(i)Publication List
(ii)Patents
(iii)Significant Contributions
Publications
(Principal investigator denoted by †)2011
144. A.S. Wahba, B. Marchand, M.A. Parniak, M. Gotte and M.J. Damha† (2011) Inhibition of HIV-1 RT RNase H activity by chemically modified nucleic acid hairpins, manuscript in preparation.
143. A.S. Wahba, T. Ilina, M.A. Parniak and M.J. Damha† (2011) Probing sugar conformational preferences during nucleotide excision by HIV-1 RT, manuscript in preparation.
142. R. Johnsson and M.J. Damha† (2011) An evaluation of cleavage rates of common protecting groups of nucleobases in 2'-deoxynucleosides, manuscript in preparation.
141. A. Knapinska, F. Madoux, P. Chase, C. Eberhart, D. Minond, B. Mercer, T. Bannister, S. Chowdhury, L. DeLuca, J.G. Lackey, M.J. Damha, H. Harding and P. Hodder† (2011) A high-throughput fluorescence polarization assay for inhibitors of C. albicans t-RNA 2'-phosphotransferase (Tpt1p), Journal of Biomolecular Screening, submitted.
140. A.S. Wahba, F. Azizi, G.F. Deleavey, F. Robert, M. Carrier, A. Kalota, A. Gewirtz, J. Pelletier, R.H.E. Hudson and M.J. Damha† (2011) Gene silencing and physicochemical properties of siRNAs incorporating 6-phenylpyrrolocytidine, ACS Chemical Biology, in press. DOI: 10.1021/cb200070k.
139. R. Johnsson, J.G. Lackey, J.J. Bogojeski and M.J. Damha† (2011) New light labile linker for solid phase synthesis of oligoribonucleotide analogues: Applications to siRNA prodrug development, Bioorganic Medicinal Chemistry Letters, 21: 3721-3725.
138. M. Hassler, Y.Q. Wu, N.M. Reddy, T.H. Chan and M.J. Damha† (2011) RNA synthesis via dimer and trimer phosphoramidite coupling, Tetrahedron Letters, 52: 2575-2578.
137. A.E. Felber, B. Castagner, G.F. Deleavey, M. Elsabahy, M.J. Damha and J.-C. Leroux† (2011) SiRNA nanocarriers based on alkylmethacrylic acid copolymers, Journal of Controlled Release, 152: 159-167.
136. M. Yahyaee, J.K. Watts, N.R. Alla, A.W. Nicholson and M.J. Damha† (2011) Energetically important C-H...F-C pseudohydrogen bonding in water: evidence and application to rational design of oligonucleotides with high binding affinity, Journal of the American Chemical Society, 133: 728-731.
2010
135. K.T. Gagnon, H. Pendergraff, G.F. Deleavey, E. Swayze, P. Potier, J. Randolph, E.B. Roesch, J. Chattopadhyaya, M.J. Damha, F. Bennett, C. Montaillier, M. Lemaitre, D.R. Corey† (2010) Allele-selective silencing of mutant Huntingtin expression with antisense oligonucleotides targeting the expanded CAG repeat, Biochemistry, 49: 10166–10178.
134. G.F. Deleavey, J.K. Watts, F. Robert, T. Alain, A. Kalota, J. Pelletier, A.M. Gewirtz, N. Sonenberg and M.J. Damha† (2010) Synergy between 2'F-ANA and rigid RNA analogues improves the potency of siRNA-mediated gene silencing, Nucleic Acids Research, 38: 4547-4557.
133. J.K. Watts, N. Martin-Pintado, I. Gómez-Pinto, J. Schwartzentruber, G. Portella, M. Orozco, C. González† and M.J. Damha† (2010) Differential stability of 2'F-ANA•RNA and ANA•RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake, and flexibility, Nucleic Acids Research, 38: 2498-2511.
132. G.F. Deleavy, J.K. Watts and M.J.
Damha† (2010) Chemical modification of siRNA, Current
Protocols in Nucleic Acid Chemistry, unit 16.3.1-16.3.22 (Doi:
10.1002/0471142700.nc1603s39).
131. A.S. Wahba, Arash
Ghorbani-Choghamarani, M.J. Damha and R.H.E. Hudson† (2010 )
A single-label phenylpyrrolocytidine providing a molecular
beacon-like response reports HIV-1 RT RNase H activity, Nucleic
Acids Research, 38: 1048-1056.
2009
130. J.G. Lackey, M.M. Somoza, D. Mitra,
F. Cerrina, and M.J. Damha* (2009) In-situ chemical synthesis
of rU-DNA chimeras on chips and enzymatic recognition, Chemistry
Today, 27: 30-33.
129. M. Elsabahy, N. Wazen, N. Bayó-Puxan, G.
Deleavey, M. Servant, M.J. Damha and J.-C. Leroux† (2009),
Delivery of nucleic acids through the controlled disassembly of
multifunctional nanocomplexes, Advanced Functional Materials,
19: 3862–3867.
128. J.G. Lackey,
D. Mitra, M Somoza, F. Cerrina and M.J. Damha† (2009),
Acetal levulinyl ester (ALE)
groups for 2'-hydroxyl of ribonucleosides in the synthesis of
oligoribonucleotides on glass and microarrays,
Journal of the American
Chemical Society, 131: 8496-8502.
127. J.K. Watts, A. Katolik, J.
Viladoms and M.J. Damha† (2009),
Studies on the hydrolytic stability of 2'-fluoroarabinonucleic acid
(2'F-ANA),
Organic & Biomolecular Chemistry,
7:1904 – 1910.
