure comprising
a spacer does not immobilize directly the aptamer onto the solid
support. The nature of the spacer may be chosen according to the
knowledge of one skilled in the art; for example the spacer may be
a non specific oligonucleotide sequence or may be polyethylene
glycol (PEG). When the spacer is a non specific oligonucleotide
sequence, said sequence may contain at least 5 nucleotides,
particularly between 5 and 15 nucleotides.
[0132] For immobilizing the aptamer onto a spacer, the aptamer may
be chemically modified with various chemical groups such as groups
enabling to covalently immobilize the aptamer, such as thiols,
amines or any other group that could react with chemical groups
present on the support or groups enabling to non-covalently
immobilize the aptamer, such as the biotin-streptavidin system.
These techniques may also be used for immobilizing the spacer onto
the solid support.
[0133] Once immobilized onto the solid support via the spacer, the
aptamer may be modified at the free end thereof (i.e. the end that
is not bound to the spacer) by, without limitation, a chemically
modified nucleotide (such as 2' omethyl or 2' fluoropyrimidine, 2'
ribopurine, phosphoramidite), a reversed nucleotide or a chemical
group (PEG, polycations, cholesterol). These and other
modifications to the presently disclosed aptamers as disclosed
elsewhere herein may be used to protect the aptamer against
enzymatic degradation.
[0134] The solid support may be an affinity chromatography column
containing a gel derived from agarose or cellulose or a synthetic
gel such as an acrylamide, a methacrylate or a polystyrene
derivative; a chip such as a chip adapted for surface plasmon
resonance; a membrane such as a polyamide, a polyacrylonitrile or a
polyester membrane; a magnetic or paramagnetic bead.
VII. Rational Drug Design
[0135] In another embodiment, the presently disclosed subject
matter relates to the use of an aptamer that specifically binds to
HbS and inhibits polymerization of HbS as disclosed herein as a
template for rational drug design.
[0136] For example, structures of RNA aptamers that recognize the
shape of HbS could be determined by spectroscopy or X-ray
crystallography. These structures could be used to guide the
rational design of drugs (mimetics) that would recognize and bind
to HbS and inhibit polymerization of HbS.
[0137] Accordingly, in one embodiment the presently disclosed
subject matter is directed to a method of using a three-dimensional
structure of an aptamer that specifically binds to HbS and inhibits
polymerization of HbS as disclosed herein in a drug screening assay
comprising:
[0138] (a) selecting a potential drug by performing rational drug
design with the three-dimensional structure of the polynucleotide
aptamer that specifically binds to HbS and inhibits polymerization
of HbS determined from one or more sets of atomic coordinates;
wherein said selecting is performed in conjunction with computer
modeling;
[0139] (b) contacting the potential drug with HbS;
[0140] (c) detecting the binding of the potential drug with the
HbS; and
[0141] (d) detecting the inhibition of polymerization of HbS by the
potential drug; wherein a potential drug is selected as a drug if
the potential drug binds to HbS and inhibits polymerization of
HbS.
[0142] Alternatively, a refined aptamer sequence can be elucidated
by modifying a known aptamer structure using software comprising
"builder" type algorithms which utilizes a set of atomic
coordinates defining a three-dimensional structure of the binding
pocket and the three-dimensional structures of the known aptamer to
computationally assemble a refined aptamer. Ample guidance for
performing rational drug design via software employing such
"scanner" and "builder" type algorithms is available in the
literature of the art (e.g., Halperin et al. (2002) Proteins
47:409-43; Gohlke & Klebe (2001) Curr Opin Struct Biol.
11:231-5; Zeng (2000) Comb. Chem. High Throughput Screen.
3:355-62).
[0143] Criteria that may be employed by software programs used in
rational drug design to qualify the binding of screened aptamer
structures with binding pockets and/or binding sites of HbS include
gap space, hydrogen bonding, electrostatic interactions, van der
Waals forces, hydrophilicity/hydrophobicity, etc. Generally, the
greater the contact area between the screened aptamer and the HbS
binding region, the lower the steric hindrance, the lower the "gap
space", the greater the number of hydrogen bonds, and the greater
the sum total of the van der Waals forces between the screened
aptamer and the HbS binding region, the greater will be the
capacity of the screened aptamer to bind with the target HbS. The
"gap space" refers to unoccupied space between the van der Waals
surface of a screened aptamer positioned within a binding pocket or
site and the surface of the binding pocket or site defined by amino
acid residues in the binding pocket or site. Gap space may be
identified, for example, using an algorithm based on a series of
cubic grids surrounding the docked molecule, with a user-defined
grid spacing, and represents volume that could advantageously be
occupied by a modifying the docked aptamer positioned within the
binding region of the HbS.
[0144] Contact area between compounds may be directly calculated
from the coordinates of the compounds in docked conformation using
the MS program (Connolly (1983) Science 221:709-713).
[0145] Suitable software employing "scanner" type algorithms
include, for example, docking software such as GRAM, DOCK, or
AUTODOCK (reviewed in Dunbrack et al. (1997) Folding and Design
2:27), AFFINITY software of the INSIGHTII package (Molecular
Simulations Inc., 1996, San Diego, Calif.), GRID (Goodford (1985)
J. Med. Chem. 28:849-857; GRID is available from Oxford University,
Oxford, UK), and MCSS (Miranker & Karplus (1991) Proteins:
Structure Function and Genetics 11:29-34; MCSS is available from
Molecular Simulations, Burlington, Mass.).
[0146] The AUTODOCK program (Goodsell & Olson (1990) Proteins:
Struct Funct Genet. 8:195-202; available from Scripps Research
Institute, La Jolla, Calif.) helps in docking screened molecules to
binding pockets in a flexible manner using a Monte Carlo simulated
annealing approach. The procedure enables a search without bias
introduced by the researcher. This bias can influence orientation
and conformation of a screened molecule in the targeted binding
pocket
[0147] The DOCK program (Kuntz et al. (1982) J. Mol. Biol.
161:269-288; available from University of California, San
Francisco), is based on a description of the negative image of a
space-filling representation of the binding pocket, and includes a
force field for energy evaluation, limited conformational
flexibility and consideration of hydrophobicity in the energy
evaluation.
[0148] Modeling or docking may be followed by energy minimization
with standard molecular mechanics force fields or dynamics with
programs such as CHARMM (Brooks et al. (1983) J. Comp. Chem.
4:187-217) or AMBER (Weiner et al. (1984) J. Am. Chem. Soc.
106:765-784). As used herein, "minimization of energy" means
achieving an atomic geometry of a chemical structure via systematic
alteration such that any further minor perturbation of the atomic
geometry would cause the total energy of the system as measured by
a molecular mechanics force-field to increase. Minimization and
molecular mechanics force fields are well understood in
computational chemistry (e.g., Burkert & Allinger, "Molecular
Mechanics", ACS Monograph 177, pp. 59-78, American Chemical
Society, Washington, D.C. (1982)).
