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Home Enzymatic Activity of Selected Nucleoside 5'-Triphosphates and Their Analogs

Enzymatic Activity of Selected Nucleoside 5'-Triphosphates and Their Analogs

By Alexandre Lebedev, Ph.D.; TriLink BioTechnologies

Nucleoside 5'-triphosphate derivatives and their analogs (NTPDA) have been extremely helpful in explaining many important details of the mechanism of reactions catalyzed by a family of NTP dependent enzymes. Different versions of NTPDAs represent various modifications of the bases, sugars, triphosphate chain and the combinations of those. Many of the modifications result in changes in the essential properties of the nucleoside 5\'-triphosphates, and most importantly their behavior in the enzymatic reactions.

  1. Substrate activity of NTPDAs often changes compared to that of the parent NTPs (usually reduced).
  2. NTPDAs may become inhibitors of the enzymatic reactions through various mechanisms. For example:
    1. NTPDAs (depending on the type of modification) may physically block the binding, catalytic or allosteric
      sites of the enzyme thus competing with the substrate, the reaction product or an allosteric regulator(s).
    2. NTPDAs may cause a termination of the enzymatic chain reaction by producing a modified product lacking the chemical function required for continuation of the enzymatic process.
    3. NTPDAs possessing a reactive group(s) may also cause a chemical modification of the crucial enzyme functions responsible for substrate recognition, catalytic action, or conformation stability of the peptide structure (or disrupt the association forces keeping the functional multiunit enzymes).

The tables on the following pages are examples of different enzymatic activities of the selected nucleoside 5'-triphosphate derivatives and their analogs. Where it is known, the mode of NTPDA action and the research or practical application(s) is briefly indicated with a reference to a primary source of information.

The data presented in the tables should not be considered as a complete compilation by any means. Rather, it is an overview of the main classes of NTPDAs and illustration of their ability to serve as tools for the different biochemical applications.

Abbreviations used in Tables:

AMV RT Avian Myeloblastosis Virus Reverse Transcriptase
ATPase Adenosine 5'-triphosphatase
ASS Adenylylsuccinate Synthesase
ATP/CTP tRNA NT ATP/CTP Dependent tRNA Nucleotidyl Transferase
DD DP DNA Dependant DNA Polymerase
DD RP DNA Dependant RNA Polymerase
RD DP RNA Dependant DNA Polymerase
RD RP RNA Dependant DNA Polymerase
RNR Ribonucleotide Reductase
PNP Polynucleotide Phosphorylase
Poly(A) Pol Polyadenylate Polymerase
PRPPS Phosphoribosylpyrophosphate Synthesase
TNDT Terminal Nucleotidyl Transferase
tRNA NT tRNA Nucleotidyl Transferase
aa tRNA S Aminoacyl tRNA Synthesase
2',5'-OAS 2',3'-Oligoadenylate Synthesase
HIV RT Human Immunodeficiency Virus Reverse Transcriptase
AC Adenylate Cyclase
GC Guanylate Cyclase
CK Creatine Kinase
HK Hexokinase
PK Pyruvate Kinase
PFK Phosphofructose Kinase


Table 1: Sugar modified nucleoside 5'-triphosphate analogs

Application Mode of Action R2 R1 Base Enzyme class References
DNA Sequencing Chain Termination H H A, C, G, T, I DD DP 1, 2
H OH A, C, G, U DD RP 3-6
F OH A, C, G, U DD RP 14
NH2 OH A, C, G, U DD RP 15-18
Me OH A, C, G, U DD RP 15, 25-27
Substrate OH F A, C, G, U DD DP 13
RNA Sequencing Chain Terminator H OH A, C, G, U RD RP 3, 9
OMe OH A, C, G, U DD RP 25
Me OH A, C, G, U DD RP 15, 25-27
N3 OH A, C, G, U DD RP 15
Synthesis Of Modified DNA Substrate OH F A, C, G, U DD DP 13
Synthesis Of Modified RNA Substrate OH OMe A DD RP 11
NH2 OH A, C, G, U DD RP 15-18
NH2 OH A tRNA-NT 19-21
Ribosomal Research Substrate NH2 OH A tRNA-NT 19-21
Enzymatic Research Inhibition H OH A, C, G, U DD RP 7
H OH A, C, G, U aa tRNA S 8
OH OMe A aa tRNA S 8
OH Ara-OH A, C RNR 10
NH2 OH A, G RD RP, DD RP 22, 23
H OH A Poly(A) Pol 24
NH2 Ara-OH G RD RP DD RP 22
N3 OH A, G RD RP DD RP 22, 23
OMe OH A aa tRNA S 8
CHO CHO A, C, G, U DD RP 30, 31
H OH U, T DD RP 64
Xylo-OH OH U, T DD RP 67
Activation OH OMe A RNR 10
OMe OH A RNR 10
Chain Termination NCS H A DD RP 17
NHC(O)CH2Br OH A DD RP 17
2', 3'-Epoxide 2', 3'-Epoxide A DD DP 28
Modification of Enzyme OH Arylazido A ATP-ase 12
NCS H A DD RP 17
NHC(O)CH2Br OH A DD RP 17
CHO CHO A ATP-ase 29
CHO CHO A aa tRNA S 32-34


