BMRB: 5245

Heteroduplex of chirally pure R-methylphosphonate/DNA duplex

Authors

Thiviyanathan, V., Vyazovkina, K.V., Gozansky, E.K., Bichenkova, E., Abramova, T.V., Luxon, B.A., Lebedev, A.V., Gorenstein, D.G.

Assembly

5'-D(*TP*GP*TP*TP*TP*GP*GP*C)-3'

Entity

1. methylphosphonate (polymer, Thiol state: not present), 8 monomers, 2511.585 Da Detail

TGTTTGGC

2. methylphosphonate (polymer, Thiol state: not present), 7 monomers, 2126.549 Da Detail

CXXXXXX

Total weight

4638.134 Da

Max. entity weight

2511.585 Da

Exptl. method

NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 53.3 %, Completeness: 61.2 %, Completeness (bb): 65.3 % Detail

Download

• NMR-STAR v3.1 (partial)
• BMRB/XML (partial)
• CSV
• TSV

Polymer type: polydeoxyribonucleotide

	Total	1H	31P
All	61.2 % (60 of 98)	59.6 % (53 of 89)	77.8 % (7 of 9)
Suger, PO4	65.3 % (47 of 72)	63.5 % (40 of 63)	77.8 % (7 of 9)
Nucleobase	50.0 % (13 of 26)	50.0 % (13 of 26)
Aromatic	50.0 % (9 of 18)	50.0 % (9 of 18)
Methyl	100.0 % (4 of 4)	100.0 % (4 of 4)

1. methylphosphonate

TGTTTGGC

2. methylphosphonate

CXXX

Show sample condition

Sample

Pressure 1 atm, Temperature 298 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	methylphosphonate			1.8 mM
2	methylphosphonate			1.8 mM
3	NaCl			100 mM
4	phosphate			10 mM
5	EDTA			0.1 mM
6	H2O			90 %
7	D2O			10 %

Hide sample codition

Chem. Shift Complete2

Sequence coverage: 6.7 %, Completeness: 34.2 %, Completeness (bb): 36.1 % Detail

Download

• NMR-STAR v3.1 (partial)
• BMRB/XML (partial)
• CSV
• TSV

Polymer type: polydeoxyribonucleotide

	Total	1H	31P
All	34.2 % (67 of 196)	33.7 % (60 of 178)	38.9 % (7 of 18)
Suger, PO4	36.1 % (52 of 144)	35.7 % (45 of 126)	38.9 % (7 of 18)
Nucleobase	28.8 % (15 of 52)	28.8 % (15 of 52)
Aromatic	30.6 % (11 of 36)	30.6 % (11 of 36)
Methyl	50.0 % (4 of 8)	50.0 % (4 of 8)

1. methylphosphonate

TGTTTGGC

2. methylphosphonate

CXXX

Show sample condition

Sample

Pressure 1 atm, Temperature 298 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	methylphosphonate			1.8 mM
2	methylphosphonate			1.8 mM
3	NaCl			100 mM
4	phosphate			10 mM
5	EDTA			0.1 mM
6	H2O			90 %
7	D2O			10 %

Hide sample codition

Release date

2002-02-07

Citation 1

Structure of hybrid backbone methylphosphonate DNA heteroduplexes: effect of R and S stereochemistry
Thiviyanathan, V., Vyazovkina, K.V., Gozansky, E.K., Bichenkova, E., Abramova, T.V., Luxon, B.A., Lebedev, A.V., Gorenstein, D.G.
Biochemistry (2002), 41, 827-838, PubMed 11790104 , DOI: , Abstract

Show more 2 citaions

Citation 2

Application of free-energy decomposition to determine the relative stability of R and S oligodeoxyribonucleotide methylphosphonates
Ferguson, D.M., Kollman, P.A.
Antisense Res. Dev. (1991), 1, 243-254, PubMed 1821645 , DOI: , Abstract

Citation 3

Synthesis of specific diastereomers of a DNA methylphosphonate heptamer, d(CpCpApApApCpA), and stability of base pairing with the normal DNA octamer d(TPGPTPTPTPGPGPC)
Vyazovkina, E.V., Savchenko, E.V., Lokhov, S.G., Engels, J.W., Wickstrom, E., Lebedev, A.V.
Nucleic Acids Res. (1994), 22, 2404-2409, PubMed 8036171 , DOI: , Abstract

Hide non-primary 2 citaions

Experiments performed 3 experiments Detail