[0149] Programs employing "builder" type algorithms include LEGEND
(Nishibata & Itai (1991) Tetrahedron 47:8985; available from
Molecular Simulations, Burlington, Mass.), LEAPFROG (Tripos
Associates, St. Louis, Mo.), CAVEAT (Bartlett et al. (1989) Special
Pub Royal Chem Soc. 78:182-196; available from University of
California, Berkeley), HOOK (Molecular Simulations, Burlington,
Mass.), and LUDI (Bohm (1992) J. Comp. Aid Molec. Design 6:61-78;
available from Biosym Technologies, San Diego, Calif.).
[0150] The CAVEAT program suggests binding molecules based on
desired bond vectors. The HOOK program proposes docking sites by
using multiple copies of functional groups in simultaneous
searches. LUDI is a program based on fragments rather than on
descriptors which proposes somewhat larger fragments to match with
a binding pocket and scores its hits based on geometric criteria
taken from the Cambridge Structural Database (CSD), the Protein
Data Bank (PDB) and on criteria based on binding data. LUDI may be
advantageously employed to calculate the inhibition constant of a
docked chemical structure Inhibition constants (Ki values) of
compounds in the final docking positions can be evaluated using
LUDI software.
[0151] During or following rational drug design, docking of an
intermediate chemical structure or of an aptamer with the HbS
binding pocket or site may be visualized via structural models,
such as three-dimensional models, thereof displayed on a computer
screen, so as to advantageously allow user intervention during the
rational drug design to optimize a chemical structure.
[0152] Software programs useful for displaying such
three-dimensional structural models, include RIBBONS (Carson (1997)
Methods in Enzymology 277:25), O (Jones et al. (1991) Acta
Crystallogr. A47:110), DINO; and QUANTA, INSIGHT, SYBYL, MACROMODE,
ICM, MOLMOL, RASMOL and GRASP (reviewed in Kraulis (1991) Appl
Crystallogr. 24:946).
[0153] Other molecular modeling techniques may also be employed in
accordance with the presently disclosed subject matter (e.g., Cohen
et al. (1990) J. Med. Chem. 33:883-894; Navia & Murcko (1992)
Current Opinions in Structural Biology 2:202-210). For example,
where the structures of test compounds are known, a model of the
test compound may be superimposed over the model of the structure
of the aptamers as disclosed herein. Numerous methods and
techniques are known in the art for performing this step, any of
which may be used (e.g., Farmer "Drug Design", Ariens (ed.), Vol.
10, pp 119-143 (Academic Press, New York, 1980); U.S. Pat. No.
5,331,573; U.S. Pat. No. 5,500,807; Verlinde (1994) Structure
2:577-587; and Kuntz (1992) Science 257:1078-108).
[0154] Following long-standing patent law convention, the terms
"a," "an," and "the" refer to "one or more" when used in this
application, including the claims. Thus, for example, reference to
"a subject" includes a plurality of subjects, unless the context
clearly is to the contrary (e.g., a plurality of subjects), and so
forth.
[0155] Throughout this specification and the claims, the terms
"comprise," "comprises," and "comprising" are used in a
non-exclusive sense, except where the context requires otherwise.
Likewise, the term "include" and its grammatical variants are
intended to be non-limiting, such that recitation of items in a
list is not to the exclusion of other like items that can be
substituted or added to the listed items.
[0156] For the purposes of this specification and appended claims,
unless otherwise indicated, all numbers expressing amounts, sizes,
dimensions, proportions, shapes, formulations, parameters,
percentages, parameters, quantities, characteristics, and other
numerical values used in the specification and claims, are to be
understood as being modified in all instances by the term "about"
even though the term "about" may not expressly appear with the
value, amount or range. Accordingly, unless indicated to the
contrary, the numerical parameters set forth in the following
specification and attached claims are not and need not be exact,
but may be approximate and/or larger or smaller as desired,
reflecting tolerances, conversion factors, rounding off,
measurement error and the like, and other factors known to those of
skill in the art depending on the desired properties sought to be
obtained by the presently disclosed subject matter. For example,
the term "about," when referring to a value can be meant to
encompass variations of, in some embodiments, .+-.100% in some
embodiments .+-.50%, in some embodiments .+-.20%, in some
embodiments .+-.10%, in some embodiments .+-.5%, in some
embodiments .+-.1%, in some embodiments .+-.0.5%, and in some
embodiments .+-.0.1% from the specified amount, as such variations
are appropriate to perform the disclosed methods or employ the
disclosed compositions.
[0157] Further, the term "about" when used in connection with one
or more numbers or numerical ranges, should be understood to refer
to all such numbers, including all numbers in a range and modifies
that range by extending the boundaries above and below the
numerical values set forth. The recitation of numerical ranges by
endpoints includes all numbers, e.g., whole integers, including
fractions thereof, subsumed within that range (for example, the
recitation of 1 to 5 includes 1, 2, 3, 4, and 5, as well as
fractions thereof, e.g., 1.5, 2.25, 3.75, 4.1, and the like) and
any range within that range.
EXAMPLES
[0158] The following Examples have been included to provide
guidance to one of ordinary skill in the art for practicing
representative embodiments of the presently disclosed subject
matter. In light of the present disclosure and the general level of
skill in the art, those of skill can appreciate that the following
Examples are intended to be exemplary only and that numerous
changes, modifications, and alterations can be employed without
departing from the scope of the presently disclosed subject matter.
The synthetic descriptions and specific examples that follow are
only intended for the purposes of illustration, and are not to be
construed as limiting in any manner to make compounds of the
disclosure by other methods.
Example 1
[0159] The primary aim of the present study was to generate one or
more RNA aptamers that would bind sickle hemoglobin (HbS) in such a
way that polymerization of HbS would be inhibited, without a
deleterious effect on hemoglobin's functional capabilities.
Preventing the polymerization of HbS would essentially cure sickle
cell anemia, since the complications of the disease arise directly
as a result of red blood cell changes brought about by HbS
polymerization. Because it is the deoxygenated form of HbS that
polymerizes, the creation and characterization of aptamers to
deoxyHbS were conducted first. However, aptamers to oxyHbS were
also created and characterized in an effort to cast a large net and
limit assumptions about which type of aptamers may be more
effective ultimately in preventing polymerization. Additionally,
aptamers that specifically bind HbS but do not have any effect on
polymerization might be useful as reagents for other scientific
studies. For example, these could be used to clear HbS or other
hemoglobins (including normal hemoglobin) from plasma for proteomic
studies or be used to identify the presence of HbS in a patient
sample, or for therapeutics.
[0160] To accomplish these goals, the "systematic evolution of
ligands by exponential enrichment" (SELEX) process was used to
select for aptamers that bind specifically to HbS in either its
oxygenated or deoxygenated states. Each aptamer pool was analyzed
for its ability to bind both oxy-HbS and deoxy-HbS at different
rounds in the selection process. However, both positive and
negative selection were used, including experiments where the bound
aptamers was recovered from the target, and experiments where the
aptamers that recognized more than one target were removed from the
pool (for example, by absorbing pools of molecules that bind both
HbA and HbS to HbA, allowing the molecules that bind only to S to
"flow through.") Once a relatively small pool of high affinity
aptamers was obtained, individual aptamers were then amplified and
tested for their ability to inhibit polymerization in a closed
anaerobic system, in which sodium dithionite was used to
deoxygenate hemoglobin.