2008
126. J.G. Lackey, D. Ron, M.J. Damha, and H.P.
Harding† (2008)
Toward the discovery of new antifungal agents: The design and
validation of a novel 2'P-RNA probe and high throughput screening
assay against 2'-phosphotransferase Tpt1p,
Nucleic Acids Symposium Series,
52: 475-476.
125. A.S. Wahba, M.J. Damha and R.H.E.
Hudson† (2008)
RNA containing pyrrolocytidine base analogs: good binding affinity
and fluorescence that responds to hybridization,
Nucleic Acids Symposium Series, 52: 399-400.
124. J.G. Lackey and M.J. Damha† (2008)
The acetal levulinyl ester (ALE) group for the 2'-hydroxyl
protection of ribonucleosides and the synthesis of
oligoribonucleotides, Nucleic
Acids Symposium Series, 52: 35-36.
123. C.G. Peng and M.J. Damha† (2008) Probing DNA polymerase activity with stereoisomeric 2'-fluoro-ß-D-arabinose (2'F-araNTPs) and 2'-fluoro-ß-D-ribose (2'F-rNTPs) nucleoside 5'-triphosphates , Canadian Journal of Chemistry, 86: 881-891.
122. J.K. Watts†, G.F. Deleavey and M.J. Damha† (2008) Chemically modified siRNA: tools and applications, Drug Discovery Today, 13: 842-855.
121. J.K. Watts, B.D. Johnston, K. Jayakanthan, A.S. Wahba, B.M. Pinto† and M.J. Damha† (2008) Synthesis and biophysical characterization of oligonucleotides containing a 4'-selenonucleotide, Journal of the American Chemical Society, 130: 8578–8579.
120. J.K. Watts and M.J. Damha† (2008) 2'-Fluoroarabinonucleic acids (2'F-ANA): history, properties and new frontiers, Canadian Journal of Chemistry, 86: 641-656.
119. H.P. Harding,† J.G. Lackey, H-C. Hsu, Y. Zhanga, J. Deng, R-M. Xu, M.J. Damha, and D. Ron (2008) An intact unfolded protein response in Trpt1 knockout mice reveals phylogenic divergence in pathways for RNA ligation, RNA , 14: 225-232.
2007
118. D. Mitra and M.J. Damha† (2007) A novel approach to the synthesis of DNA and RNA lariats, Journal of Organic Chemistry, 72: 9491-9500 .
117. D. Sabatino and M.J. Damha† (2007) Synthesis and properties of oligonucleotides containing a seven-membered (oxepane) sugar ring, Nucleosides, Nucleotides, Nucleic Acids , 26: 1185–1188.
116. C.-G. Peng and M.J. Damha† (2007) DNA polymerase recognition of 2'-deoxy-2'-fluoroarabinonucleoside 5'-triphosphates (2'F-araNTPs), Nucleosides, Nucleotides, Nucleic Acids , 26: 1189–1193.
115. R.A. Donga, M. Hassler, T.-H. Chan and M.J. Damha† ( 2007 ) Oligonucleotide synthesis using ionic liquids as soluble supports, Nucleosides, Nucleotides, Nucleic Acids , Nucleosides, Nucleotides, Nucleic Acids , 26: 1287 – 1293.
114. C.-G. Peng and M.J. Damha† (2007) G-quadruplex induced stabilization by 2'-deoxy-2'-fluoro-D-arabinonucleic acids (2'F-ANA), Nucleic Acids Research, 35: 4977-4988.
113. D. Sabatino and M.J. Damha† (2007) Oxepane nucleic acids (ONA): synthesis, characterization and properties of oligonucleotides bearing a 7-membered carbohydrate ring, Journal of the American Chemical Society, 129: 8259 -8270.
112. R.A. Donga, T.-H. Chan and M.J. Damha† (2007) Ion tagged synthesis of an oligoribonucleotide pentamer: The continuing versatility of TBDMS chemistry, Canadian Journal of Chemistry, 85: 274-282.
111. C.G. Peng and M.J. Damha†
(2007)
Polymerase-directed synthesis of 2'-deoxy-2'-fluoro-arabinonucleic
acids,
Journal of the American Chemical Society, 129: 5310
-5311.
110. J.G. Lackey, D. Sabatino and M.J. Damha† (2007)
Solid-phase synthesis and on-column deprotection of RNA from 2'-(and
3'-)O-levulinated
(Lv) ribonucleoside monomers,
Organic Letters, 9: 789-792 .
109. J.K. Watts, N. Choubdar, K. Sadalapure, F. Robert, A.S. Wahba, J. Pelletier, B.M. Pinto† and M.J. Damha† (2007) 2'-Fluoro-4'-thioarabino-modified oligonucleotides: Conformational switches linked to siRNA activity, Nucleic Acids Research, 35:1441-1451.
108. B. Patureau, R.H.E. Hudson† and M.J. Damha† (2007) Induction of RNase H activity by arabinose-peptide nucleic acid chimeras, Bioconjugate Chemistry , 18: 421-430.
2006
107. J.B. Opalinska, A. Kalota, J. Chattopadhyaya, M.J. Damha and A.M. Gewirtz† (6) Nucleic acids therapeutics for hematologic malignancies – theoretical considerations, Annals of the New York Academy of Sciences, 1082: 124-136.
