Dr. Salifu Seidu-Larry - Academia.edu (original) (raw)

Uploads

Papers by Dr. Salifu Seidu-Larry

Advances in Experimental Medicine and Biology, 2016

The carbon 5 of pyrimidine nucleobases is a privileged position in terms of nucleoside modificati... more The carbon 5 of pyrimidine nucleobases is a privileged position in terms of nucleoside modification in both DNA and RNA. The simplest modification of uridine at this position is methylation leading to thymine. Thymine is an integral part of the standard nucleobase repertoire of DNA that is synthesized at the nucleotide level. However, it also occurs in RNA, where it is synthesized posttranscriptionally at the polynucleotide level. The cytidine analogue 5-methylcytidine also occurs in both DNA and RNA, but is introduced at the polynucleotide level in both cases. The same applies to a plethora of additional derivatives found in nature, resulting either from a direct modification of the 5-position by electrophiles or by further derivatization of the 5-methylpyrimidines. Here, we review the structural diversity of these modified bases, the variety of cofactors that serve as carbon donors, and the common principles shared by enzymatic mechanisms generating them.

European Journal of Nutrition & Food Safety

Food labels are important public health tool that provides consumers with nutritional information... more Food labels are important public health tool that provides consumers with nutritional information to make informed and healthier food choices. This study aimed at determining the level of knowledge and understanding of nutritional information on food labels and its impact on food choices among students at the University of Cape Coast, Ghana. A cross-sectional study employing random sampling was used to recruit 200 study participants. A pre-tested structured questionnaires were used to obtain data on socio demographic characteristics, frequency of food label use and nutritional knowledge of the students. Pertaining to the frequency of food label use, 27.5% of students always use food labels, while 11% never use food labels. While most of the students were aware that packaged foods have labels, most of them do not refer to information on the labels when making purchases. Expiry date was considered the most important information on food labels, while the students may refer to labels mo...

Journal of the Science of Food and Agriculture

multifunctional bioconjugate module for versatile

Nucleic Acids Research, 2011

A multifunctional reagent based on a coumarin scaffold was developed for derivatization of naive ... more A multifunctional reagent based on a coumarin scaffold was developed for derivatization of naive RNA. The alkylating agent N3BC [7-azido-4-(bromomethyl)coumarin], obtained by Pechmann condensation, is selective for uridine. N3BC and its RNA conjugates are pre-fluorophores which permits controlled modular and stepwise RNA derivatization. The success of RNA alkylation by N3BC can be monitored by photolysis of the azido moiety, which generates a coumarin fluorophore that can be excited with UV light of 320 nm. The azidocoumarinmodified RNA can be flexibly employed in structure-function studies. Versatile applications include direct use in photo-crosslinking studies to cognate proteins, as demonstrated with tRNA and RNA fragments from the MS2 phage and the HIV genome. Alternatively, the azide function can be used for further derivatization by click-chemistry. This allows e.g. the introduction of an additional fluorophore for excitation with visible light.

International Journal of Pest Management

Chemical communications, 2012

A propargyl containing guanosine phosphoramidite was synthesized and incorporated into siRNA, ena... more A propargyl containing guanosine phosphoramidite was synthesized and incorporated into siRNA, enabling click-ligation with an azido fluorophore onto the nucleobase sugar edge. Duplex stability was not affected by labeling at this new site, which allowed deconvolution of the effects of label, structure and attachment site on RNAi activity.

This work is centered on the synthesis and chemical recognition of modified RNA. Phosphoramidites... more This work is centered on the synthesis and chemical recognition of modified RNA. Phosphoramidites of m5U, Ψ, m1G, m2G and m22G were synthesized and were incorporated into RNA oligomers by standard SPS. The synthesized oligomers were used for two purposes: (i) the total construction of tRNA via enzyme catalyzed ligation, and (ii) investigations of modifications in siRNAs. The construction of human mitochondrial tRNAIle (i) with and without modification was achieved in a one-pot 3 fragments ligation using T4-DNA-ligase with a DNA-splint. The yield for the ligation was 20-30 % and the products were further investigated for the stability of the tertiary structure via UV-melting curve analysis. The unmodified tRNA was found to be significantly less stable than the fully modified tRNA. In the second case (ii) RNAi efficiency and the immunostimulation in cells were investigated with 22 nucleotide long double-stranded siRNAs that were synthesized containing the modifications m1G, m2G, m22G,...