Materials and Methods
[0161] Preparation of Hemoglobin
[0162] After obtaining informed consent, venous blood was drawn
from an untransfused patient with homozygous SS disease. Red cells
were washed 5 times with PBS, hemolyzed in 3.5 volumes of distilled
water, and stromata were removed by centrifugation at 20,000 g for
25 minutes. Hemoglobin-rich extract was dialyzed into 0.05M
tris-Cl, pH 8.3, and purified HbS was obtained by separation on a
DEAE Sephadex A-50 anion exchange column, developing with a
gradient of 0.05M Tris-HCl, pH 8.3 to 0.05M Tris-HCl pH 7.3. The
HbS was dialyzed against 2 mM HEPES, pH 7.4 for the SELEX process
and against 1M potassium phosphate buffer, pH 7.1 for use in the
polymerization assays, and stored in small aliquots at -80.degree.
C. Hemoglobin concentrations were determined by standard methods.
When necessary, hemoglobin was concentrated with Amicon Ultra 30K
centrifugal filters (Millipore, Billerica, Mass.). Proportions of
hemoglobins at different oxidation states within a solution were
determined by the method of Benesch, Benesch and Yung (Benesch,
Benesch, & Yung (1973) Anal Biochem. 55:245-248).
[0163] Selection of Aptamers Through Systematic Evolution of
Ligands by Exponential Enrichment (SELEX)
[0164] The initial oligonucleotide library was the Sel2 library
(Trilink Biotechnologies, San Diego, Calif.) comprising the
sequence 5'-GGGAGGACGAUGCGG(N.sub.40)--CAGACGACUCGCUGAGGAUCCGAGA-3'
(SEQ ID NO:1), where N.sub.40 represents a random sequence of 40
nucleotides. Template DNA was synthesized with the Klenow fragment
of DNA polymerase I (New England Biolabs, Ipswich, Mass.). Two
separate selections were performed. Both selections shared the
first four rounds, which were carried out as described below, using
deoxygenated HbS as the target protein. For these rounds, binding
was carried out at 37.degree. for 5 minutes. After round 4, the
resulting RNA pool was utilized to continue with two separate
selections. The first targeted HbS in its oxygenated state.
Measurements of the oxidation states of HbS in a freshly-thawed
aliquot showed approximately 83-95% to be oxygenated hemoglobin, so
freshly thawed HbS was used in the binding steps. Incubation was
carried out at room temperature for 10 minutes at a ratio of 5
moles RNA per mole of protein in round 5, increasing to 9 moles RNA
per mole of protein by round 14. Bound RNA was collected by
capturing the protein on a nitrocellulose membrane, eluting and
extracting the RNA. RT-PCR reactions were performed on the eluted
RNA with AMV Reverse Transcriptase (Roche, Indianapolis, Ind.) and
Platinum Taq Polymerase (Invitrogen, Grand Island, N.Y.).
Transcription was performed with the Durascribe T7 kit (Epicentre,
Madison, Wis.), which incorporates the modified nucleotides
2'-fluorine-dCTP and 2'-fluorine-dUTP into the sequences to
generate nuclease-resistant RNA.
[0165] The second selection targeted deoxygenated HbS. Paired
rounds were performed in which cycles of selection against
deoxy-HbS were alternated with cycles of subtractive binding with
oxy-HbS, described below. In order to deoxygenate the HbS prior to
incubation, it was thawed, exposed to a vacuum by injection into a
vacuum tube with a septum cap, and rocked at room temperature for 1
hour. The hemoglobin was then removed from the tube, and incubation
with RNA aptamer library was immediately carried out at room
temperature for 10 minutes at a ratio of 3 moles RNA per mole of
protein in round 1 then stepwise up to 7 moles RNA per mole protein
by round 9. For subtractive binding, the oligo pool was incubated
with oxy-HbS at room temperature for 10 minutes and the unbound
flow-through material was collected and saved, following protein
capture on a nitrocellulose membrane. Butanol extraction was
employed to concentrate the unbound oligos. Subtractive binding
followed by standard binding was done for multiple "paired" rounds,
with RNA ratios for the oxy-HbS rounds similar to those for the
deoxy-HbS rounds, except for the final cycle of subtractive
binding, in which the ratio was 5 moles RNA per mole protein. This
lower ratio allowed the oxygenated protein to bind and retain a
higher fraction of oxy-HbS-targeted aptamers in the pool. Oxy-HbS
oligo selection rounds 1-7 and deoxy-HbS oligo selection rounds 1-5
were performed in low salt binding buffer (20 mM HEPES pH 7.4, 50
mM NaCl, 2 mM CaCl.sub.2, 0.01% BSA) and low salt wash buffer (20
mM HEPES pH 7.4, 50 mM NaCl, 2 mM CaCl.sub.2). Oxy-HbS selection
rounds 8-14 and deoxy-HbS selection rounds 6-9 were performed in
high salt binding buffer (20 mM HEPES pH 7.4, 150 mM NaCl, 2 mM
CaCl.sub.2, 0.01% BSA) and high salt wash buffer (20 mM HEPES pH
7.4, 150 mM NaCl, 2 mM CaCl.sub.2). The last cycle of subtractive
binding for deoxy-HbS aptamers, using oxy-HbS as the target, was
done in low salt buffers, again to decrease the stringency of
aptamer-protein binding.
[0166] Binding Assays
[0167] Aptamers were dephosphorylated with bacterial alkaline
phosphatase (Invitrogen, Grand Island, N.Y.) and 5' end-labelled
with .alpha.-.sup.32P-ATP (Perkin Elmer, Waltham, Mass.) using
T.sub.4 polynucleotide kinase (New England Biolabs, Ipswich,
Mass.). RNA was diluted to 2,000 cpm/ul in the appropriate binding
buffer and heated at 65.degree. C. for 5 minutes. For the oligomer
pool targeting oxyHbS, the hemoglobin was thawed and used to make a
dilution series in binding buffer. For the oligo pool targeting
deoxyHbS the hemoglobin was thawed, exposed to a vacuum and rocked
at room temperature for 1 hour, and used immediately to make a
dilution series in binding buffer. For both assays, 5 ul of labeled
RNA (10,000 cpm) was added to each tube of the dilution series,
such that the final protein concentrations ranged from 0.078 uM to
10 uM, in 2-fold increments. Each mixture was incubated (at
37.degree. C. for 5 minutes for rounds 0 and 4, and at room
temperature for 10 minutes for subsequent rounds) and passed over a
nitrocellulose membrane to capture the HbS and bound RNA, with the
non-bound RNA captured on a nylon membrane. The fractions of bound
and unbound RNA were quantified with a Beckman LS-3801
scintillation counter, and the nonspecific binding subtracted.
[0168] Cloning, Sequencing and RNA Preparation
[0169] At rounds 7 and 9 of selection targeting deoxy-HbS and
rounds 11 and 14 of selection targeting oxy-HbS, cDNA was
synthesized from RNA and used for cloning and sequencing of
individual aptamers. DNA oligos were ligated into the pCR2.1-TOPO
vector using the TOPO cloning kit (Invitrogen, Grand Island, N.Y.)
and T.sub.4 DNA ligase (New England Biolabs, Ipswich, Mass.).