106. N. Ferrari, D.
Bergeron, A.-L. Tedeschi, M.M. Mangos, L. Paquet, P.M. Renzi and
M.J. Damha† (2006)
Characterization of antisense oligonucleotides comprised of
2'-deoxy-2'-fluoro-b-D-arabinonucleic
acid (FANA): specificity, potency and duration of activity,
Annals of the New York Academy of Sciences,
1082: 91–102.
105. R.A. Donga, S.M. Khaliq-Uz-Zaman,
T.-H. Chan and M.J. Damha† (2006)
A novel approach to oligonucleotide synthesis using an imidazolium
ion tag as a soluble support,
Journal of Organic Chemistry,
71: 7907-7910.
104. T. Dowler, D. Bergeron, A.-L. Tedeschi,
L. Paquet, N. Ferrari† and M.J. Damha† (2006)
Improvements in siRNA properties mediated by 2'-deoxy-2'-fluoro-ß-D-arabinonucleic
acid (FANA),
Nucleic Acids Research,
34:1669-1675.
103. R. Mourani and M.J. Damha† (2006)
Synthesis, characterization and biological properties of small
branched RNA fragments containing chiral (Rp and Sp) 2',5'-phosphorothioate
linkages,
Nucleosides Nucleotides and Nucleic Acids,
25: 203-229.
102. D. Gendron, S. Carriero, D. Garneau, J.
Villemaire, R. Klinck, S. AbouElela, M.J. Damha† and B. Chabot† (2006)
Modulation of 5' splice site selection using tailed oligonucleotides
carrying splicing signals,
BMC Biotechnology,
6:5 (12 pages).
101. A. Kalota, L. Karabon, C Swider, E. Viazovkina, M. Elzagheid,
M.J. Damha† and A. Gewirtz† (2006)
A Novel 2'-deoxy-2'-fluoro-[ß]-D-arabinonucleic acid (2'F-ANA)
modification of DNA creates a highly efficient, and long lasting,
gene silencing oligonucleotide (ON),
Nucleic Acids Research, 34: 451-461.
100. J.K. Watts, K. Sadalapure, N. Choubdar, B.M. Pinto† and M.J.
Damha† (2006)
Synthesis and conformational analysis of 2'-fluoro-5-methyl-4'-thioarabinouridine
(4'S-FMAU),
Journal of Organic Chemistry, 71: 921-925.
2005
99. C.-G. Peng and M.J. Damha† (2005)
Synthesis and hybridization studies of oligonucleotides containing
1-(2-Deoxy-2-a-C-hydroxymethyl-ß-D-ribofuranosyl)thymine
(2'-a-hm-dT),
Nucleic Acids Research, 33: 7019-7028.
98. R.N. Hannoush and M.J. Damha† (2005)
Preference for ribose over deoxyribose in loop-closing base pairs of
extra stable nucleic acid hairpins,
Nucleosides Nucleotides and Nucleic Acids, 24:
1519-1530.
97. M. F. Khalid, M.J. Damha, S. Shuman and B. Schwer† (2005) Structure-function analysis of yeast RNA debranching enzyme (Dbr1), a manganese-dependent phosphodiesterase, Nucleic Acids Research, 33: 6349-6360 .
96. R.N. Hannoush,
K.-L. Min and M.J. Damha† (2004) Diversity-oriented solid-phase synthesis and biological
evaluation of
oligonucleotide hairpins as HIV-1 RT RNase H inhibitors, Nucleic
Acids Research, 32: 6164-6175.
95. C.G. Peng, R.N. Hannoush and M.J. Damha† (2005)
Synthesis of a “taller” 2’,5’-linked ribonucleic acids: 2’-a-C-hydroxymethyl
2’,5’-linked RNA,
Journal of Biomolecular Structure & Dynamics, 22:
856-857.
2004 and earlier
94. A. Galarneau, K.-L. Min, M.M. Mangos and M.J.
Damha†
(2004) Assay for evaluating Ribonuclease H – mediated
degradation of RNA/antisense oligonucleotide duplexes in “DNA
Synthesis: Methods and Protocols” P. Herdewijn (ed.), The Humana
Press Inc., Totowa, New Jersey,
65-80.
93. B.
Lamontagne, R.N. Hannoush, M.J. Damha and S. Abou-Elela†, (2004)
Molecular requirements for duplex recognition and cleavage by RNase
III: discovery of an RNA-dependent DNA cleavage activity by
yeast Rnt1p, Journal of Molecular Biology, 338: 401-418.
92. R. Hannoush, S. Carriero, K.-L. Min and M.J.
Damha†
(2004) Selective Inhibition of HIV-1 Reverse transcriptase
(HIV-1 RT) RNase H by small RNA hairpins and dumbbells,
ChemBioChem, 5: 527-533.
91. S. Carriero and M.J. Damha† (2003)
Template-mediated synthesis of Lariat DNA and RNA, Journal of
Organic Chemistry, 68: 8328-8338.
90. S. Carriero and M.J. Damha† (2003)
Inhibition of pre-mRNA splicing by synthetic branched nucleic acids,
Nucleic Acids Research, 31: 6157-6167.
89. R.N. Hannoush, A.-Yu. Denisov, K. Gehring and
M.J. Damha† (2003) A new RNA fold: RNA hairpins
containing unusually stable 2',5'-linked r(UUCG) loops, Journal
of Biomolecular Structure & Dynamics, 20: 836-837.
88. A.-Y. Denisov, R.N. Hannoush, K. Gehring and M.J. Damha† (2003) A novel RNA motif based on the structure of unusually stable 2',5'-linked r(UUCG) loops, Journal of the American Chemical Society, 125: 11525-11531.