Frontiers in Immunology, 2017

Nucleic Acids Research, 2011

Chemistry & Biology, 2011

Using a combination of advanced RNA synthesis techniques and single molecule spectroscopy, the de... more Using a combination of advanced RNA synthesis techniques and single molecule spectroscopy, the deconvolution of individual contributions of posttranscriptional modifications to the overall folding and stabilization of human mitochondrial tRNA Lys is described. An unexpected destabilizing effect of two pseudouridines on the native tRNA folding was evidenced. Furthermore, the presence of m 2 G10 alone does not facilitate the folding of tRNA Lys , but a stabilization of the biologically functional cloverleaf shape in conjunction with the principal stabilizing component m 1 A9 exceeds the contribution of m 1 A alone. This constitutes an unprecedented cooperative effect of two nucleotide modifications in the context of a naturally occurring RNA, which may be of general importance for tRNA structure and help understanding several recently described decay pathways for hypomodified tRNAs.

Advances in experimental medicine and biology, 2016

The carbon 5 of pyrimidine nucleobases is a privileged position in terms of nucleoside modificati... more The carbon 5 of pyrimidine nucleobases is a privileged position in terms of nucleoside modification in both DNA and RNA. The simplest modification of uridine at this position is methylation leading to thymine. Thymine is an integral part of the standard nucleobase repertoire of DNA that is synthesized at the nucleotide level. However, it also occurs in RNA, where it is synthesized posttranscriptionally at the polynucleotide level. The cytidine analogue 5-methylcytidine also occurs in both DNA and RNA, but is introduced at the polynucleotide level in both cases. The same applies to a plethora of additional derivatives found in nature, resulting either from a direct modification of the 5-position by electrophiles or by further derivatization of the 5-methylpyrimidines. Here, we review the structural diversity of these modified bases, the variety of cofactors that serve as carbon donors, and the common principles shared by enzymatic mechanisms generating them.

Advances in Experimental Medicine and Biology, 2016

The carbon 5 of pyrimidine nucleobases is a privileged position in terms of nucleoside modificati... more The carbon 5 of pyrimidine nucleobases is a privileged position in terms of nucleoside modification in both DNA and RNA. The simplest modification of uridine at this position is methylation leading to thymine. Thymine is an integral part of the standard nucleobase repertoire of DNA that is synthesized at the nucleotide level. However, it also occurs in RNA, where it is synthesized posttranscriptionally at the polynucleotide level. The cytidine analogue 5-methylcytidine also occurs in both DNA and RNA, but is introduced at the polynucleotide level in both cases. The same applies to a plethora of additional derivatives found in nature, resulting either from a direct modification of the 5-position by electrophiles or by further derivatization of the 5-methylpyrimidines. Here, we review the structural diversity of these modified bases, the variety of cofactors that serve as carbon donors, and the common principles shared by enzymatic mechanisms generating them.

European Journal of Nutrition & Food Safety

Food labels are important public health tool that provides consumers with nutritional information... more Food labels are important public health tool that provides consumers with nutritional information to make informed and healthier food choices. This study aimed at determining the level of knowledge and understanding of nutritional information on food labels and its impact on food choices among students at the University of Cape Coast, Ghana. A cross-sectional study employing random sampling was used to recruit 200 study participants. A pre-tested structured questionnaires were used to obtain data on socio demographic characteristics, frequency of food label use and nutritional knowledge of the students. Pertaining to the frequency of food label use, 27.5% of students always use food labels, while 11% never use food labels. While most of the students were aware that packaged foods have labels, most of them do not refer to information on the labels when making purchases. Expiry date was considered the most important information on food labels, while the students may refer to labels mo...