Transformations were performed using One Shot TOP 10 cells
(Invitrogen, Grand island, NY), and following overnight growth,
mini-preps were performed with the Qiaprep spin miniprep kit
(Qiagen, Valencia, Calif.) to produce DNA for sequencing.
Sequencing was carried out at the Johns Hopkins Genetic Resources
Core Facility. Large quantities of aptamer for analysis were
generated from clone DNA by transcription using the Durascribe T7
kit (Epicentre, Madison, Wis.). RNA was purified by running on a
12% denaturing gel and eluted in dH.sub.2O.
[0170] Polymerization Assays
[0171] Sickle hemoglobin in 1 M potassium phosphate buffer, pH 7.1
was thawed on ice, concentrated in an Amicon Ultra 30K centrifugal
filter tube (Millipore, Billerica, Mass.) at 4.degree. C. and kept
on ice. Aptamers in distilled H.sub.2O or H.sub.2O alone as a
control were thawed on ice, aliquoted into tubes for each
individual replicate, heated at 65.degree. C. for 5 minutes, and
placed on ice. SM20, a non-related aptamer targeting the
plasminogen activator inhibitor-1 (PAI-1) and possessing flanking
sequences identical to those generated here, was used as a negative
aptamer control. To deoxygenate sodium dithionite powder (Sigma,
St. Louis, Mo.), it was placed in a tube with a rubber septum cap
and flushed with nitrogen gas by inserting one needle for gas inlet
and one needle for gas outlet into the cap (Adachi & Asakura
(1979) J. Biol. Chem. 254:7765-7771). A buffer solution of 1.6 M
potassium phosphate buffer pH 7.8 was deoxygenated similarly in
separate tubes flushed with nitrogen gas. The dithionite powder and
buffer were exposed to nitrogen for 11/2 hours, flushing with new
nitrogen gas every 1/2 hour, then placed on ice. Sodium dithionite
stock solution and subsequent dilutions were then made using a
Hamilton gas-tight syringe to transfer buffer from one tube to
another (Adachi & Asakura (1979) J. Biol. Chem. 254:7765-7771).
Each replicate was run in a closed 1 cm quartz cuvette (Starna
Cells, Atascadero, Calif.) that had been flushed with nitrogen gas
through a septum cap as described above, and placed on ice. Cold
1.6 M potassium phosphate buffer pH, 7.8 and HbS were added to the
tube containing aptamer, mixed well, and added to the
nitrogen-filled cuvette using a Hamilton gas-tight syringe. The
syringe was immediately washed and used to transfer sodium
dithionite solution from its dilution tube into the cuvette. The
final concentrations of all components in the cuvette were 0.12 mM
HbS, 0.48 mM sodium dithionite, and 0.01 mM aptamer in 1.49 M
potassium phosphate, pH 7.9. After addition of dithionite, the
contents were briefly mixed and put in a 37.degree. C. water bath.
The cuvette was removed one minute after incubation began and
turbidity measured with a Beckman DU-640B spectrophotometer
(Beckman Coulter, Inc., Brea, Calif.) at a wavelength of 700 nm
(Adachi & Asakura (1979) J. Biol. Chem. 254:7765-7771;
Harrington (1998) Comp. Biochem. Physiol. 119B(2):305-309; Eaton
& Hofrichter (1987) Blood 70:1245-1266; Knee & Mukerji
(2009) Biochemistry 48:9903-9911; Magdoff-Fairchild et. al. (1976)
Proc. Nat. Acad. Sci. 73(4):990-994). Measurements were also taken
at 540, 560 and 576 nm in order to calculate the fractions of HbS
in various oxygenation states. After the spectrophotometric
measurement, the cuvette was immediately returned to 37.degree. C.
Subsequent readings were done in a similar manner every 3 minutes
through the 34 minute time point, then every 5 minutes from the 40
minute to the 70 minute time points.
Results
[0172] Different Sets of Aptamers Generated Targeting Oxy-HbS
Versus Deoxy-HbS
[0173] One of the goals of the present study was to generate
aptamers that bind to HbS in either its oxygenated or deoxygenated
states specifically and further to identify aptamers that when
bound result in inhibition of polymerization of deoxy-HbS. While
aptamers binding selectively to oxy- or deoxyhemoglobin were
targeted, it was also recognized that aptamers binding to both
oxygenated and deoxygenated Hb would likely be identified and would
be of value, potentially inhibiting HbS polymerization as well.
Clones were obtained and sequenced at rounds 11 and 14 of the
oxy-HbS aptamer selection and rounds 7 and 9 of the deoxy-HbS
aptamer selection. 57 total aptamers were identified that bound to
deoxy-HbS. Of these, several aptamers were represented multiple
times; many sequences were represented only once. 15 total aptamers
were identified that bound oxy-HbS.
[0174] The unique sequences for the identified clones are shown in
Table 1. Only one of the clones is represented in both the oxy and
deoxy aptamer pool. Several aptamers identified in the group
targeting deoxy-HbS were further amplified and analyzed for their
ability to inhibit polymerization. Although the remainder of the
discussion below applies to these deoxy-HbS aptamers that have been
partially characterized for their anti-polymerization activity, all
clones selected against both deoxy and oxy hemoglobin may
potentially inhibit HbS polymerization as well.