87. S. Carriero, M.M. Mangos, K.A. Agha, A.M. Noronha and M.J. Damha† (2003) Branchpoint sugar stereochemistry determines the hydrolytic susceptibility of branched RNA fragments by yDBR, Nucleosides, Nucleotides & Nucleic Acids, 22: 1599-1602.
86. K.A. Agha and M.J. Damha† (2003) Synthesis and binding properties of a homopyrimidine 2',5'-linked xylose nucleic acid (2',5'-XNA), Nucleosides, Nucleotides & Nucleic Acids, 22: 1175-1178.
85. R.N. Hannoush, A.Y. Denisov, K. Gehring and M.J. Damha† (2003) Structure of 2',5'-linked tetraribonucleotide loops: a novel RNA motif, Nucleosides, Nucleotides & Nucleic Acids, 22: 1687-1690.
84. E. Viazovkina, K.-L. Min, A. Galarneau and M.J. Damha† (2003) Synthesis and properties of oligonucleotide chimeras containing 5'-amino-2'-deoxy-2'-fluoroarabinonucleotides, Nucleosides, Nucleotides & Nucleic Acids, 22: 1335-1338.
83. M. Elzagheid, A.L. Tedeschi and M.J. Damha† (2003) Synthesis of 2',3'-dideoxy-2'-fluoro-3'-thioarabinothymidine and its 3'-phosphoramidite derivative, Nucleosides, Nucleotides & Nucleic Acids, 22: 1343-1346.
82. E. Viazovkina, M.M. Mangos and M.J. Damha† (2003) Synthesis and properties of 2'-deoxy-2',2"-difluoro-ß-D-ribofuranosyl oligonucleotides and 2'-deoxy-2',2"-difluoro-a-D-ribofuranosyl oligonucleotides, Nucleosides, Nucleotides & Nucleic Acids, 22: 1251-1254.
81. M. Elzagheid, E. Viazovkina and M.J. Damha† (2003) A new synthesis of 9-(2-deoxy-2-fluoro-b-D-arabinofuranosyl)guanine (araF-G), Nucleosides, Nucleotides & Nucleic Acids, 22: 1339-1342.
80. S. Carriero and M.J. Damha† (2003) Synthesis of lariat-DNA via the chemical ligation of a dumbbell complex, Organic Letters, 5: 273-276.
79. M.M. Mangos, K.-L. Min, E. Viazovkina, A. Galarneau, M. Elzagheid, M.A. Parniak and M.J. Damha† (2003) Efficient RNase H-directed cleavage of RNA using DNA or 2'F-ANA constructs containing acyclic nucleotide inserts, Journal of the American Chemical Society, 125: 654-661.
78. J.Lacombe, E. Viazovkina, P.N. Bernatchez, A. Galarneau, M.J. Damha and Martin G. Sirois† (2002) Antisense inhibition of Flk-1, a receptor for vascular endothelial growth factor (VEGF), by oligonucleotides comprised of 2'-deoxy-2-fluoro-ß-D-arabino and 2'-deoxynucleosides, Canadian Journal of Physiology and Pharmacology, 80: 951-961.
77. M.I. Elzagheid, E. Viazovkina, and M.J. Damha† (2002) Synthesis of protected 2'-deoxy-2'-fluoro- ß-D-arabinonucleosides, Current Protocols in Nucleic Acid Chemistry, Unit 1.7 (19 pages).
76. E. Viazovkina, M.M. Mangos, M.I. Elzagheid, and M.J. Damha† (2002) Synthesis of 2'-fluoroarabino nucleoside phosphoramidites and their use in the synthesis of 2'F-ANA, Current Protocols in Nucleic Acid Chemistry, Unit 4.15 (22 pages).
75. M.M. Mangos and M.J. Damha† (2002) Flexible and frozen sugar-modified nucleic acids - modulation of biological activity through furanose ring dynamics in the antisense strand, Current Topics in Medicinal Chemistry, 2: 1145-1169.
74. K.-L. Min, E. Viazovkina, A. Galarneau, M.A. Parniak,† and M.J. Damha† (2002), Oligonucleotides comprised of alternating 2'-deoxy-2'-fluoro-D-arabinonucleosides and D-2'-deoxyribonucleosides (2'F-ANA/DNA "Altimers") Bioorganic & Medicinal Chemistry Letters, 12: 2651-2654.
73. D.R. Yazbeck and M.J.Damha† (2002) Molecular requirements for degradation of RNA in DNA/RNA hybrids by E. coli RNase H1, Nucleic Acids Research, 30: 3015-3025.
72. S. Carriero and M.J. Damha† (2002) Solid-phase synthesis of branched oligonucleotides, Current Protocols in Nucleic Acid Chemistry, 4.14.1-4.14.32, John Wiley & Sons.
71. C.-N. Lok, E. Viazovkina, K.-L. Min, E. Nagy, C.J. Wilds, M.J. Damha† and M.A. Parniak† (2002) Potent gene-specific inhibitory properties of mixed-backbone antisense oligonucleotides comprised of 2'-deoxy-2'-fluoro-D-arabinose and 2'-deoxynucleotides, Biochemistry, 41: 3457-3467.
70. A.Y.
Denisov, A.M. Noronha, C.J. Wilds, J.-F. Trempe, R.T. Pon, K.
Gehring, and M.J. Damha† (2001) Solution structure of an
arabinonucleic acid (ANA)/RNA duplex in a chimeric hairpin:
comparison with 2'F-ANA/RNA and DNA/RNA hybrids", Nucleic Acids
Research, 29: 4284-4293.