Table 2: Base modified nucleoside 5'-triphosphate analogs

Application Mode of Action R Base Enzyme Class References
DNA Sequencing Substrate H 7-Deaza (A,G,I) DD DP 38-41
H N4-Me-C DD DP 46
Synthesis Of Modified DNA Substrate H Benzimidazole DD DP 35
H 5-Me-C DD DP 42-44
H 7-Deaza (A,G) Hum. telomerase 45
H N6,N6-Etheno-2,6-DAP DD DP 47
H Dihydrothymidine DD DP 48
Synthesis Of Modified RNA Substrate OH 5-Br-U DD RP 49
OH 5-I-U DD RP 49
OH 5-I-C tRNA NT 50
OH 5-Formyl U (β anomer) DD RP 53-56
OH 2-Thio U DD RP 59
OH 5-Br-C DD DP 59
OH Formycin A DD RP 60
PCR Substrate H N4-Me-C DD DP 46
Enzymatic Research Substrate H Benzimidazole RNR 10
H 5-Br-U DD RP 36,37
OH 8-Azido-A DD RP 51
OH 5-Formyl U (α anomer) DD RP 53-56
OH 4-Thio-U DD RP 57-59
OH Xanthine ASS 61
Inhibition H 7-Deaza (A,G) Hum. telomerase 45
OH 8-Azido-A aa tRNA S 8
OH 8-Br-A aa tRNA S 8
OH 8-Cl-A aa tRNA S 8
OH 9-Purinyl aa tRNA S 8
Modification of Enzyme H 5-I-U DD RP 49
Ribosomal Research Photomodification of Ribosomal protiens OH 3-(Azidooxymethylphenyl)-G DD DP 52


Table 3: Nucleoside 5'-triphosphate analogs with modified γ-phosphates

Application Mode of Action X Nucleoside Enzyme Class References
Enzymatic Research Substrate Anilide rA DD RP 141
4-Azidoanilide r(A, C, G) DD RP 142 - 144
4-Azidoanilide rA aa tRNA S 145-150
1-(5-sulfonatenapthyl)-amide rA DD RP 160, 161
1-(5-sulfonatenapthyl)-amide r(A,C,G,U) SVPD 162
1-(5-sulfonatenapthyl)-amide d(C, T) SVPD 162
Inhibition Anilide rA aa tRNA S 138-140
4-Azidoanilide rA aa tRNA S 145-150
4-Azidoanilide rA, Etheno-rA CK 151-153
2,4,6-(Me)3-C6H4-C(O)O- rA aa tRNA S 155, 156
BrCH2C(O)NH-C6H4O- rG Ribosome 159
4-(N-2-Chloroethyl, N-methylamino)-benzylamide dA, dT RD DP, DD DP, HK 163-165
N-Methyl,N-(4-azidobenzyl)-amide rA aa tRNA S 124, 148
Enzyme Modification N3 rG DD RP 154
2,4,6-(Me)3-C6H4-C(O)O- rA ATP-ase 157
FSO2-C6H4-C(O)O- rA PK 158
4-(N-2-Chloroethyl, N-methylamino)-benzylamide dA, dT RD DP, DD DP, HK 163-165
N-Methyl,N-(4-azidobenzyl)-amide rA aa tRNA S 124, 148
Cyclic trimetaphosphate* rA, Etheno-rA aa tRNA S 166
Cyclic trimetaphosphate* rA DD RP 167, 168
Enzyme Photo- Modification 4-Azidoaniline r(A, C, G) DD RP 142 - 144
4-Azidoaniline rA aa tRNA S 145-150
4-Azidoaniline rA, Etheno-rA CK 151-153
4-Azidobenzylamide rG DD RP 154