TABLE-US-00001 TABLE 1 Complete Aptamer Sequences (unique or
representative of an identical family DeoxyHbS Aptamer Sequences
Clone deoxy 1 (SEQ ID NO: 2) 5'
GGGAGGACGAUGCGGccgauuagaacugggcugcgaucggagauccu
cuagguuuCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 2 (SEQ ID NO: 3)
5' GGGAGGACGAUGCGGgccgagggauucgguguagacucugcacaguc
cugaaaagCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 3-A (SEQ ID NO: 4)
5' GGGAGGACGAUGCGGccgauuagaacugggcugaggcguucugcauu
ucggugauCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 3-B (SEQ ID NO: 5)
5' GGGAGGACGAUGCGGccgauuagaacugggcuguuccgacucugcau
ccggugauCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 5 (SEQ ID NO: 6)
5' GGGAGGACGAUGCGGuuggugaagggaggucagcauaucuucccgcg
ggaagcgaCGGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 7-A (SEQ ID NO: 7)
5' GGGAGGACGAUGCGGauccacggguaagggugagggacgacaucaag
gcgagauuCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 8 (SEQ ID NO: 8)
5' GGGAGGACGAUGCGGuacgauuagaacuggugccgaacagcgcucgu
ugaagacaCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 9 (SEQ ID NO: 9)
5' GGGAGGACGAUGCGGaggaaguaggguucguccauugggcgaguggc
cuguguuaCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 10 (SEQ ID NO: 10)
5' GGGAGGACGAUGCGGcacgguauaguggaguggguaggcaucgcucg
acgagugaCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 15 (SEQ ID NO: 11)
5' GGGAGGACGAUGCGGgaguagggagguaaucgccaccccaacgcgga
gacagcgaCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 19-C-1 (SEQ ID NO:
12) 5' GGGAGGACGAUGCGGucgauagggggacggaccgcgcuggaaacuca
acguagcaCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 20 (SEQ ID NO: 13)
5' GGGAGGACGAUGCGGcacugaugggaguuggaucagugucgagcggu
aucugcagCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 22 (SEQ ID NO: 14)
5' GGGAGGACGAUGCGGgaguagggagguaaucgucaccccaacgcgga
gacagcgaCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 24 (SEQ ID NO: 15)
5' GGGAGGACGAUGCGGaagcauacaguuuagugugcuagggugggacu
cagugauCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 28-A (SEQ ID NO:
16) 5' GGGAGGACGAUGCGGuccuacuuuccccaauuuguaacagcucuccg
cacagcagCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 30 (SEQ ID NO: 17)
5' GGGAGGACGAUGCGGcgguguagggaucgucagucucggaaugaccu
cacagaagCAGACGACUCGGUGAGGAUCCGAGA 3' Clone deoxy 31 (SEQ ID NO: 18)
5' GGGAGGACGAUGCGGccagcaggaggaugggugccgcacucggauau
ucacguguCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 33-A (SEQ ID NO:
19) 5' GGGAGGACGAUGCGGgacuaagcacaacucaacuagaacgaaccuau
uccaucauCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 34-D (SEQ ID NO:
20) 5' GGGAGGACGAUGCGGaacggaggaguguccucucagcugacagucgu
gcauacuaCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 37-A (SEQ ID NO:
21) 5' GGGAGGACGAUGCGGaacucgauccaucaucgugacugcguacgugu
caacuaagCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 40 (SEQ ID NO: 22)
5' GGGAGGACGAUGCGGgacggucauagagccggccgacauuagagccg
ggaauccaCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 44-A (SEQ ID NO:
23) 5' GGGAGGACGAUGCGGuggagaggggaaucguccugcgcacucugucu
ccugagagCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 45 (SEQ ID NO: 24)
5' GGGAGGACGAUGCGGuguauccgccaguaugauuaacaucuauaagu
cccuauguCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 46 (SEQ ID NO: 25)
5' GGGAGGACGAUGCGGcuaaccuuguuagggccccauacagcaucgag
ugacggauCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 47 (SEQ ID NO: 26)
5' GGGAGGACGAUGCGGugcacaggaggugguacacugcgcucgauuca
ucagcgcaCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 48 (SEQ ID NO: 27)
5' GGGAGGACGAUGCGGcaugugagggaggagguccgcgucauaaacuc
caggaccaCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 50 (SEQ ID NO: 28)
5' GGGAGGACGAUGCGGaagcaauagcucgccguacaguuguccugccg
cucguguuCAGACGACUCGCUGAGGAUCCGAGA 3' Clone deoxy 52 (SEQ ID NO: 29)
5' GGGAGGACGAUGCGGgaguagggagguaagcaguggacuaacgagau
ucggugagCAGACGACUCGCUGAGGAUCCGAGA 3' Clone EMdeoxy 8 (SEQ ID NO:
30) 5' GGGAGGACGAUGCGGcgagcaaccggaacucggcucuuaugaccagc
caacuuaaCAGACGACUCGCUGAGGAUCCGAGA 3' Clone EMdeoxy 8-A (SEQ ID NO:
31) 5' GGGAGGACGAUGCGGcgagcaaccugaacucggcuauuaggaccagc
caacuuaaCAGACGACUCGCUGAGGAUCCGAGA 3' Clone EMdeoxy 11 (SEQ ID NO:
32) 5' GGGAGGACGAUGCGSgaucggaaccagcgugacgacgcgcggaucaa
cuccggugCAGACGACUCGCUGAGGAUCCGAGA 3' Clone EMdeoxy 11-A (SEQ ID NO:
33) 5' GGGAGGACGAUGCGGgaucggaaccagcgugacgaagcgcggaucaa
cuccggugCUGACGACUCGCUGAGGAUCCGAGA 3' Clone EMdeoxy 12 (SEQ ID NO:
34) 5' GGGAGGACGAUGCGGccgauuagaacugggucccgcuguacccuagg
gaucgaCAGACGACUCGCUGAGGAUCCGAGA 3' OXyHbS Apt-Inner Sequences Clone
oxy 1 (SEQ ID NO: 35) 5'
GGGAGGACGAUGCGGagacccaagcgccacgucuggcaugugaggga
ggagguacCAGACGACUCGCUGAGGAUCCGAGA 3' Clone oxy 2 (SEQ ID NO: 36) 5'
GGGAGGACGAUGCGGagagccaagcgccacgucuggcaugugagggg
ggagguacCAGACGACUCGGUGAGGAUCCGAGA 3' Clone oxy 3-8 (SEQ ID NO: 37)
5' GGGAGGACGAUGCGGaaacucaucgguagccuuccugcggucagucu
auuaggacCAGACGACUCGCUGAGGAUCCGAGA 3' Clone oxy 4-8 (SEQ ID NO: 38)
5' GGGAGGACGAUGCGGcaauuaccucagccucccuagacacgucgucu
auuaggacCAGACGACUCGGUGAGGAUCCGAGA 3' Clone oxy 5-A (SEQ ID NO: 39)
5' GGGAGGACGAUGCGGcagucuuccgguaagcacggaggugaggggag
cuuagcguCAGACGACUCGCUGAGGAUCCGAGA 3' Clone oxy 6 (SEQ ID NO: 40) 5'
GGGAGGACGAUGCGGauaugccaugggucgcucgagugaggucgucu
auuaggacCAGACGACUCGGUGAGGAUCCGAGA 3' Clone oxy 7 (SEQ ID NO: 41) 5'
GGGAGGACGAUGCGGagagccaagcgccacgucuggcaugugaggga
ggagguacCAGACGACUCGCUGAGGAUCCGAGA 3' Clone oxy 8 (SEQ ID NO: 42) 5'
GGGAGGACGAUGCGGauuggcgcuauuaggaccagcuccguccgcaa
cuggucccGAGACGACUCGCUGAGGAUCCGAGA 3' Clone ocy 9 (SEQ ID NO: 43) 5'
GGGAGGACGAUGCGGgaacagacccauggcaaucucgcgacgucuuc
ggccgcugCAGACGACUCGCUGAGGAUCCGAGA 3' Clone oxy 10 (SEQ ID NO: 44)
5' GGGAGGACGAUGCGGuacaacagguucauacggcgcguuguuccuug
gcugacgCAGACGACUCGCUGAGGAUCCGAGA 3' Clone oxy 11 (SEQ ID NO: 45) 5'
GGGAGGACGAUGCGGcacuauuaggaccagcgccuguugucucgaua
agcuccgcCAGACGACUCGCUGAGGAUCCGAGA 3' Clone oxy 12 (SEQ ID NO: 46)
5' GGGAGGACGAUGCGGauuggcgcuauuaggaccagcuccguccgcaa
cugaucccGAGACGACUCGCUGAGGAUCCGAGA 3' Clone oxy 13-A (SEQ ID NO: 47)
5' GGGAGGACGAUGCGGcuauuaggaccagccguguagaauucguagcg