69. R. N. Hannoush and M.J. Damha† (2001)
Remarkable stability of hairpins containing 2',5'-Linked RNA Loops,
Journal of the American Chemical Society, 123: 12368-12374.
68. S.L. Ooi, C. Dann III, K. Nam, D. Leahy, M.J. Damha, J.D. Boeke† (2001) The Yeast lariat debranching enzyme, Methods In Enzymology, Volume 342, Ribonucleases Part A: Functional Roles and Mechanisms, Harcourt Publishers Ltd., 233-250.
67. M.J. Damha,† A.M. Noronha, C.J. Wilds, J.F.-Trempe, A. Denisov and K.Gehring (2001) Properties of arabinonucleic acids (ANA & 2'F-ANA): Implications for the design of antisense therapeutics that invoke RNase H cleavage of RNA, Nucleosides & Nucleotides, 20: 429-440.
66. S. Carriero, R.S. Braich, R.H.E. Hudson, D. Anglin, J.D. Friesen and M.J. Damha† (2001) Inhibition of in-vitro pre-mRNA splicing in S. cerevisiae by branched oligonucleotides, Nucleosides & Nucleotides, 20: 873-877.
65. R.N. Hannoush and M.J. Damha† (2001) Extra stable 2',5'-linked RNA loops, Nucleosides & Nucleotides, 20: 1201-1204.
64. A.M. Noronha, D. Arion, M.A. Parniak† and M.J. Damha† (2001) Effect of substituting arabinonucleosides for deoxynucleotides in the DNA priming strand on the polymerase action of HIV-1 RT, Nucleosides Nucleotides, 20: 1205-1209.
63. J.F.
Trempe, C.J. Wilds, A. Danisov, M.J. Damha† and K. Gehring (2001)
NMR structure of a 2'F-ANA/RNA duplex and relevance to the
activation of RNaseH, J. Am. Chem. Soc., 123: 4896-4903.
62. R.N. Hannoush and M.J. Damha† (2001)
Structure and thermodynamics of hairpins containing 2',5'-Linked RNA
loops, Journal of Biomolecular Structure & Dynamics, 18: 906.
61. C.J. Wilds and M.J. Damha† (2000)
2'-Deoxy-2'-fluoro-ß-D-arabinonucleosides and oligonucleotides
(2'F-ANA): synthesis and physicochemical studies, Nucleic Acids
Research, 28: 3625-3635.
60. A.M. Noronha, C. J. Wilds, C.N. Lok, K.
Viazovkina, D. Arion, M.A. Parniak and M.J. Damha† (2000)
Synthesis and biophysical properties of arabinonucleic acids (ANA):
CD spectra, melting temperatures, and RNase H susceptibility of
ANA/RNA hybrids, Biochemistry, 39: 7050-7062.
59. C. J. Wilds and M.J. Damha† (1999)
Duplex recognition by oligonucleotides containing 2’-deoxy-2’-fluoro-D-arabinose
and 2'-deoxy-2'-fluoro-D-ribose. Intermolecular [2'OH-phosphate]
contacts versus sugar puckering in the stabilization of triple
helical complexes, Bioconjugate Chemistry (ACS), 10: 299-305.
58. M.J .Damha,† C. Wilds, A.M. Noronha, I.
Brukner, G. Borkow and M.A. Parniak (1998) Hybrids of RNA and
arabinonucleic acids (ANA and 2'F-ANA) are substrates of
ribonuclease H, Journal of the American Chemical Society,
121: 12976-12977.
57. M.J. Damha† and A.M. Noronha (1998)
Recognition of nucleic acid double helices by homopyrimidine
2',5'-linked RNA, Nucleic Acids Research, 26: 5152-5156.
56. A.M. Noronha and M.J. Damha† (1998)
Triple helices containing arabinonucleotides in the third (Hoogsteen)
strand: effects of inverted stereochemistry at the 2’-position of
the sugar moiety, Nucleic Acids Research, 26: 2665-2671.
55. M.J. Damha† and R.S. Braich (1998)
Synthesis of a branched DNA/RNA chimera similar to the msDNA
molecule of Myxococcus xanthus, Tetrahedron Letters, 39:3907-3910.
54. M. Wasner, D. Arion, G. Borkow, A. Noronha,
A. H. Uddin, M. A. Parniak, and M.J. Damha† (1998)
Physicochemical and biochemical properties of 2',5'-linked RNA and
2',5'-RNA:3',5'-RNA ‘hybrid’ duplexes, Biochemistry, 37:
7478-7486.
53. R.H.E. Hudson, S. Robidoux and M.J. Damha† (1998)
Divergent synthesis of nucleic acid dendrimers, Tetrahedron
Letters, 39: 1299-1302.
52. S. Robidoux, R. Klinck, K. Gehring, and M.J.
Damha† (1997) Association of branched oligonucleotides into
the i-motif, Journal of Biomolecular Structure & Dynamics,
15: 517-527.
51. S. Robidoux and M.J. Damha† (1997)
2-Deoxyribose and arabinose, but not ribose, stabilize the cytosine
(I-DNA) structure, Journal of Biomolecular Structure & Dynamics,
15: 529-535.
50. A.H. Uddin, P.A.E. Piunno, R.H.E. Hudson, M.J.
Damha† and U.J. Krull† (1997) A fiber optic biosensor for
fluorimetric detection of triple-helical DNA, Nucleic Acids
Research, 25: 4139-4146.