*Nucleoside 5'-Trimetaphosphate

Table 4: Nucleoside 5'-triphosphate analogs with modified triphosphate chain

Application Mode of Action X Y R1 R2 R3 Nucleoside Enzyme Class References
DNA Sequencing Substrate O O O- O- S- dA, dT DD DP 110-117
O O O- O- S- d(A,C,G,T) DD DP 118
O O O- O- BH3 5-(Me,Et,Br,or I) C DD DP 137
Synthesis Of Modified DNA Substrate O O O- O- S- dA, dT DD DP 110-117
O O O- O- Me dT DD DP, TDNT, HIV-RT, AMV-RT 133, 134
Enzymatic Research Inhibition CF2 O O- O- O- rG DD DR 66
CH2 O O- O- O- rA Various enzymes 67-70
CH2 O O- O- O- rA PFK 72
O CH2 O- O- O- rA AC 73
NH O O- O- O- rA, rG Various enzymes 74-82
O NH O- O- O- rA Various enzymes 67-69
Substrate CH2 O O- O- O- rA CK 71
CH2 O O- O- O- rA DD DP 66
O CH2 O- O- O- rA CK 71
O NH O- O- O- rA DD RP, CK 83
O O O- O- S- r(A,C,G,U) Myosine 84, 85
O O O- O- S- rA Kinases 86-92
O O O- O- S- rA PRPPS 93
O O O- O- S- rA, rG DD RP 94-99
O O O- O- S- rA 2\',5\' OAS 100, 101
O O O- O- S- rA PNP 102, 103
O O O- O- S- rA tRNA NT 104
O O O- O- S- rA RNA ligase 105
O O O- O- S- rA GS 106
O O O- O- S- rA AS 107, 108
O O O- O- S- rA UDP GPP, GP UT 109
O O O- O- S- dA, dT DD DP 110-117
O O O- O- S- dA AMV RT 119
O O O- S- O- rA Kinases 86-92, 120-122
O O O- S- O- rA aa tRNA S 123, 124
O O O- S- O- rA ATP-ase 125
O O O - S - O - dA DD DP 110-111
O O S - O - O - rA Kinases 126-129
O O S - O - O - rA, rG ATP and GTP-ases 125, 130-132
O O O - O - Me dT DD DP, TDNT, 133, 134
O O O - O - BH3 d(A,C,G,T) HIV-RT, AMV-RT DD DP 135, 136


Table 5: Sugar and Base modified nucleoside 5'-triphosphate analogs

Application Mode of Action R1 R2 Base Enzyme Class References
DNA Sequencing Chain Terminator NH2 H 5-(2-Br-vinyl)-U DD DP 35
NH2 H 5-(2-Br-vinyl)-U AMV RT 35
N3 H 5-(2-Br-vinyl)-U DD DP 35
N3 H 5-(2-Br-vinyl)-U AMV RT 35
RNA Sequencing Inhibition of DNA synthesis H OH 5-F-C DNA Primase 7
H OH 5-F-U DNA Primase 7
Enzymatic Research Inhibition N3 H Ribavirin RD RP 22
Xylo-OH OH 5-F-U DD RP 64
Xylo-OH OH 5-Cl-U DD RP 64
Xylo-OH OH 5-Br-U DD RP 64
Xylo-OH OH 5-I-U DD RP 64
Xylo-OH OH 5-Ethyl-U DD RP 64
Xylo-OH OH 5-Propyl-U DD RP 64
Xylo-OH OH 5-Butyl-U DD RP 64
Modification of Enzyme CHO CHO Etheno-A Nitrogenase 65
Photo-Modification of Enzyme OH OH 8-Azido-A DD RP 62
Arylazido OH 8-Azido-A ATP-ase 63

 

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