augugacgCAGACGACUCGCUGAGGAUCCGAGA 3' Clone oxy 13-B (SEQ ID NO: 48)
5' GGGAGGACGAUGCGGuucgcgcuauuaggaccagugcgaacgugggu
auacauguCAGACGACUCGCUGAGGAUCCGAGA 3' Clone EMoxy 2-B (SEQ ID NO:
49) 5' GGGAGGACGAUGGGGaacacacgggacgagccuggcgguugucgccu
auuaggacCAGACGACUCGCUGAGGAUCCGAGA 3' Clone EMoxy 3 (SEQ ID NO: 50)
5' GGGAGGACGAUGCGGguccaugcuuuaaacugcaauuucccguuuac
acgggcuguCAGACGACUCGCUGAGGAUCCGAGA 3' Clone EMoxy 3-M (SEQ ID NO:
51) 5' GGGAGGACGAUGCGGaccaccgaaucacgaggugcgagacauugguu
ccccgccgCAGACGACUCGCUGAGGAUCCGAGA 3' Clone EMoxy 4 (SEQ ID NO: 52)
5' GGGAGGACGAUGCGGgggacaauaguccacgacuacaugucggugcg
ucggagguCAGACGACUCGCUGAGGAUCCGAGA 3' Clone EMoxy 6-A (SEQ ID NO:
53) 5' GGGAGGACGAUGCGGcuauuaggaccagcugccaauguuaagucuac
cccagcagCAGACGACUCGCUGAGGAUCCGAGA 3' Clone EMoxy 6-C (SEQ ID NO:
54) 5' GGGAGGACGAUGCGGcuuacguauggucacggaggugugggggaaca
uacagcagCAGACGACUCGGUGAGGAUCCGAGA 3' Clone EMoxy 8 (SEQ ID NO: 55)
5' GGGAGGACGAUGCGGuuggugaccuauucaggcguaggcauauaaac
uacgaggcCAGACGACUCGGUGAGGAUCCGAGA 3' Clone EMoxy 8 (SEQ ID NO: 56)
5' GGGAGGACGAUGCGGcuauuaggaccagcugccaauguuaagucuac
cccagcggCAGACGACUCGCUGAGGAUCCGAGA 3' Clone EMoxy 11 (SEQ ID NO: 57)
5' GGGAGGACGAUGCGGgcacgacacgccgauuagaacugggcgaucuu
ggucgagcCAGACGACUCGGUGAGGAUCCGAGA 3' Clone EMoxy 12 (SEQ ID NO: 58)
5' GGGAGGACGAUGCGGcgauacgaccgcaugaguauaccgucgugcuu
cccggcugCAGACGACUCGCUGAGGAUCCGAGA 3' Clone EMoxy 13 (SEQ ID NO: 59)
5' GGGAGGACGAUGCGGauuggcgcuauuaggaccagcuccguccgcaa
ccggucccCAGACGACUCGGUGAGGAUCCGAGA 3' Clone EMoxy 14 (SEQ ID NO: 60)
5' GGGAGGACGAUGCGGauuggcgcuauuaggaccagcuccguccgcaa
cuggucccCAGACGACUCGCUGAGGAUCCGAGA 3'
[0175] Aptamer Pools Generated that Bind Specifically to
Deoxy-HbS
[0176] Binding of the deoxy HbS-selected aptamers to oxy- and
deoxy-hemoglobin was assessed at various rounds of selection. FIG.
1 shows that by the end of the selection process, the aptamers
selected against deoxy hemoglobin bind to deoxy hemoglobin in a
dose dependent saturable manner.
[0177] Aptamer Deoxy-3-A Inhibits Polymerization of Deoxygenated
HbS
[0178] In order to evaluate individual aptamers' ability to inhibit
polymerization, aptamers were amplified and added to an anaerobic
solution of deoxygenated HbS, in which spectrophotometric
measurements of turbidity at a wavelength of 700 nm reflected the
extent of polymerization. It was necessary to develop a system in
which HbS would reliably and reproducibly polymerize using the
smallest possible concentration in order to minimize the quantities
of aptamer necessary for testing. In HbS polymerization studies,
shorter lag times and higher polymerization rates are associated
with higher temperature, higher hemoglobin concentration, the use
of potassium phosphate buffer, and higher buffer concentrations;
therefore, in order to enhance polymerization in a low
concentration HbS system, we utilized a buffer solution of 1.49 M
potassium phosphate buffer and conducted the incubations at
37.degree. C. Sodium dithionite at a concentration of 0.48 mM was
used to deoxygenate HbS. Test assays (data not shown) showed that
this concentration of sodium dithionite in our system consistently
resulted in solutions of 93-96% deoxygenated HbS.
[0179] Each aptamer was tested at a concentration of 0.01 mM (an
aptamer to heme molar ratio of 1:12). From the initial set of
activity assays, an aptamer denoted deoxy-3-A (SEQ ID NO:4) was
identified as causing reduced polymerization, with increased lag
times and decreased maximal polymerization over the time frame of
the experiment (FIG. 2). This is proof of principle that an RNA
aptamer can alter the polymerization of HbS, and shows that this
agent could be useful as a therapy for sickle cell anemia. It also
describes a specific, unique, but modifiable aptamer reagent that
has this property. FIG. 2 summarizes data for 4 separate
experiments with the deoxy 3-A aptamer (SEQ ID NO:4), demonstrating
consistent inhibition of HbS polymerization in multiple runs as
compared to a control aptamer (SM20) or water control. Preliminary
results from two additional aptamers, Deoxy-1 (SEQ ID NO:2) and
Deoxy EM8-A (SEQ ID NO:31), have shown some inhibition of
polymerization as well (FIGS. 3 and 4). FIG. 5 summarizes data for
the Oxy 3-B aptamer (SEQ ID NO:37), demonstrating consistent
inhibition of HbS polymerization in multiple runs as compared to
water control.
[0180] To determine if deoxy 3-A inhibited polymerization of HbS in
a dose-dependent manner, HbS polymerization studies were performed
as previously described in the presence of increasing
concentrations of the deoxy-3A aptamer from 0.3125 micromolar to 10
micromolar final concentration. Water only controls as well as
non-specific aptamer controls were performed. FIG. 6A shows a clear
concentration-dependent inhibition of polymerization by the
deoxy-3A aptamer. Additionally, the dose response was quantified by
determining the slope of the polymerization curves as a function of
deoxy 3-A aptamer concentration (FIG. 6B). The slopes, as measured
from time points 22-50 minutes in the dose response curves, were
calculated and plotted as a function of aptamer concentration to
display the dose-dependent effects of this aptamer in inhibiting
polymerization.
[0181] Lipofectin Facilitates Entry of Deoxy 3-A Aptamer into
Sickle Red Blood Cells
[0182] To determine if lipofectin could facilitate entry of the
deoxy 3-A aptamer into sickle red blood cells, sickle red blood
cells obtained with consent from patients were washed and subjected
to transfection using a standard protocol with Lipofectin reagent
in the presence or absence of fluorescently labeled deoxy 3-A
aptamer. The cells were vigorously washed in high salt buffer
following transfection to remove any non-specifically bound
aptamer. Increased fluorescence intensity of the population
demonstrates successful transfer of deoxy 3-A into red blood cells.
Fluorescent microscopy following transfection confirmed the
introduction of the deoxy 3-A aptamer into a subset of the red
blood cells (FIG. 7).