49. G. Borkow, D. Arion, A.M. Noronha, M.
Scartozzi, M.J. Damha and M.A. Parniak† (1997) Inhibitory
potency of R-region specific antisense oligonucleotides against in
vitro DNA polymerization and template-switching reactions catalysed
by HIV-1 reverse transcriptase, International Journal of
Biochemistry & Cell Biology, 29: 1285-1295.
48. C.J. Wilds, J.F. Lunetta, Y.S. Tsantrizos† and
M.J. Damha† (1997) Biophysical studies and synthesis of
oligonucleotides containing a peptide/aromatic backbone, Journal
of Biomolecular Structure & Dynamics, 14: 806.
47. A. Noronha and M.J. Damha† (1997)
Hybridization Properties of Arabinonucleic Acids (ANA. Influence of
stereochemistry at 2’ on the stability of double and triple helices,
Journal of Biomolecular Structure & Dynamics, 14: 805-806.
46. M. Wasner, A. Uddin, G. Borkow, D. Arion, M.A.
Parniak† and M.J. Damha† (1997) Selective association and
antisense properties of 2',5'-linked oligoribonucleotides,
Journal of Biomolecular Structure & Dynamics, 14: 805.
45. S. Robidoux, R. Klinck, K. Gehring, and M.J.
Damha† (1997) Association of branched oligonucleotides into
C-tetraplexes: 2-deoxyribose and arabinose, but not ribose,
stabilize the C-tetrad structure, Journal of Biomolecular
Structure & Dynamics, 14: 804.
44. R.S. Braich and M.J. Damha† (1997)
Effect of vicinal 2',5' and 3',5'-phosphodiester linkages on the
formation of hairpin DNA, Journal of Biomolecular Structure &
Dynamics, 14: 803.
43. R.S. Braich and M.J. Damha† (1997)
Regiospecific solid-phase synthesis of branched oligonucleotides:
effect of vicinal 2',5' (or 2',3'-) and 3',5'-phosphodiester
linkages on the formation of hairpin DNA, Bioconjugate Chemistry,
8: 370-377.
42. P.M. Macdonald†, M.J. Damha†, K. Ganeshan, R.
Braich and S.V. Zabarylo (1996), Phosphorus-31 CPMAS NMR
characterization of oligonucleotides covalently bound to a solid
support, Nucleic Acids Research 24: 2868-2876.
41. A.H. Uddin, M.A. Roman, J. Anderson and M.J.
Damha† (1996) A novel N3-functionalized thymidine linker for
the stabilization of triple helical DNA, Chemical Communications,
171-172.
40. R.H.E. Hudson, A. Uddin and M.J. Damha† (1995)
Association of branched nucleic acids. Structural and
physicochemical analysis of antiparallel T.AT triple-helical DNA,
Journal of the American Chemical Society, 117: 12470-12477.
39. M.J. Damha†, B. Meng, C.G. Yannopoulus, D.
Wang and G. Just (1995) Structural basis for the RNA
selectivity of oligonucleotides containing alkylsulfide
internucleoside linkages and 2'-O-substituted 3'-deoxyribose,
Nucleic Acids Research 19: 3967-3973.
38. D. Wang, B. Meng, M.J. Damha and G. Just† (1995)
Synthesis of 2'-substituted sulfide-linked dinucleosides,
Nucleosides & Nucleotides, 14: 1961-1985.
37. S. Robidoux, Y. Guo and M.J. Damha† (1995)
Tricyclic oxadiazaphosphorine oxide guanosines: a new strategy to
functionalize guanosines at the exocyclic amino group,
Tetrahedron Letters, 36: 6651-6654.
36. P.A.E. Piunno, U.J. Krull†, R.H.E. Hudson,
M.J. Damha, and H. Cohen (1995) Optic DNA sensor for
fluorimetric nucleic acid analysis, Analytical Chemistry, 67:
2635-2646.
35. K. Ganeshan, K. Nam, R.H.E. Hudson, T. Tadey,
R. Braich, W.C. Purdy, J.D. Boeke and M.J. Damha† (1995)
Novel approaches to the synthesis and analysis of branched RNA,
Nucleosides & Nucleotides, 14: 1009-1013.
34. R.H.E. Hudson, K. Ganeshan and M.J. Damha† (1994)
Branched oligonucleotides: synthesis and biological applications, in
"Carbohydrate Modifications in Antisense Research", P.D. Cook and
Y.S. Sanghvi (eds.), American Chemical Society Symposium Series
580: 133-152, Washington, DC.
33. K. Nam, R.H.E. Hudson, K. Ganeshan, K.B.
Chapman, M.J. Damha† and J.D. Boeke† (1994) Yeast lariat
debranching enzyme: substrate and sequence specificity, The
Journal of Biological Chemistry 269: 20613-621.
32. M.J. Damha†, P.A. Giannaris and P. Marfey (1994)
Antisense L/D-oligodeoxynucleotide chimeras: synthesis, nuclease
stability, base-pairing properties, and activity at directing
ribonuclease H, Biochemistry 33: 7877-7885.
31. P.A. Giannaris and M.J. Damha† (1994)
Hybridization properties of oligoarabinonucleotides, Canadian
Journal of Chemistry 72: 909-918.
30. P.A.E. Piunno, U.J. Krull†, R.H.E. Hudson,
M.J. Damha, and H. Cohen (1994) A fiber optic biosensor for
fluorimetric detection of DNA hybridization, Analytica Chimica
Acta 288: 205-214.
29. P.A. Giannaris and M.J. Damha† (1993)
Oligoribonucleotides containing 2',5'-phosphodiester linkages
exhibit binding selectivity for 3',5'-RNA over 3',5'-ssDNA,
Nucleic Acids Research 21: 4742-4749.