Journal of the Science of Food and Agriculture

multifunctional bioconjugate module for versatile

Nucleic Acids Research, 2011

A multifunctional reagent based on a coumarin scaffold was developed for derivatization of naive ... more A multifunctional reagent based on a coumarin scaffold was developed for derivatization of naive RNA. The alkylating agent N3BC [7-azido-4-(bromomethyl)coumarin], obtained by Pechmann condensation, is selective for uridine. N3BC and its RNA conjugates are pre-fluorophores which permits controlled modular and stepwise RNA derivatization. The success of RNA alkylation by N3BC can be monitored by photolysis of the azido moiety, which generates a coumarin fluorophore that can be excited with UV light of 320 nm. The azidocoumarinmodified RNA can be flexibly employed in structure-function studies. Versatile applications include direct use in photo-crosslinking studies to cognate proteins, as demonstrated with tRNA and RNA fragments from the MS2 phage and the HIV genome. Alternatively, the azide function can be used for further derivatization by click-chemistry. This allows e.g. the introduction of an additional fluorophore for excitation with visible light.

International Journal of Pest Management

Chemical communications, 2012

A propargyl containing guanosine phosphoramidite was synthesized and incorporated into siRNA, ena... more A propargyl containing guanosine phosphoramidite was synthesized and incorporated into siRNA, enabling click-ligation with an azido fluorophore onto the nucleobase sugar edge. Duplex stability was not affected by labeling at this new site, which allowed deconvolution of the effects of label, structure and attachment site on RNAi activity.

This work is centered on the synthesis and chemical recognition of modified RNA. Phosphoramidites... more This work is centered on the synthesis and chemical recognition of modified RNA. Phosphoramidites of m5U, Ψ, m1G, m2G and m22G were synthesized and were incorporated into RNA oligomers by standard SPS. The synthesized oligomers were used for two purposes: (i) the total construction of tRNA via enzyme catalyzed ligation, and (ii) investigations of modifications in siRNAs. The construction of human mitochondrial tRNAIle (i) with and without modification was achieved in a one-pot 3 fragments ligation using T4-DNA-ligase with a DNA-splint. The yield for the ligation was 20-30 % and the products were further investigated for the stability of the tertiary structure via UV-melting curve analysis. The unmodified tRNA was found to be significantly less stable than the fully modified tRNA. In the second case (ii) RNAi efficiency and the immunostimulation in cells were investigated with 22 nucleotide long double-stranded siRNAs that were synthesized containing the modifications m1G, m2G, m22G,...

Frontiers in Immunology, 2017

Nucleic Acids Research, 2011

Chemistry & Biology, 2011

Using a combination of advanced RNA synthesis techniques and single molecule spectroscopy, the de... more Using a combination of advanced RNA synthesis techniques and single molecule spectroscopy, the deconvolution of individual contributions of posttranscriptional modifications to the overall folding and stabilization of human mitochondrial tRNA Lys is described. An unexpected destabilizing effect of two pseudouridines on the native tRNA folding was evidenced. Furthermore, the presence of m 2 G10 alone does not facilitate the folding of tRNA Lys , but a stabilization of the biologically functional cloverleaf shape in conjunction with the principal stabilizing component m 1 A9 exceeds the contribution of m 1 A alone. This constitutes an unprecedented cooperative effect of two nucleotide modifications in the context of a naturally occurring RNA, which may be of general importance for tRNA structure and help understanding several recently described decay pathways for hypomodified tRNAs.

Advances in experimental medicine and biology, 2016

The carbon 5 of pyrimidine nucleobases is a privileged position in terms of nucleoside modificati... more The carbon 5 of pyrimidine nucleobases is a privileged position in terms of nucleoside modification in both DNA and RNA. The simplest modification of uridine at this position is methylation leading to thymine. Thymine is an integral part of the standard nucleobase repertoire of DNA that is synthesized at the nucleotide level. However, it also occurs in RNA, where it is synthesized posttranscriptionally at the polynucleotide level. The cytidine analogue 5-methylcytidine also occurs in both DNA and RNA, but is introduced at the polynucleotide level in both cases. The same applies to a plethora of additional derivatives found in nature, resulting either from a direct modification of the 5-position by electrophiles or by further derivatization of the 5-methylpyrimidines. Here, we review the structural diversity of these modified bases, the variety of cofactors that serve as carbon donors, and the common principles shared by enzymatic mechanisms generating them.