[0183] HbS Retains the Ability to Form New Polymer when Growing
Filament Ends are Provided by Mechanical Disruption
[0184] To evaluate the ability of HbS to form new polymer when
growing filament ends were provided by mechanical disruption,
polymerization assays were performed as previously described. At
the end of the assay, cuvettes containing HbS or HbS plus aptamer
were shaken in an effort to break long filaments and supply new
ends for a polymerization reaction. HbS in the presence of the
deoxy 3-A aptamer was capable of forming new polymer, demonstrating
that the aptamer is not merely causing protein denaturation over
time as a mechanism of action (FIG. 8).
REFERENCES
[0185] All publications, patent applications, patents, and other
references mentioned in the specification are indicative of the
level of those skilled in the art to which the presently disclosed
subject matter pertains. All publications, patent applications,
patents, and other references are herein incorporated by reference
to the same extent as if each individual publication, patent
application, patent, and other reference was specifically and
individually indicated to be incorporated by reference. It will be
understood that, although a number of patent applications, patents,
and other references are referred to herein, such reference does
not constitute an admission that any of these documents forms part
of the common general knowledge in the art.
[0186] Although the foregoing subject matter has been described in
some detail by way of illustration and example for purposes of
clarity of understanding, it will be understood by those skilled in
the art that certain changes and modifications can be practiced
within the scope of the appended claims.
Sequence CWU 1
1
65180RNAArtificial SequenceSynthetic Oligonucleotide Template,
wherein n is a, c, g, or u 1gggaggacga ugcggnnnnn nnnnnnnnnn
nnnnnnnnnn nnnnnnnnnn nnnnncagac 60gacucgcuga ggauccgaga
80280RNAArtificial SequenceSynthetic Aptamer 2gggaggacga ugcggccgau
uagaacuggg cugcgaucgg agauccucua gguuucagac 60gacucgcuga ggauccgaga
80380RNAArtificial SequenceSynthetic Aptamer 3gggaggacga ugcgggccga
gggauucggu guagacucug cacaguccug aaaagcagac 60gacucgcuga ggauccgaga
80480RNAArtificial SequenceSynthetic Aptamer 4gggaggacga ugcggccgau
uagaacuggg cugaggcguu cugcauuucg gugaucagac 60gacucgcuga ggauccgaga
80580RNAArtificial SequenceSynthetic Aptamer 5gggaggacga ugcggccgau
uagaacuggg cuguuccgac ucugaauccg gugaucagac 60gacucgcuga ggauccgaga
80680RNAArtificial SequenceSynthetic Aptamer 6gggaggacga ugcgguuggu
gaagggaggu cagcauaucu ucccgcggga agcgacggac 60gacucgcuga ggauccgaga
80780RNAArtificial SequenceSynthetic Aptamer 7gggaggacga ugcggaucca
cggguaaggg ugagggacga caucaaggcg agauucagac 60gacucgcuga ggauccgaga
80880RNAArtificial SequenceSynthetic Aptamer 8gggaggacga ugcgguacga
uuagaacugg ugccgaacag cgcucguuga agacacagac 60gacucgcuga ggauccgaga
80980RNAArtificial SequenceSynthetic Aptamer 9gggaggacga ugcggaggaa
guaggguucg uccauugggc gaguggccug uguuacagac 60gacucgcuga ggauccgaga
801080RNAArtificial SequenceSynthetic Aptamer 10gggaggacga
ugcggcacgg uauaguggag uggguaggca ucgcucgacg agugacagac 60gacucgcuga
ggauccgaga 801180RNAArtificial SequenceSynthetic Aptamer
11gggaggacga ugcgggagua gggagguaau cgccacccca acgcggagac agcgacagac
60gacucgcuga ggauccgaga 801280RNAArtificial SequenceSynthetic
Aptamer 12gggaggacga ugcggucgau agggggacgg accgcgcugg aaacucaacg
uagcacagac 60gacucgcuga ggauccgaga 801380RNAArtificial
SequenceSynthetic Aptamer 13gggaggacga ugcggcacug augggagugg
gaucaguguc gagcgguauc ugcagcagac 60gacucgcuga ggauccgaga
801480RNAArtificial SequenceSynthetic Aptamer 14gggaggacga
ugcgggagua gggagguaau cgucacccca acgcggagac agcgacagac 60gacucgcuga
ggauccgaga 801579RNAArtificial SequenceSynthetic Aptamer
15gggaggacga ugcggaagca uacaguuuag ugugcuaggg ugggacucag ugaucagacg
60acucgcugag gauccgaga 791680RNAArtificial SequenceSynthetic
Aptamer 16gggaggacga ugcgguccua cuuuccccaa uuuguaacag cucuccgcac
agcagcagac 60gacucgcuga ggauccgaga 801780RNAArtificial
SequenceSynthetic Aptamer 17gggaggacga ugcggcggug uagggaucgu
cagucucgga augaccucac agaagcagac 60gacucgcuga ggauccgaga
801880RNAArtificial SequenceSynthetic Aptamer 18gggaggacga
ugcggccagc aggaggaugg gugccgcacu cggauauuca cgugucagac 60gacucgcuga
ggauccgaga 801980RNAArtificial SequenceSynthetic Aptamer
19gggaggacga ugcgggacua agcacaacuc aacuagaacg aaccuauucc aucaucagac
60gacucgcuga ggauccgaga 802080RNAArtificial SequenceSynthetic
Aptamer 20gggaggacga ugcggaacgg aggagugucc ucucagcuga cagucgugca
uacuacagac 60gacucgcuga ggauccgaga 802180RNAArtificial
SequenceSynthetic Aptamer 21gggaggacga ugcggaacuc gauccaucau
cgugacugcg uacgugucaa cuaagcagac 60gacucgcuga ggauccgaga
802280RNAArtificial SequenceSynthetic Aptamer 22gggaggacga
ugcgggacgg ucauagagcc ggccgacauu agagccggga auccacagac 60gacucgcuga
ggauccgaga 802380RNAArtificial SequenceSynthetic Aptamer
23gggaggacga ugcgguggag aggggaaucg uccugcgcac ucugucuccu gagagcagac
60gacucgcuga ggauccgaga 802480RNAArtificial SequenceSynthetic
Aptamer 24gggaggacga ugcgguguau ccgccaguau gauuaacauc uauaaguccc
uaugucagac 60gacucgcuga ggauccgaga 802580RNAArtificial
SequenceSynthetic Aptamer 25gggaggacga ugcggcuaac cuuguuaggg
ccccauacag caucgaguga cggaucagac 60gacucgcuga ggauccgaga
