Table 1.
Sequences of putative G-quadruplex forming oligonucleotides in the genome of HSV-1. Sequence repeats within HSV-1 main strains and G-scores are shown.
| Name | Sequence | G-scorea | Strains | Positions |
Repeats and genes |
||
|---|---|---|---|---|---|---|---|
| Leading strand (5′ → 3′) | Lagging strand (5′ → 3′) | Leading strand | Lagging strand | ||||
| gp054a | GGGGTTGGGGCTGGGGTTGGGG | 63 | F | 71527–71620 | – | 4 UL36 | – |
| 17 | 71612–71705 | – | 4 UL36 | – | |||
| H129 | 71561–71654 | – | 4 UL36 | – | |||
| KOS | 71580–71757 | – | 4 UL36 | – | |||
| gp054b | GGGGTTGGGGTTGGGGTTGGGG | 63 | F | 71587–71608 | – | 1 UL36 | – |
| 17 | 71672–71693 | – | 1 UL36 | – | |||
| H129 | 71621–71642 | – | 1 UL36 | – | |||
| KOS | 71616–71637 | – | 1 UL36 | – | |||
| gp054c | GGGGTTGGGGTTGGGGCTGGGG | 63 | F | 71593–71632 | – | 1 UL36 | – |
| 17 | 71678–71717 | – | 1 UL36 | – | |||
| H129 | 71627–71666 | – | 1 UL36 | – | |||
| KOS | 71574–71661 | – | 2 UL36 | – | |||
| gp054d | GGGGCTGGGGCTGGGGCTGGGG | 63 | F | 71623–71722 | – | 4 UL36 | – |
| 17 | 71708–71807 | – | 4 UL36 | – | |||
| H129 | 71657–71756 | – | 4 UL36 | – | |||
| KOS | 71652–71739 | – | 3 UL36 | – | |||
| gp054e | GGGGCTGGGGCTGGGGTTGGGG | 63 | F | 71707–71728 | – | 1 UL36 | – |
| 17 | 71792–71813 | – | 1 UL36 | – | |||
| H129 | 71741–71762 | – | 1 UL36 | – | |||
| KOS | 71562–71745 | – | 2 UL36 | – | |||
| gp054f | GGGGCTGGGGTTGGGGTTGGGG | 63 | F | 71581–71626 | – | 2 UL36 | – |
| 17 | 71666–71711 | – | 2 UL36 | – | |||
| H129 | 71615–71660 | – | 2 UL36 | – | |||
| KOS | 71568–71655 | – | 3 UL36 | – | |||
| unb | GGGGTTGGGGTTGGGGTTGGGG | 63 | F | 4121–4142 | 30075–30096 | 1 TRL | 1 IRL |
| 17 | 4138–4159 | 29987–30008 | 1 TRL | 1 IRL | |||
| H129 | 4114–4135 | 29892–29913 | 1 TRL | 1 IRL | |||
| KOS | – | – | – | – | |||
| un1 | GGGGGAGAGGGGAGAGGGGGGGAGAGGGG | 62 | F | 8966–9147 | 34922–35103 | 5 TRL (b) | 5 IRL (b′) |
| 17 | 9049–9213 | 34898–35062 | 5 TRL (b) | 5 IRL (b′) | |||
| H129 | 9010–9174 | 34804–34968 | 5 TRL (b) | 5 IRL (b′) | |||
| KOS | 8997–9161 | 34768–34932 | 5 TRL (b) | 5 IRL (b′) | |||
| un2 | GGGGGCGAGGGGCGGGAGGGGGCGAGGGG | 62 | F | 150989–151306 | 25157–25474 | 9 TRS (c) | 9 IRS (c′) |
| 17 | 151064–151381 | 25090–25407 | 9 TRS (c) | 9 IRS (c′) | |||
| H129 | 150962–151279 | 25087–25404 | 9 TRS (c) | 9 IRS (c′) | |||
| KOS | 150854–151171 | 25009–25326 | 9 TRS (c) | 9 IRS (c′) | |||
| un3 | GGGAGGAGCGGGGGGAGGAGCGGG | 36 | F | 93–296/151880–152083 | 26047–26250 | 8 TRL, 8 TRS (a) | 8 IR (a′) |
| 17 | 106–309/151929–152132 | 25955–26158 | 8 TRL, 8 TRS (a) | 8 IR (a′) | |||
| H129 | 106–333/151771–151974 | 25896–26111 | 9 TRL, 8 TRS (a) | 9 IR (a′) | |||
| KOS | 118–309/151734–151925 | 25889–26080 | 8 TRL, 8 TRS (a) | 8 IR (a′) | |||
a
G-score: propensity of a sequence to fold into unimolecular G-quadruplex assigned by the QGRS software.