28. I. Idziak, G. Just†, M.J. Damha and P.A.
Giannaris (1993) Synthesis and hybridization properties of
amide-linked thymidine dimers incorporated into
oligodeoxynucleotides, Tetrahedron Letters 34: 5417-5420.
27. B. Meng, S.H. Kawai, D. Wang, G. Just†, P.A.
Giannaris and M.J. Damha† (1993) A sulfide-incorporating
oligonucleotide analogue with selective hybridization properties,
Angew.Chemie Int. Ed. Engl. 32: 729-731.
26. R.H.E. Hudson and M.J. Damha† (1993)
Nucleic acid dendrimers: Novel biopolymer structures, Journal of
the American Chemical Society, 115: 2119-2124.
25. S.H. Kawai, D. Wang, P.A. Giannaris, M.J.
Damha† and G. Just (1993) Solid-phase synthesis and
hybridization properties of DNA containing sulfide-linked
dinucleosides, Nucleic Acids Research, 21: 1473-1479.
24. M.J. Damha† and K.K. Ogilvie† (1993)
Oligoribonucleotide synthesis - the silyl-phosphoramidite method in
“Protocols for Oligonucleotide and Analogs: Synthesis and
Properties” S. Agrawal (ed.), Methods in Molecular Biology,
pp.81-114, The Humana Press Inc., Totowa, New Jersey.
23. R.H.E. Hudson and M.J. Damha† (1993)
Association of branched nucleic acids, Nucleic Acids Research
Symposium Series, 29: 97-99.
22. M.J. Damha†, K. Ganeshan, R.H.E. Hudson and
S.V. Zabarylo (1992) Solid-phase synthesis of branched
oligoribonucleotides related to mRNA splicing intermediates,
Nucleic Acids Research, 20: 6565-6573.
21. M.J. Damha†, Y. Guo, S.V. Zabarylo, K.
Ganeshan and P.A. Giannaris (1992) Tricyclic
oxadiazaphosphorine oxide guanosines: a new strategy to the
protection of guanine bases during RNA synthesis, Tetrahedron
Letters, 33: 6739-6743.
20. P.A. Giannaris and M.J. Damha† (1992)
Binding properties of 2',5'-linked oligoribonucleotides:
evolutionary selection for the 3',5'-phosphodiester bonds in
ribonucleic acids, Proceedings of the 10th Annual Graduate
Students Symposium pp. 22-30, SUNY at Buffalo, New York.
19. M.J. Damha†, P.A. Giannaris, P. Marfey and
L.S. Reid (1991) Oligodeoxynucleotides containing unnatural
L-2'-deoxyribose Tetrahedron Letters, 32: 2573-2576.
18. M.J. Damha†, P.A. Giannaris and N. Kahn (1991)
2',5'-Linked oligoribonucleotides form stable complexes with
complementary RNA and DNA, Nucleic Acids Research Symposium
Series, 24: 290.
17. M.J. Damha†, R.H.E. Hudson, K. Ganeshan, S.V.
Zabarylo, and Y. Guo (1991) Synthesis and properties of
branched and hyperbranched oligonucleotides, Nucleic Acids
Research Symposium Series, 24: 203-204.
16. M.J. Damha†, P.A. Giannaris and S.V. Zabarylo
(1990) An improved procedure for derivatization of
controlled-pore glass beads for solid-phase oligonucleotide
synthesis, Nucleic Acids Research, 18: 3813-3821.
15. F. Lafortune, M.J. Damha, X. Tang, K.G.
Standing, J.B. Westmore† and K.K. Ogilvie (1990)
Time-of-flight secondary ion mass spectrometry of branched RNA
fragments: mRNA splicing intermediates, Nucleosides & Nucleotides
9: 445-446.
14. M.J. Damha† and S.V. Zabarylo Automated
Solid-Phase Synthesis of Branched Oligonucleotides (1989)
Tetrahedron Letters, 30: 6295-6298.
13. M.J. Damha, N. Usman and K.K. Ogilvie† (1989)
Solution and solid-phase synthesis of arabinonucleotides,
Canadian Journal of Chemistry, 67: 831-837.
12. M.J. Damha (1988)
Developments in the chemical synthesis of oligonucleotides and their
analogues, Ph.D. Thesis (Supervisor:
Kelvin K. Ogilvie), McGill University, Montreal, QC, Canada.
11. F. Lafortune, W. Ens, K.G. Standing, J.B.
Westmore†, M.J. Damha and K.K. Ogilvie† (1989) Time-of-flight
secondary ion mass spectrometry of protected isomeric
oligonucleotides, Advances in Mass Spectrometry, 11:
1402-1403.
10. M.J. Damha and K.K. Ogilvie† (1988)
Conformational properties of branched RNA fragments in aqueous
solution, Biochemistry, 27: 6403-6416.
9. M.J. Damha and K.K. Ogilvie† (1988)
Synthesis and spectroscopic analysis of branched RNA fragments: mRNA
splicing intermediates, Journal of Organic Chemistry, 53:
3710-3722.
8. F. Lafortune, K.G. Standing, J.B. Westmore†,
M.J. Damha and K.K. Ogilvie† (1988) Differentiation between
protected diastereomeric trinucleotides by time-of-flight SIMS,
Organic Mass Spectrometry, 23: 228-230.
7. M.J. Damha, N. Usman and K.K. Ogilvie† (1987)
The rapid chemical synthesis of arabinonucleotides, Tetrahedron
Letters, 28: 1633-1636.