802680RNAArtificial SequenceSynthetic Aptamer 26gggaggacga
ugcggugcac aggagguggu acacugcgcu cgauucauca gcgcacagac 60gacucgcuga
ggauccgaga 802780RNAArtificial SequenceSynthetic Aptamer
27gggaggacga ugcggcaugu gagggaggag guccgcguca uaaacuccag gaccacagac
60gacucgcuga ggauccgaga 802880RNAArtificial SequenceSynthetic
Aptamer 28gggaggacga ugcggaagca auagcucgcc guacaguugu ccugccguuc
guguucagac 60gacucgcuga ggauccgaga 802980RNAArtificial
SequenceSynthetic Aptamer 29gggaggacga ugcgggagua gggagguaag
cagcggacua acgagauucg gugagcagac 60gacucgcuga ggauccgaga
803080RNAArtificial SequenceSynthetic Aptamer 30gggaggacga
ugcggcgagc aaccggaacu cggcuauuau gaccagccaa cuuaacagac 60gacucgcuga
ggauccgaga 803180RNAArtificial SequenceSynthetic Aptamer
31gggaggacga ugcggcgagc aaccugaacu cggcuauuag gaccagccaa cuuaacagac
60gacucgcuga ggauccgaga 803280RNAArtificial SequenceSynthetic
Aptamer 32gggaggacga ugcgggaucg gaaccagcgu gacgaagcgc ggaucaacuc
cggugcagac 60gacucgcuga ggauccgaga 803380RNAArtificial
SequenceSynthetic Aptamer 33gggaggacga ugcgggaucg gaaccagcgu
gacgaagcgc ggaucaacuc cggugcugac 60gacucgcuga ggauccgaga
803478RNAArtificial SequenceSynthetic Aptamer 34gggaggacga
ugcggccgau uagaacuggg ucgcgcugua cccuagggau cgacagacga 60cucgcugagg
auccgaga 783580RNAArtificial SequenceSynthetic Aptamer 35gggaggacga
ugcggagacc caagcgccac gucuggcaug ugagggagga gguaccagac 60gacucgcuga
ggauccgaga 803680RNAArtificial SequenceSynthetic Aptamer
36gggaggacga ugcggagagc caagcgccac gucuggcaug ugagggggga gguaccagac
60gacucgcuga ggauccgaga 803780RNAArtificial SequenceSynthetic
Aptamer 37gggaggacga ugcggaaacu caucgguagc cuuccugcgg ucagucuauu
aggaccagac 60gacucgcuga ggauccgaga 803880RNAArtificial
SequenceSynthetic Aptamer 38gggaggacga ugcggcaauu accucagccu
cccuagacac gucgucuauu aggaccagac 60gacucgcuga ggauccgaga
803980RNAArtificial SequenceSynthetic Aptamer 39gggaggacga
ugcggcaguc uuccgguaag cacggaggug aggggagcuu agcgucagac 60gacucgcuga
ggauccgaga 804080RNAArtificial SequenceSynthetic Aptamer
40gggaggacga ugcggauaug ccaugggucg cucgagugag gucgucuauu aggaccagac
60gacucgcuga ggauccgaga 804180RNAArtificial SequenceSynthetic
Aptamer 41gggaggacga ugcggagagc caagcgccac gucuggcaug ugagggagga
gguaccagac 60gacucgcuga ggauccgaga 804280RNAArtificial
SequenceSynthetic Aptamer 42gggaggacga ugcggauugg cgcuauuagg
accagcuccg uccgcaacug gucccgagac 60gacucgcuga ggauccgaga
804380RNAArtificial SequenceSynthetic Aptamer 43gggaggacga
ugcgggaaca gacccauggc aaucucgcga cgucuucggc cgcugcagac 60gacucgcuga
ggauccgaga 804479RNAArtificial SequenceSynthetic Aptamer
44gggaggacga ugcgguacaa cagguucaua cggcgcguug uuccuuggcu gacgcagacg
60acucgcugag gauccgaga 794580RNAArtificial SequenceSynthetic
Aptamer 45gggaggacga ugcggcacua uuaggaccag ugccuguugu cucgauaagc
uccgccagac 60gacucgcuga ggauccgaga 804680RNAArtificial
SequenceSynthetic Aptamer 46gggaggacga ugcggauugg cgcuauuagg
accagcuccg uccgcaacug aucccgagac 60gacucgcuga ggauccgaga
804780RNAArtificial SequenceSynthetic Aptamer 47gggaggacga
ugcggcuauu aggaccagcc guguagaauu cguagcgaug ugacgcagac 60gacucgcuga
ggauccgaga 804880RNAArtificial SequenceSynthetic Aptamer
48gggaggacga ugcgguucgc gcuauuagga ccagugcgaa cguggguaua caugucagac
60gacucgcuga ggauccgaga 804980RNAArtificial SequenceSynthetic
Aptamer 49gggaggacga ugcggaacac acgggacgag ccuggcgguu gucgucuauu
aggaccagac 60gacucgcuga ggauccgaga 805081RNAArtificial
SequenceSynthetic Aptamer 50gggaggacga ugcgggucca ugcuuuaaac
ugcaauuucc cguuuacacg ggcugucaga 60cgacucgcug aggauccgag a
815180RNAArtificial SequenceSynthetic Aptamer 51gggaggacga
ugcggaccac cgaaucacga ggugcgagac auugguuccc cgccgcagac 60gacucgcuga
ggauccgaga 805280RNAArtificial SequenceSynthetic Aptamer
52gggaggacga ugcgggggac aauaguccac gacuacaugu cggugcgucg gaggucagac
60gacucgcuga ggauccgaga 805380RNAArtificial SequenceSynthetic
Aptamer 53gggaggacga ugcggcuauu aggaccagcu gccaauguua agucuacccc
agcagcagac 60gacucgcuga ggauccgaga 805480RNAArtificial
SequenceSynthetic Aptamer 54gggaggacga ugcggcuuac guauggucac
ggaggugugg gggaacauac agcagcagac 60gacucgcuga ggauccgaga
805580RNAArtificial SequenceSynthetic Aptamer 55gggaggacga
ugcgguuggu gaccuauuca ggcguaggca uauaaacuac gaggccagac 60gacucgcuga
ggauccgaga 805680RNAArtificial SequenceSynthetic Aptamer
56gggaggacga ugcggcuauu aggaccagcu gccaauguua agucuacccc agcggcagac
60gacucgcuga ggauccgaga 805780RNAArtificial SequenceSynthetic
Aptamer 57gggaggacga ugcgggcacg acacgccgau uagaacuggg cgaucuuggu
cgagccagac 60gacucgcuga ggauccgaga 805880RNAArtificial
SequenceSynthetic Aptamer 58gggaggacga ugcggcgaua cgaccgcaug
aguauaccgu cgugcuuccc ggcugcagac 60gacucgcuga ggauccgaga
805980RNAArtificial SequenceSynthetic Aptamer 59gggaggacga
ugcggauugg cgcuauuagg accagcuccg uccgcaaccg guccccagac 60gacucgcuga
ggauccgaga 806080RNAArtificial SequenceSynthetic Aptamer
60gggaggacga ugcggauugg cgcuauuagg accagcuccg uccgcaacug guccccagac
60gacucgcuga ggauccgaga 806111RNAArtificial SequenceRNA aptamer
consensus sequence 61gaacugggcu g 116215RNAArtificial SequenceRNA
aptamer consensus sequence 62caccccaacg cggag 156312RNAArtificial
SequenceRNA aptamer consensus sequence 63gucuauuagg ac
126413RNAArtificial SequenceRNA aptamer consensus sequence
64cuauuaggac cag 136513RNAArtificial SequenceRNA aptamer consensus
sequence 65cgauuagaac ugg 13
* * * * *