6. K.K. Ogilvie†, M.J. Damha, N. Usman and R.T.
Pon (1987) Developments in the chemical synthesis of
naturally occurring DNA and RNA with normal and unusual Linkages,
Pure & Applied Chemistry, 28: 325.
5. R.T. Pon, N. Usman, M.J. Damha and K.K.
Ogilvie† (1986) Prevention of guanine modification and chain
cleavage during the solid-phase synthesis of oligonucleotides using
phosphoramidite derivatives, Nucleic Acids Research, 14:
6453-6470.
4. M.J. Damha and K.K. Ogilvie† (1986)
Modification of guanine bases: reaction of N2-acylated guanine
nucleosides with dichloro-N,N-diisopropylaminophosphine, Journal
of Organic Chemistry, 51: 3559-3560.
3. R.T. Pon, M.J. Damha and K.K. Ogilvie† (1985)
Modification of guanine bases by nucleoside phosphor-amidite
reagents during the solid-phase synthesis of oligonucleotides,
Nucleic Acids Research, 13: 6447-6465.
2. M.J. Damha, R.T. Pon and K.K. Ogilvie† (1985)
Chemical synthesis of branched RNA: novel trinucleoside diphosphates
containing vicinal 2',5'- and 3',5'-phosphodiester linkages,
Tetrahedron Letters, 26: 4839-4842.
1. R.T. Pon, M.J. Damha and K.K. Ogilvie† (1985)
Necessary protection of the 06-position of guanine during the
solid-phase synthesis of oligonucleotides by the amidite approach,
Tetrahedron Letters, 26: 2525-2528.
Patents
Total of 14 patent filings since 1997; 5 issued. Selected patents:
-P.A.E. Piunno, R.H.E. Hudson, U.J.Krull, A.H. Uddin,
M.J. Damha . Nucleic Acid Biosensor Diagnostics.
International Patent Application WO9858079A1, International filing
date April 30, 1998 (priority date: CIPO 2,208,165 June 18, 1997).
-
M.J. Damha , M. A. Parniak, A. Noronha, C. Wilds, D. Arion, G.
Borkow. Antisense oligonucleotide constructs based on b-arabinose
and its analogues; International Application WO 9967378,
International filing date June 17, 1999 (priority date CA 2,241,361
June 19, 1998).
-
M.J. Damha , M.A. Parniak, C.-N. Lok, K. Viazovkina. Chimeric
antisense of arabinofuranose and deoxyribose nucleotides;
International Patent Application WO 02020773, International filing
date September 4, 2001 (priority date: US 60/230,414 Sept. 6,
2000).
-
M.J. Damha , M.A. Parniak, M. Mangos, K.-L. Min, K. Viazovkina,
Acyclic linker-containing oligonucleotides and uses thereof;
International Patent Application WO 03037909, International filing
date October 29, 2002 (priority date: US 60/330,719 October 29,
2001).
-
M.J. Damha , M.A. Parniak. Oligonucleotides comprising
alternating segments and uses thereof; International Patent
Application WO 03064441, International filing date January 31, 2003
(priority date: US 60/352,873 January 31, 2002).
-
M.J. Damha , R.N. Hannoush, K.-L. Min S. Carrier; Inhibition of
HIV Reverse Transcriptase by Nucleic Acid Mini Hairpins; US
patent application US 10/748,475 (priority date: US 60/437,568;
Filing date: December 31, 2002).
-
M.J. Damha , T.H. Chan, Weishi Miao, Xun He, Robert Donga;
Ionic liquid supported synthesis; International Patent Application
PCT/CA/2006/000355 (priority date: US60/661,480 March 14, 2005)
Significant
Contributions to Research and/or to Practical Applications
Oligonucleotide Chemistries for Gene Silencing (Publications #134, 133, 120, 109, 106, 104, 101, 100,
75, 74, 70, 67, 63, 58). These articles describe arabinose-modified
nucleic acids that trigger the hydrolysis of mRNA by the action of
ribonucleases (RNaseH, Ago2).
These are the predominant methods of activity of most antisense and
siRNA oligonucleotides under clinical development.
Impact: These
discoveries have received significant attention by the nucleic acids
community for two reasons: Firstly, these compounds represented the
first examples of RNase H-competent oligomers that lacked
D-2-deoxyribofuranose.
Prior to 1998,
Design and Synthesis of
HIV-1 Reverse Transcriptase Inhibitors (Publication #96,
92). Paper #95 was
featured on the cover of
Nucleic Acids Research (issue 21), and discloses the exciting
discovery that short hairpin RNAs interfere specifically with the
function of the RNase H domain of HIV-1 Reverse Transcriptase at the
low μM range, without affecting E. coli or human RNase
H. Remarkably, the
Synthesis and Biological
Investigations on Branched RNA/DNA (Publications #119, 118,
90, 87, 72, 55, 52, 45, 43, 40, 34, 33, 23, 22).
Our work on branched and dendritic oligonucleotides (e.g.,
Hudson and Damha, JACS 1993 and publications listed above) have
been often cited in the context of "chiral dendrimers" and as one of
the first dendrimers ever made from biological monomers. Impact:
These reports have made
available new classes of branched RNA molecules used by our group
and others for recognition of spliceosomal factors and more
fundamentally, for mechanistic studies of mRNA splicing and
debranching that occurs at the cellular level. Others are exploiting
our branching synthetic strategies to prepare dendrimers for gene
delivery, and for the construction of novel 3D DNA assemblies.
News